Rice Genome Landscape: Table of Contents

This landscape is a work in progress and is designed to provide an overview of the policies involved with the patenting of the rice genome. We also provide an analysis of the genes and proteins that are claimed in United States patents and patent applications that have significant homology to the fully-sequenced rice genome.

Team Members
Contributors

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1. Introduction

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2. Background Information About Rice

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3. Genome Patenting: Policies and Implications

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4. Mapping of Rice Patents and Applications Onto the Rice Genome

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5. Granted Patents on Rice

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6. Patent Applications on Rice

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7. Bulk Sequence Applications

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8. Rice Genome Patents in Other Jurisdictions

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9. Key Players in Rice Genome Patenting

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10. Conclusions and Implications

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Appendix

Rice Genome Landscape Contributors

Kerry Fluhr

Email:

k.fluhr@cambia.org

Location:

Australia

Institution:

CAMBIA

Kerry Fluhr

Kerry obtained a B.A. in Biochemistry from Ithaca College, followed by a Ph.D. in Biological Chemistry from the University of Michigan, where her research focus was in the area of mechanistic enzymology. 

Following graduate school, she completed a postdoctoral fellowship at the University of Washington, where she studied Type III-secreted exotoxins in gram-negative bacteria. Kerry is also a USPTO-registered Patent Agent, and prior to joining CAMBIA, she worked for several years at a Seattle-based law firm. Her work involved the preparation, prosecution, and analysis of patents and patent applications relating to biotechnology and medical devices.

As a patent analyst at CAMBIA, Kerry focuses on patent landscapes, patent tutorials, and other IP-related projects.

Wei Yang

Email:

wei@cambia.org

Location:

Australia

Institution:

CAMBIA

Wei Yang

Wei is originally from China, where he obtained his B.Sc degree in biochemistry from Wuhan University. He worked at China National Rice Research Institute (CNRRI) as a research scientist before joining CAMBIA in 1996 and obtained a PhD in plant molecular biology from the Research School of Biological Sciences, Australian National University.

Wei's PhD work on apomixis is shown in the BioForge apomixis project and is available to use under a BiOS license.  He then worked as a Research Scientist at CAMBIA on Arabidopsis transgenomics. 

Wei has now shifted focus from scientific research to intellectual property and is working with the IP group in biotechnology-related patent analysis and assisting in  Chinese-related IP issues.

Kerry Mills

Email:

k.mills@cambia.org

Location:

Australia

Institution:

CAMBIA

Kerry Mills

Kerry studied for her BA and BSc at ANU, completing her honours year working on HIV at the John Curtin School of Medical Research in 1996. She then moved to Melbourne for her PhD at the Walter and Eliza Hall Institute (WEHI), studying surface proteins of the malaria parasite, Plasmodium falciparum.

In 2003, she moved to Heidelberg, Germany, where she studied the earliest infection events of the Hepatitis B virus. She has now returned to her home town to work with CAMBIA.

Marie Connett-Porceddu

Email:

cambia@cambia.org

Location:

Australia (2007), France

Institution:

CAMBIA (2005-2007)

Marie Connett-Porceddu

Marie was CAMBIA's Deputy Chief Executive Officer 2005-2007.  She led CAMBIA's Patent Lens development team, including the addition of biological sequence search tools, status and family information, and expansion from a life sciences database to all patent categories.  She also coordinated the launch of the BiOS License and BiOS-compatible agreements covering materials transfer and data access, and the BiOS Initiative

Marie has a PhD from Cornell University where she worked on the molecular genetic and biochemical mechanisms underlying a pollen production deficiency.  Her MBA was earned in the Moore Business School of USC.  She has a BA in Modern Languages and Literatures, is registered with the USPTO bar as a patent agent, has co-owned businesses in two countries and has experience with intellectual property business rules in an array of different countries. 

She is now the CEO of A Rocha International.

Richard Jefferson

Email:

raj@cambia.org

Location:

Australia

Institution:

CAMBIA

Richard Jefferson

Richard obtained a PhD in Molecular Biology at the University of Colorado, followed by an NIH fellowship at the Plant Breeding Institute in Cambridge where he was responsible for creating and distributing amongst the most widely cited and licensed plant biotechnologies. CAMBIA, an international non-profit institute based in Australia was founded in 1991 and is dedicated to development of tools and enabling technologies to promote equitable life sciences-enabled innovation worldwide.

The CAMBIA BiOS Initiative (www.bios.net) - the biological open source movement is an integrated response to increasing science and technology complexity, patent thickets and innovation system inefficiencies. As part of this work, CAMBIA created the Patent Lens, (www.patentlens.net), an independent, public-good global resource for increasing patent transparency. 

Richard has worked and taught extensively in the developing world, supporting the Rockefeller Foundation's biotechnology network for over ten years, and has worked as senior staff for the FAO, and consultant for other UN Agencies. He has been profiled in media including The Economist, Newsweek, Nature Biotechnology and Red Herring. CAMBIA's work has recently featured in cover editorials in most major life sciences journals.

In 2003 he was named by Scientific American to the List of the World's 50 most influential technologists, cited as the World Research Leader for 2003 for Economic Development. Richard is an Outstanding Social Entrepreneur of the Schwab Foundation, for which is a regular panelist at the Davos meetings of the World Economic Forum. 

View full Curriculum Vitae.

Carol Nottenburg

Email:

c.nottenburg@cougarlaw.com

Location:

United States

Institution:

Cougar Patent Law

Carol Nottenburg

Carol holds a Ph.D. in Genetics from Stanford University and a J.D. magna cum laude from University of Puget Sound (now Seattle University) School of Law. She was a biomedical scientist in the academic world for many years before earning her law degree. Her legal focus is patents and their strategic integration with business goals.

In private law practice, she often counselled clients on freedom to operate issues and saw the need for more pragmatic learning tools about patents. Carol was the Director of Intellectual Property and Chief Legal Officer for CAMBIA until 2004 and oversaw the creation of the CAMBIA IP Resource.

She has now returned to private practice as principal of Cougar Patent Law (www.cougarlaw.com) and is retained as a consultant for CAMBIA.

Neil Bacon

Email:

neil@cambia.org

Location:

Australia

Institution:

CAMBIA

Neil Bacon

Neil is from Hamilton, New Zealand, where he caught a B.Sc (Phys) at Waikato Uni.  He did a short stint of seismic surveying in the Bass Strait with Esso and enjoyed a few stormy days of seas rougher than he imagined possible. He worked at the CSIRO Division of Fossil Fuels and did a part-time M.Sc. (Phys) at the UNSW.

Since then he's been doing IT work, initially embedded engineering applications and telecommunications and finally more general IT, in the UK, NZ, Belgium and Australia. Neil moved back to Australia from Belgium to be warm and live near a nice surf beach, but something went wrong with the plan and he ended up in Canberra - oh well, it's great for cycling. Neil has worked extensively on CAMBIA Sequence Software

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Rice Genome Landscape Executive Summary

Rice is a hugely important food crop for the world's population.  It's importance goes beyond food security; rice plays a large economic and cultural role as well in many countries.  Rice production must increase in order to sustain those who depend upon it.  Besides traditional breeding methods, biotechnological methods are being applied to improve production.  Some of these methods rely upon knowledge of the rice genome and use of genetic sequences. 

This landscape is meant to support policymakers in assessing the implact of patent activity affecting access to the genetic material of rice.  Lack of coherent information about the current holdings of patents in this field can hamper effective policies and research and development.  To this purpose, the patent landscape presented here examines patents and patent applications directed to any part of the rice genome, directly analyzing the degree to which granted and pending patents cover the rice genome. 

The landscape was produced by first compiling a comprehensive collection of patent sequences that are recited in the claims of United States granted patents and patent applications. Sequences were compiled from both NCBI and the USPTO.  A program (MEGABLAST) was used to identify nucleotide sequences that are highly similar to sequences in the rice genome. To qualify as a “hit”, the sequence had to be at least 150 nucleotides in length and have a a probability value of 1e-200 or less. Matches with such values are highly statistically significant.  Major findings include:

While there is relatively low amount of rice gene patenting in the U.S., patenting of rice genome in key rice-growing countries was not assessed.  The amount of patenting in these other countries will depend on a number of factors, including whether and to what extent such patents are allowable, the effect of publication of sequences in U.S. patent applications and other publications, and the status of a patent system in these countries.  Because of the undisputed importance of rice, further analysis of patenting in other countries is warranted.  It is hoped that the information in this patent landscape will guide new analyses. 

Chapter 1: Introduction

rice7-sushi

With the increasing importance of patents, it is highly advantageous for scientists and business developers to be versed in the field of intellectual property. An understanding of patents is necessary to fully comprehend business opportunities, particularly in the area of agriculture.

In this intellectual property landscape, we analyze the patents, patent applications, claim drafting strategies, and key players in the area of rice (Oryza sativa) genome patents. In particular, we highlight bulk sequence applications and patents and applications with broadening claim language (such as hybridisation and percent identity language). To demonstrate these important aspects of genome patents, we will provide example patents and patent applications from various assignees and discuss their associated claims.

With this landscape and others now present on the Patent Lens, we strive to provide a readable and understandable overview of patents in some key areas of the life sciences. In this way, we hope to contribute to the public awareness of intellectual property issues that surround key research tools. The information in these reports is not exhaustive, but highlights issues that are likely to be of particular importance to those doing work in the area. In this regard, these reports can be used to open the door to the patent world and to provide a platform from which additional self-directed investigation can be performed.

This landscape is NOT intended as a legal opinion or as a substitute for legal advice, nor is it intended to make the user an expert in patents. Furthermore, the nature of the patenting systems worldwide means that new patents and patent applications may appear at anytime.  Similarly, patents may lapse or patent applications may expire or be replaced by new applications. So, although we give extensive coverage of the intellectual property surrounding rice genome sequences, this landscape should be viewed as an insight and snapshot of the subject. 

Patent Landscapes are "Works in Progress"

CAMBIA is in the process of developing new tools to enable our readers to use and understand patent information. As we develop these tools, we plan to incorporate new functionality into this and other landscapes. In addition, we are working on exanding our analysis of patenting of the rice genome to include amino acid sequences and additional related nucleotide sequences.

Rice Genome Landscape: Overview

Rice_China

Introduction

The goal of this report is to contribute to public awareness of intellectual property issues surrounding the genetic sequences of rice. Rice is an important economic crop, as well as a major subsistence crop for large populations. Because rice is a close genetic relation of other cereals such as wheat, maize (corn), and sorghum, patent claims over genetic sequences of rice can result in exclusionary treatment of genetic resources of these cereals. Also, as the first cereal genome that has been sequenced, the patenting behaviour of rice sequences may serve as a model for how sustenance crop genes are patented in the future.

Although the rice genome is relatively small compared to other flowering plants, we found hundreds of patent applications claiming rice sequences. As a part of our analysis, we mined the sequences claimed in U.S. patents and patent applications and identified sequences that had significant homology to the rice genome and provide links to these patents.

Because of the volume of patent activity in this area, a detailed discussion of all the patents and patent applications is beyond the scope of this landscape. Though our analysis of patents and patent applications below is not exhaustive, we highlight issues from which users can perform additional self-directed investigation.

Rice and Intellectual Property

Due to a variety of factors, such as drought, climate change, soil erosion, urbanization, and pollution, rice growers are faced with the challenge of producing more rice for more people, but with fewer resources. While government-based rice breeding operations have done extraordinarily well improving rice yield and quality using more traditional breeding methods, biotechnology will likely be a essential component of strategies aimed at meeting this challenge.

In the advent of gene patenting, access to enabling technologies may be impeded by intellectual property, material transfer agreements (MTAs), or other contractual arrangements. Gene patents, in particular, have the potential to monopolize genes and proteins associated with desirable agronomic traits. Patents also impact the gene-based tools needed to improve rice, such as transformation and genotyping techniques.

The inherent relatedness of plant genomes has the potential to expand the reach of patent claims well beyond their expected scope. In particular, the similarity between the rice genome and the genomes of other cereal makes it possible that patent claims to rice sequences will also literally extend to other crops. Similarly, patent claims to the genes of other crops may encompass portions of the rice genome.

Intellectual property also has an impact on a larger scale by shifting the demographics of rice research from publicly-funded organizations to private companies. This shift has changed who solves problems for whom, and who has access to the tools of innovation.

In addition, patent craft has evolved in the era of sequence patents. New patent strategies have emerged, and old ones have been re-tooled to claim biological sequence "inventions" as broadly as possible. For example bulk sequence applications, which we define as those claiming more than 1,000 sequences, are frequently filed although they are likely to issue with claims to only a few sequences. However, during the pendency of the application, the uncertainty of which sequences will be claimed in the final patent may be used to influence contracts and agreements that often have limitations and consequences far greater than an enforced patent.

Access to Patent Data is Limited in Rice-Growing Jurisdictions

Access to patent sequence data in the major rice-growing jurisdictions is limited or non-existent, which makes it extremely difficult to fully assess the impact of patents where they matter most. Since the vast majority of rice produced in the world is consumed in the same country that it was produced, domestic patent laws are key for determining access to innovation tools.

For example in India, it is currently not possible to conduct a full-text search of domestic patents or patent applications; only bibliographic information is available. How can anyone assess whether they have freedom-to-operate in India if they cannot access the claims or specifications of Indian patents? The uncertainty regarding the metes and bounds of patents can lead to exploitation of parties not privy to the inner workings of the Indian patent office.

CAMBIA’s Analysis

CAMBIA’s goal is to facilitate access to science-enabled innovation by creating tools that promote patent transparency. To this end we have created the Patent Lens, which includes a free patent search tool that allows users to search the full text of patents and applications from the United States, Europe, and Australia as well as world (PCT) applications. In addition, we provide a BLAST-type tool that permits searching of sequences that are disclosed in the specification or recited in the claims of U.S. patents and patent applications.

The rice genome patent landscape outlines many of the key issues associated with patenting of the rice genome. Inspired by the analysis published by Jensen and Murray in 2005 (Science 310: 239-240), we have carried out an analysis of genes that are claimed in both U.S. granted patents and patent applications. Unlike Jensen and Murray, we included patent applications in our analysis.

This landscape cannot provide an exhaustive treatment of rice genome sequences patented in all jurisdictions. Because the U.S. Patent and Trademark Office (USPTO) provides sequence data in electronic form, we were able to do this analysis with U.S. patents and applications, and we have supplemented this with some information we were able to find on counterpart filings in other countries that report to a European Patent Office (EPO) database. Unfotunately, however, many jurisdictions do not make sequence information available electronically. For example, although sequence information for China filings has been discussed in a peer-reviewed journal article, we found it is not actually available. 

Our analysis of U.S. patent applications shows that around 74% of the rice genome is recited in the claims of patent applications, but very small percentage ends up in granted patents. Numerous bulk sequence applications claim more than 100,000 rice genome nucleotide and/or amino acid sequences. Bulk sequence applications create uncertainty as to which sequences will issue when the patent is granted. While the application is pending, agreements can be made that benefit from this uncertainty. However, the patent office is stemming the tide on bulk sequence applications by limiting the number of sequences that are claimed in a granted patent to fewer than ten, and in many cases, only one or two sequences.

Our analysis of granted U.S. applications shows that a number of promoters, transcriptional activators and important structural genes are encumbered by patent claims. Pages in our landscape contain tables that provide information about these granted patents, as well as links to the Patent Lens.

Implications

One of the most important lessons in compiling this landscape was how difficult it was to access and analyse the data. If it was difficult for us, how difficult would it be for a small business enterprise wanting to enter this research area?

There are three major obstacles in our ability to conduct a thorough analysis of the rice genome; the lack of available patent data in key rice-growing jurisdictions, the lack of public information about patent licensing, and a lack of knowledge of case law in the rice-growing jurisdictions. While it is usually possible to determine who is the initial assignee of a patent application, it is virtually impossible to determine who is the rights holders of a granted patent with any degree of certainty. This makes it difficult to determine how to best conduct any negotiations regarding the patent.

This landscape is a work in progress, as the patent world is dynamic as new patents are filed, published, granted, or abandoned, and continuation applications are filed every day. Also, the landscape is changing as patent jurisdictions are increasing their capacity for search and analysis by individuals outside the patent office. CAMBIA plans to facilitate access to patent data from difficult jurisdictions and create new interactive patent landscaping tools to simplify the creation of new, dynamic, interactive patent landscapes.

Why is rice important?

Food Security

Food security, which is the condition of having enough food to provide adequate nutrition for a healthy life, is a critical issue in the developing world. About 3 billion people, nearly half the world's population, depend on rice for survival. In Asia as a whole, much of the population consumes rice in every meal. In many countries, rice accounts for more than 70% of human caloric intake. As seen in Figure 1, the total consumption of rice (expressed as % of total calorie intake) varies widely between different regions. In Asia in total, just over 30% of all calories come from rice.

But within a region, rice intake varies even more widely. Figure 2 shows fifteen of the countries most reliant on rice for energy. The graphs show that although total Asian rice intake is around 30%, people in countries such as Cambodia, Bangladesh and Myanmar rely on rice for over 70% of their calories. Africans as a whole gain less than 10% of their calories from rice, but in countries such as Madagascar and Sierra Leone, people use rice for nearly 50% of their energy needs.

Region%calorieRice2

Figure 1: Rice as a percentage of total caloric intake by region (2000).*

Rice Calorie Supply by Country

Figure 2: Rice as a percentage of total caloric intake (top 15 countries)*

* Data in Figures 1 and 2 was extracted from Table 16 of the IRRI World Rice Statistics.

Rice yields have been increasing since the 1960s, but since the 1990s, growth in rice production has been slower than population growth. Indeed, it is anticipated that rice production will need to increase by 30% by 2025 in order to sustain those who need it for sustenance. However, climate change, especially access to water, soil erosion and other problems threaten rice yields. A study by the International Water Management Institute suggested that by 2020, one third of Asia could face water shortages.

The Economic Importance of Rice

Because of high domestic consumption of rice in rice-producing countries, the economic importance of rice differs from that of traditional exports. Worldwide, only 5-6% of rice is exported. Japan, for example, consumes their entire domestic production and has to import around 8% of their rice each year. However, this imported rice is not released to the domestic market, ensuring a high local price. Thus the pressures of world trade on these countries are not as great as for exported crops. It also makes these countries vulnerable to local catastrophes, such as crop failure due to inclement weather (eg too much or too little rain), pests (such as insect swarms) or diseases (such as rice fungal diseases).

Furthermore, because both rice growers and people who rely on rice for sustenance tend to be poor, there is a constant pressure from rice growers to keep prices as high as possible, and from consumers to keep the price low. This strain is in constant force in all rice-growing countries, but is particularly important in the poorest countries.

For a good overview of this subject, please refer to the United Nations Conference on Trade and Development website.

The Cultural Importance of Rice

Beyond providing sustenance, rice plays an important cultural role in many countries. Products of the rice plant are used for a number of different purposes, such as fuel, thatching, industrial starch, and artwork.

Growing, selling and eating rice is integral to the culture of many countries. In Japan, rice was historically a product for the wealthy and is now a highly-prized crop. Many rituals surround the preparation of the rice beds, the sowing of the crop, and the harvest. In China, it has been suggested that rice has been cultivated for 3000 - 4000 years, where it gradually rose to become an important part of aristocratic life. China's rural culture has developed around the growing of rice, and foods made from rice are the basis of festivals such as the Land Opening Festival, which marks the start of the rice cultivation season, and the Spring Festival. Even in Western countries, rice is an important part of culture. Imagine Italy without risotto or Spain without paella!

Biotechnology Methods are Needed for Rice Improvement

In order to keep up with the increasing demand for rice, improvements are needed in rice performance parameters such as yield, quality, disease resistance, and other desirable growth characteristics. Conventional breeding methods will not be sufficient to yield the needed improvements in rice, and it is likely that biotechnology methods will be necessary to tap into the significant yield potential of rice.

This especially true in the case of hybrid rice. Many farmers have switched to growing hybrid rice due to the higher yields that it tends to produce. Technically, it is feasible to create intervarietal and intersubspecific hybrid rice strains by conventional breeding methods. However, it is impossible to exploit distant heterosis (the introduction of enhancing genes from other species or genera) without using molecular methods because crosses between plants of different species or genera normally leads to sterile offspring.

rice_panorama

What is Hybrid Rice?

Hybrid rice is rice that has been created by crossing two different parental strains. Such crosses generally result in an F1 generation that is more robust than either of the parental strains. The improved qualities of the F1 generation is referred to as "hybrid vigour" or "heterosis". The hybrid vigour may result in superior agronomic qualities such as higher yield, stronger resistance to diseases, more efficient use of soil nutrients, and better weed control. Hybrid vigour and other superior qualities arising from crossing genetically different plants has been well known and used by traditional crop breeders for decades.

In the past, the production of hybrid rice strains was limited by rice's inherent propensity to self-pollinate. In 1974, Chinese scientists overcame this when they developed the first generation of hybrid rice using a three-line hybrid system based on cytoplasmic male sterile (CMS) lines and hybrid combinations. In 1996, an even more efficient second generation of hybrid rice was developed based on photoperiod-sensitive genetic male sterility (PGMS) lines.

Traditional rice production (i.e., non hybrid rice) relies on rice varieties. A rice variety is a rice line that is a group of rice plants distiguished by common characteristics of significance to agriculture and often has been assigned a commercial name. When rice is produced from a variety, a single line is planted and it fertilizes by self-pollination. When a rice variety is reproduced, it retains its distiguishing characteristics, and farmers can keep seeds for replanting next season.

In contrast, hybrid rice is the product of a cross between two distinct rice lines, and due to the difficulty of making hybrids, they are generally only produced by seed companies.   Farmers do not save seeds for replanting because self-fertilization will result in genetic segregation of traits.  Therefore, farmers need to buy new hybrid seeds every year. This may produce an economic hardship for the farmer, who has to balance the benefits of hybrid vigour with the annual cost of purchasing new seeds.

References

Hybrid rice for food security (2004). FAO Factsheet.

Yuan L.P. (2002) The second generation of hybrid rice in China. Sustainable rice production for food security, Proceedings of the 20th Session of the International Rice Commission, Food and Agriculture Organization of the United Nations.

Intellectual Property Affects Rice Innovation

Most, if not every, current application of new technology to agricultural productivity requires access to proprietary enabling technologies belonging to others. To actually deliver commercial innovations in agriculture that are derived from modern biotechnology requires "Freedom to Operate". Freedom to Operate refers to the permissive use of technology and materials in the research, development and delivery of products and processes.

Obtaining Freedom to Operate first requires an analysis of the intellectual property surrounding the technology area of interest. Intellectual property, and patents in particular, have potential to impact the production of rice. Patents on rice genes and proteins can have an effect on the research level by affecting access to the biotechnology tools used for rice improvement. It can also have an impact on a larger scale by influencing the structure of the industry that produces rice.

Impact of Rice Gene Patents on Rice Performance Improvements

In the area of rice performance, it is straightforward to envision how patents may have an impact. Many of the desirable agronomic traits are controlled by genes, proteins, or regulatory elements that are the subject of patents. In addition, the enabling technologies, such as Agrobacterium-mediated plant transformation, that allow rice researchers to create strains exhibiting desirable agronomic traits are the subject of patent applications or granted patents. With this landscape and other features of the Patent Lens, we hope to enable readers to determine the patent status of the genes associated with important agronomic traits.

Impact of Patents on Industry Structure

Patents can also have an impact on rice production on a larger scale. For example, a thicket of patents or pending patents may actually discourage investment in the downstream innovation often required to convert an interesting invention into a useful product. Patents may shift the demographics of the rice industry and affect who solves problems for whom.

Why is the rice genome important to non-rice growers?

1. Rice is a model cereal plant.

Rice, apart from being a staple food for several billion people, is also a model system for cereals. For the rest of the world, other cereal crops, such as wheat, corn, sorghum and barely (among others) form the basis of most people's "daily bread". Rice is of particular use as a model for these other cereals because of the small size of its genome (430 Mb), its relatively short generation time and its relative genetic simplicity (it is diploid, or has two copies of each chromosome). Moreover, rice is quite easy to transform genetically. Wheat, in contrast, has a genome 40 times as large as rice, and can be diploid, but is more commonly tetraploid (4x), such as in durum wheat, or hexaploid (6x), such as in bread wheat. Each additional set of chromosomes adds complexity to genetic studies. But how can rice act as a model for other cereals? The most striking feature of the cereals is that, despite huge differences in genome size and ploidy, the genomes of rice and the other cereals are highly conserved. This conservation occurs not only in the sequences of the genes present, but in the order of the genes, or "synteny".

2. Similarity between rice and other plants.

Rice and other plants, especially other cereals, are amazingly similar on a genetic level. For example, the genes are often present on the chromosomes in the same order (synteny), and moreover, the genes themselves are very similar at a sequences level (homology). This is important if the granted rice patent covers, through "homology" or "percent identity" language, a gene in other another cereal, such as maize or wheat. This means that when when patents contain broadening language, including percent identity language, they may literally cross-cover other species. That is, a patent on a rice gene with, for example, percent identity language, may actually cover genes in wheat, or barley, or even bamboo! This means that researchers in another field may be unwittingly infringing patents on rice.  (Note however, that because of recent changes in U.S. patent law, a court is likely to interpret the claim to cover only rice.)

3. Rice is the first major crop genome to be sequenced.

Patenting and research behavior resulting from rice genome data may have an impact on how other crops are handled in the future. In the years since the rice genome was sequenced, there have been tremendous improvements in high-throughput DNA sequencing. As a result, there has been an explosion in the number and variety of genomes that have been sequenced. It is likely that the disclosures and claims of some of the more recently-sequenced plant genomes will be modeled on the patenting behaviour of the rice genome.

Because many rice genome patents were filed before the related crop species were sequenced, there was relatively little sequence-based prior art to be found by patent examiners. As a result, earlier plant genome patents are likely to be broader in scope than later applications.

Innovation Support from CAMBIA

CAMBIA is continuously working to develop new tools and functionalities to support innovators worldwide.

CAMBIA provides tools such as the Patent Lens to enable patent and patent sequence searching.

The complexity of the patent system, unfortunately, can result in fear, uncertainty and doubt about what valid intellectual property rights exist. The existence of a patent does not necessarily mean that the claims are in force (e.g., maintenance fees or annuities might not have been paid) or valid (e.g., a court may have invalidated one or more claims). For this and other reasons, CAMBIA provides the Patent Lens, a free online resource that aims to increase transparency in the patent system. 

The Patent Lens is a fast, free, full-text searchable patent database containing documents from the largest patenting jurisdictions for the life sciences.  It holds over 8 million patent documents and is updated regularly.

The Patent Lens provides not only the ability to search and look at technology described in patents, but also to explore where patents may not be in force.  The patent status and patent family database allows patent searchers to check for information provided by the national patent offices on the dynamic status of patents and related patent applications in over 40 countries.

CAMBIA'S Patent Sequence Server

Finding nucleotide and amino acid sequences associated with patent applications and granted patents is often a hit-or-miss situation. Sequence listings are not always provided with a published application or patent, and when they are, they are not always in a text format that is compatible with conventional sequence analysis tools such as BLAST. To address this issue, CAMBIA has created a sequence server that allows a user to enter a patent (or patent publication number) and retrieve any sequences associated with that patent or application. The sequence server also provides links to the sequence at GenBank (if available) as well as BLAST.

CAMBIA provides tutorial material to explain patent law to non-patent professionals.

The Patent Lens facilitates learning about what patent rights apply where, by providing tutorials, IP analyses, and information about patents around the world.

Patent Landscapes

CAMBIA'S technology landscapes provide an overview of the patenting activity in important technology areas. We are in the process of integrating new patent informatics tools and features into the landscapes as we develop them. As such, our patent landscapes are "works in progress" that will continue to evolve with the new tools.

BiOS licenses

BiOS (Biological Open Source) is a legally enforceable framework to enable the sharing of the capability to use patented and non-patented technology, which may include materials and methods, within a dynamically expanding group of those who all agree to the same principles of responsible sharing, a “protected commons”.  Those who join a BiOS "concordance" agree not to assert IP rights against each others's use of the technology to do research, or to develop products either for profit or for public good.  BiOS-compatible agreements can support both freedom to operate, and freedom to cooperate.

Chapter 2: Rice Background

rice13-terrace

Rice is one of the most important cereal crops and feeds more than a third of the world's population (Khush, 1997). Rice is a monocarpic annual plant that usually grows between 1 and 1.8 meters tall with long slender leaves 50–100 cm long and 2–2.5 cm broad. Its small, wind-pollinated flowers are characteristic of grasses. The seed is a grain normally 5–12 mm long and 2–3 mm thick (see "Rice" in Wikipedia).

While rice is believed to have evolved around 130 million years ago (Chang, 1976), it is only considered to have been cultivated within the last nine thousand years (Patarapuwadol, 2005). There are two domesticated species: Oryza sativa, the most common, grown throughout Asia, Australia, the Americas and Africa; and Oryza glaberrima, grown on a small scale in western Africa.

There are three main varieties of Oryza sativa:

Within each variety, there are many cultivars, each favoured for particular purposes or regions. A japonica variety was the first to undergo genome sequencing, and is the focus of this landscape.

rice_closeup

Apart from the two domesticated species of Oryza, there are a further twenty-one wild species. Nine of the wild species are tetraploid. The remaining species, inclusive of the two cultivated ones, are diploid. The International Rice Research Institute (IRRI) has registered and preserved over 80,000 varieties of rice. Of these, 76,000 are said to be O. sativa  (Jackson 1997). All varieties of rice have 12 chromosomes.

Rice has the smallest genome size of all common cereals (see table below, comparing Oryza sativa against that of other plants).

Organism

Common Name

Genome Size

Oryza sativa

rice

    430 Mb

Sorghum bicolor

sorghum

    772 Mb [1]

Lycopersicon esculentum

tomato

    950 Mb

Zea mays

maize

  2365 Mb

Hordeum vulgare

barley

  5000 Mb

Triticum aestivum

wheat

17000 Mb

(Genome sizes were taken from the NCBI's Genomic Biology web pages.)

References

[1] Bowers JE, Abbey C, Anderson S, Chang C, Draye X, Hoppe AH, Jessup R, Lemke C, Lennington J, Li Z, Lin YR, Liu SC, Luo L, Marler BS, Ming R, Mitchell SE, Qiang D, Reischmann K, Schulze SR, Skinner DN, Wang YW, Kresovich S, Schertz KF, Paterson AH (2003) A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165:367-386

[2] Chang TT (1976) The origin, evolution, cultivation, dissemination, and diversification of Asian and African rices. Euphytica 25(1):425-41

[3] Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant molecular biology 35 (1-2), 25-34

[4] Jackson MT (1997) Conservation of rice genetic resources: the role of the International Rice Genebank at IRRI. Plant Molecular Biology 35(1-2): 61-67

Who are the top rice growers in the world?

The World's Top 10 Rice Growers (Compiled from 2005 IRRI Data)

No

Country

Rice Production
(thousand metric tons)

1

China

183,354

2

India

130,513

3

Indonesia

53,985

4

Bangladesh

40,054

5

Vietnam

36,341

6

Thailand

27,000

7

Myanmar

24,500

8

Philippines

14,615

9

Brazil

13,141

10

Japan

11,342

The Genomic Structure of Rice

The genome of Oryza sativa consists of 12 chromosomes, one circular mitochondrial DNA, and a circular chloroplast DNA. Additional information about the rice genome may be found at the TIGR Rice Genome Annotation site. Chromosomes are often drawn as in Figure 1 below: with a short and long arm and an intervening centromeric region. Figure 2 depicts the shapes and relative sizes of the Oryza sativa chromosomes. Table 1 shows the size (in Mbp) and predicted number of genes for each chromosome from Oryza sativa ssp. japonica (Nipponbare). 

Chr Figure

Rice chromosomes

Figure 1

Figure 2

Table 1

Chromosome

Size
(Mb)

Predicted Number

of Genes

Chr1

45.1

4467

Chr2

36.8

3011

Chr3

37.3

3197

Chr4

35.9

2679

Chr5

30.0

2426

Chr6

32.1

2342

Chr7

30.4

2507

Chr8

28.5

2286

Chr9

23.8

1618

Chr10

23.7

1724

Chr11

30.8

1834

Chr12

27.8

1870

Mitochondria

0.491

96

Chloroplast

0.135

159

Total

~383Mb

30216

Similarity Between Rice and Other Cereals

1. Rice has significant synteny with other cereals.

Synteny, or preservation of the order of genes on a chromosome, can be a marker for evolutionary history, or a key to functional relationships between genes. Over time, chromosomal rearrangements take place, and therefore the degree of synteny can give us information about shared ancestry. In organisms with a known shared ancestry, synteny can be used to predict the presence of genes in more than one species. Moreover, it means that genes present in one species are likely to be present in closely-related species. For example, the degree of synteny between rice and other cereals means that genes present in one or both rice species may well be present in other species.

But how great is the degree of synteny between rice and other cereals? Very great. In fact, if you look at any rice chromosome, the degree of synteny between it and, for example, maize is astounding (see Figure 1). This principle holds true for all the cereals, and means that genes present in one cereal will almost certainly be present in the same order in another. When Goff et al (2002 Science 296: 92-100) assessed the known proteins from maize, wheat and barley, 98% had homologues in the rice genome.

What is the significance of synteny between cereals? Why is this of concern when talking about patenting the rice genome? Depending on the language used in the patent, this could potentially mean that a patent on an important rice gene could cover, without separate patents, that gene in wheat, in corn, in sorghum, in rye, in sugar cane, etc. But is there significant homology between rice and other cereals at the level of individual genes?

2. Rice is homologous to other plants.

Just because the same "genes" exist in the same order on a chromosome in rice and wheat, for example, does not necessarily mean that the sequences of the individual genes or resulting proteins are identical or highly similar. There are examples of conserved genes that tolerate a great degree of diversity, and others that are virtually identical across a wide evolutionary range. Furthermore, many sequences that "drive" expression of important genes are patented. So what degree of homology exists between rice and other cereals? Homology is usually expressed in terms of "percent identity", although "percent similarity" is also used. Percent identity is more precise, as it means the percent to which two genes or proteins match exactly over a given seqeuence. When we look, as an example, at the homology between rice and wheat (Figure 2), we see that many rice genes are present that share nucleotide identity of 80% or more with wheat.

The same is true for maize. As shown in Goff et al. (2002 Science 296: 92-100), the regions of homology between rice and maize of greater than 80% over 100 bp. Virtually every part of the maize genome finds a homologue in rice, where the sequence identity is greater than 80%.

Figure 1: Comparison of chromosome 3 of the rice variety
japonica with the maize species Zea mays.

Rice/Maize Synteny

Image re-printed from http://www.gramene.org/

Note that to a large extent, the rice genes (centre) are present
in the same order on one or more maize chromosomes.

Figure 2: Comparison of the rice genome (chromosomes 1-12) with the wheat genome.

RiceWheatSynteny

Each coloured box represents a match of 80% or greater at the nucleotide level with a
wheat gene. The chromosomal location of the corresponding wheat gene is colour-coded
(wheat chromosome 1 is purple, wheat chromsome 4 is yellow and so on).

Image kindly provided by Dr Mark Sorrells, Department of Plant Breeding & Genetics,
Cornell, Ithaca, NY

Sequencing of the Rice Genome

Rice has the smallest genome of all common cereals (Khush GS, 1997). Rice was the first cereal to be fully sequenced, and both the indica and japonica genome sequences were published in 2002 (Yu J, et al. and Goff SA, et al.). The indica genome is 420 Mb in size and contains between 32,000 to 50,000 genes. The japonica variety is larger, at 466 Mb, and contains around 46,022-55,615 genes. For this landscape, we analyzed the japonica rice genome.

The genome was sequenced by both public and private groups, as described below.

varieties of Rice  fom IRRI

1. Public Efforts at Sequencing - the IRGSP

In 1997, a consortium of publicly funded laboratories called the International Rice Genome Sequencing Project (IRGSP) was established to map the rice genome. The consortium includes labs from ten countries: Japan, the United States of America, China, Taiwan, Korea, India, Thailand, France, Brazil, and the United Kingdom. The IRGSP adopted the "clone-by-clone shotgun sequencing strategy" so that each specific position on the genetic map was associated with a sequenced clone. IRGSP’s policy is that all rice sequence data must be released into the public domain. In December 2004, the completed rice genome sequence was made available through the NCBI database.

Research such as the genome-sequencing project has provided a wealth of molecular marker data, together with phenotypic, ecological, and archaeological data and has significantly helped our understanding of the evolutionary history of the genus Oryza (Khush GS, 1997). It has also assisted efforts to assimilate useful genes from wild species to cultivated rice through inter-specific hybridisation. Organizations such as IRRI have been using this knowledge to help modify rice in an endeavour to reduce poverty and hunger and to improve the health of rice farmers and consumers.

More information about the IRGSP participants are provided on the next page of the landscape.

2. Private Efforts at Sequencing

Private firms and other interested parties have also contributed to the sequencing of the rice genome. Key players in the private sphere were Monsanto, Syngenta and Myriad Genomics. Monsanto released all of its data into the public sphere, but not before they had filed patent applications on more than 200,000 sequences. Syngenta also released their sequence information, but not exactly in a timely manner. More information about the role of these companies is provided later in this landscape.

References

Goff SA, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 296(5565):92-100.

Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant molecular biology 35 (1-2), 25-34

Yu J, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 296(5565):79-92. 

 The International Rice Genome Sequencing Project (IRGSP)

The IRGSP is a consortium of public institutions that was established in 1997 to sequence the rice genome using Nipponbare, a cultivar of Oryza sativa ssp. japonica. It consisted of a number of publicly-funded organisations, including:

Rice Genome Research Program (RGP)
A Japanese-government-funded joint project of the National Institute of Agrobiological Sciences (NIAS) and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF). The program itself was part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Program.

The Institute for Genomic Research (TIGR)
A not-for-profit institute involved in the sequencing and analysis of genomes. Based in Rockville, Maryland, USA.

National Center for Gene Research Chinese Academy of Sciences (NCGR)
Established by the Ministry of Science and Technology, the Shanghai local government, and the Chinese Academy of Sciences (CAS) in 1992. The NCGR was responsible for sequencing chromosome 4 from rice.

Arizona Genomics Institute (AGI)
The AGI, CSHL, Washington University and University of Wisconsin (ACWW) consortium was granted funds in 1999 (from USDA/NSF/DOE/CSREES) to sequence and annotate the short arms of chromsomes 3 and 10 as part of the IRGSP.

Cold Spring Harbor Laboratory (CSHL)
A private, not-for-profit, organisation based in Cold Spring Harbor, NY. Involved in sequencing chromosomes 3, 5, 9, 10, and 11 from Oryza sativa L. ssp. japonica cv. Nipponbare. 

Plant Genome Initiative at Rutgers (PGIR)
PGIR was established to participate in the international efforts to sequence the rice genome.  It is a high-throughput sequencing facility, of medium capacity, also involved in sequencing the maize genome. Based at the Waksman Institute, Rutgers University, The State University of New Jersey, New Jersey.

Genoscope (France)
The French National Sequencing Center, founded in 1997 in Evry, near Paris. Involved in sequencing chromosome 12 from rice.

Academia Sinica Plant Genome Center (ASPGC)
Based at the Institute of Botany, Academia Sinica, Taipei, Taiwan. Support derived from National Science Council, Council of Agriculture, Academia Sinica and the Institute of Botany. This group was involved in the sequencing of chromosome 5.

Indian Initiative for Rice Genome Sequencing (IIRGS)
Founded through efforts of the Department of Biotechnology, and the Indian Council of Agriculture. The Initiative is based in New Delhi and was involved in sequencing of the long arm of chromosome 11

Korea Rice Genome Research Program (KRGRP)
Sponsored by the Rural Development Administration, Suwon, Korea, under direction of the Science and Technology Policy Institute. The program was responsible for generating more than 100,000 rice ESTs.

National Center for Genetic Engineering and Biotechnology (BIOTEC)
Thai component of rice sequencing efforts.

Wisconsin Rice Genome Project (GCOW)
Based at the University of Wisconsin-Madison, within the University of Wisconsin Biotechnology Center. Involved in sequencing chromosome 11. 

John Innes Centre (JIC)
An international centre of excellence in plant science and microbiology, based in the  Norwich Research Park, Norwich, UK. Funded by both local and international funding bodies, including the Biotechnology and Biological Sciences Research Council (BBSRC).

Brazilian Rice Genome Initiative (BRIGI)
Involved in sequencing of chromosome 9.

IRGSP adopted an incremental (clone-by-clone) shotgun process so that each sequenced clone can be associated with a specific position on the genetic map. This sequencing process was therefore slower than the whole-genome shotgun sequencing strategy adopted by other rice sequencing projects, but the result was the most complete sequence of the entire rice genome. The project was completed 3-years ahead of schedule in 2005 with help from the Monsanto draft rice genome sequence data. Total international funding was ~US$150 million (CSREES figures).

Other Rice Genome Sequencing Efforts

In addition to the public rice genome sequence efforts, there have been several notable commercially-funded efforts to determine the nucleotide sequence of rice. For additional information, see the NCBI Oryza sativa (rice) genome view.

  1. Monsanto

  2. Syngenta and Myriad Genetics

  3. The Rice Full-Length cDNA Consortium (Japan)

  4. Beijing Genomics Institute (BGI)

     

1. Monsanto

In April 2000, Monsanto was the first private company to announce a working draft of genetic map of rice (japonica type). Monsanto’s sequencing had been done under contract by universities that received both public funds and funding from Monsanto. Although Monsanto's sequencing was carried out simultaneously with the public sequencing initiative, the Monsanto data were not released to the public until June 2000, when Monsanto launched the now-defunct rice-research.org database to provide access for publicly funded researchers to its draft rice genome sequences. Shortly before Monsanto released the rice sequence data, they filed U.S. patent applications claiming more than 200,000 rice genes, promoters, and other sequences. See the Monsanto page in Chapter 10 for more information about Monsanto's patenting of the rice genome.

2. Syngenta and Myriad Genetics

In January 2001, Myriad Genetics and Syngenta announced that they had also completed DNA sequencing of the entire rice genome. Excerpts from Nature News 5 April 2002:

"We can use the rice genome to help improve wheat and corn right now. The genes are interchangeable," says a member of the commercial sequencing team, Stephen Goff of the Torrey Mesa Research Institute, San Diego….

The publicly funded International Rice Genome Sequence Project, is set to deliver a complete sequence based on a slower, more expensive, but more complete, technique in 2004. 

"This will be gold standard", says plant biologist Michael Bevan of the John Innes Institute, Norwich, UK. "These papers are landmarks, but they're only part of the story.”….

In the end, Syngenta has made its sequence freely available, through its own website, to non-profit institutions…

Bevan is sanguine about this arrangement. "Syngenta put a lot of resources into the project, and they need to see returns," he says. "Hopefully they will have extracted all the juice they want from the genome in a year or so and will make it fully accessible."

New Scientist (Coghlan, A., New Scientist Print Edition 14:19, 2001) also published an article about Syngenta and Myriad Genetics' sequencing project. Quote from the New Scientist article:

"Rice has become the first crop plant to have its entire genome sequenced. Syngenta, the Basel-based multinational that funded the breakthrough, expects the rice genome to unlock genetic secrets of all cereals, from wheat and barley to maize and sorghum."

3. The Rice Full-Length cDNA Consortium (National Institute of Agrobiological Sciences, RIKEN, and the Foundation for Advancement of International Science Genome Sequencing and Analysis Group

In this project, 28,469 full-length complementary DNA clones from Oryza sativa were sequenced by a consortium in Japan. The research team was led by Dr. Shoshi Kikuchi at the Department of Molecular Genetics, National Institute of Agrobiological Sciences in Ibaraki, Japan. The results of this sequencing effort were published in Science (Science 301:376-379, 2003). Other participants included the Foundation for Advancement of International Science Genome Sequencing and Analysis Group, and RIKEN.

The consortium collected 3'- EST sequences of 175,642 cDNA clones from rice, clustered them into 28,469 nonredundant groups, and sequenced all representative clones from each group. Through homology searches, they assigned protein functions to roughly 75.86% of the clones.

Shortly before the Science paper was published, the consortium filed a patent application claiming 28,469 cDNA sequences. Later in this landscape, we show a claim analysis of this patent application.  Note, however, that any of the sequences filed earlier by Monsanto would constitute prior art against RIKEN's claims.

A related scientific publication was authored by Nagata et al. in 2004 (Mol Biol Evol. 21(10):1855-70). This publication disclosed a comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data.

4. Beijing Genomics Institute (BGI)

All above rice sequencing projects used Nipponbare, a cultivar of the rice subspecies japonica (Oriza sativa ssp. japonica), as the target rice cultivar. Beijing Genomics Institute, however, chose to sequence Oryza sativa ssp. indica, the major rice subspecies cultivated in China and many other Asian-pacific regions. Sequencing a different type of rice is important because it aids in understanding of the differences between different rice species. 

BGI's sequencing project was initiated in May 2000, and used 93-11, a cultivar of Oryza sativa L. ssp. indica, as target material. This particular cultivar of indica is the paternal cultivar of a "super" hybrid rice breed called Liang-You-Pei-Jiu or LYP9, which has 20 to 30% higher yield per hectare than the average of other rice crops in the fields. A working draft of the 93-11 genome sequence was completed in October 2001 and published in Science 296: 79-92, 2003.

BGI then launched a Rice Information System (BGI-RIS) to host the rice sequence data from 93-11. In addition, the sequence information of japonica rice from Syngenta has also been included in this system based on an agreement between BGI and Syngenta. More detailed information about BGI-RIS can be found in Nucleic Acids Research, 32: D377-D382.  

Chapter 3: Genome Patenting Issues

rice3-ricebowl

There are many issues associated with genome patenting that make it different from patenting articles of manufacture. This chapter discusses some of the issues relating to the patenting of genes, for example, why gene sequences are patentable, how patent craft has evolved in the post-genomic era, and how to search for biological sequences that are the subject of a patent or patent application.

Why are gene and protein sequences patentable?

The mantra is that "anything under the sun made by man" is patentable. Using this criteria, it would appear that genes and proteins, which exist naturally within living organisms, would not be patentable. However, patent laws in many jurisdictions, including the United States, Europe and Australia, allow patent applications to claim nucleotide and amino acid sequences as compositions of matter as long as they have been isolated from their cell of origin. Isolated nucleotide and amino acid sequences claimed under "composition of matter" claims in a U.S. patent are like any other patented technology in this respect. If used in a way that is covered by the claims of a patent that is in force, the user may be subject to being stopped by injunction or be required to pay royalties.

The road to allowing patents on sequences began with a U.S. Supreme Court case involving a genetically-engineered bacterium for cleaning up oil spills.  In this oft-cited case of Diamond v. Chakrabarty (447 U.S. 303 (1980)), the Supreme Court had no difficulty finding that a living, genetically-altered organism may qualify for patent protection.  From there, patent law in the U.S. evolved to allowing patents on many types of biotechnology products, including transgenic plants and eventually for DNA and protein sequences.  The rationale for concluding that DNA sequences - and by extension, protein sequences - are patentable is that the claimed sequences are human-made; they are "purified and isolated" sequences (Amgen, Inc v. Chugai Pharm. Co. Ltd., 13 U.S.P.Q. 2d 1737 (D. Mass. 1989), aff'd in part, rev'd in part, vacated in part, 927 F.2d 1200 (Fed. Cir. 1990), cert. denied, 502 U.S. 856 (1991)).  This view is very controversial and at times contentious, even within the U.S. courts. 

In the 1990s, the U.S. Patent Office granted many patents claiming "purified" or "isolated" nucleotide and amino acid sequences.  The year 2001 however, brought a change that severly limited the ability to obtain claims reciting sequences.  The U.S. Patent Office released the "Utility Examination Guidelines", which set out procedures for ensuring that patent applications complied with the utility requirement of patent law (Federal Register, Vol. 66, 1092-1099).   A claimed invention now had to have a "specific and substantial" or a "well-established" utility.  The impact was huge for claims to sequences.  Under these rules, a claim to "A cDNA consisting of the sequence set forth in SEQ ID No: 1." is unpatentable unless there is a known function for the sequence.  In addition, more restrictive rules may well be implemented in the near future. 

Thus, in the United States, after a period of granting expansive patent claims, it has become increasingly more difficult to obtain patent claims to DNA or amino acid sequences. 

Broadening Claim Language in Gene Patents

The claims define the scope of a patent. There are different types of claim language that are used in gene-based patents and patent applications that broaden the scope of the claim beyond the actual sequences that are disclosed in a specification. For the purposes of this landscape, we refer to this type of claim language as "broadening language".

Examples of different types of broadening language include the following:

Hybridisation Language

Percent Identity Language

Amino Acid Substitutions

Any Nucleotide Sequence that Encodes a Given Amino Acid

Hybridisation Language

Hybridisation language in claims allows an applicant to claim a particular nucleotide sequence, as well as any nucleotide sequence that hybridises to that sequences under a given set of experimental conditions. See a tutorial on the basis for hybridisation language for a more detailed description. An example of a claim with hybridisation language is claim 1 from US Patent No. 5747327:

A cloned DNA which encodes phospholipase D originated from a plant, wherein said DNA comprises a nucleotide sequence selected from the group consisting of nucleotides 182-2617 of SEQ ID NO:1 and nucleotides 107-2542 of SEQ ID NO:3 or a sequence complementary thereto or a sequence which specifically hybridizes to said cloned DNA or said complementary sequence in a hybridization solution containing 0.5M sodium phosphate buffer, pH 7.2, containing 7% SDS, 1 mM EDTA and 100 mg/ml of salmon sperm DNA at 65° C. for 16 hours and washing twice at 65° C. for twenty minutes in a washing solution containing 0.5×SSC and 0.1% SDS.

Percent Identity Language

Percent identity language, which is also sometimes expressed as percent similarity language, allows an applicant to claim not only the sequence of interest, but any sequence that is for example, 70, 80, or 90% identical to that sequence. This dramatically broadens the scope of the claim by increasing the number of individual sequences that meet the criteria of the claim. Percent identity or similarity language may be used with either nucleotide and amino acid sequences.

A potential difficulty with determining the meaning of a claim with percent identity language is that applications do not always specify the parameters for calculating the percent identity. There are many different algorithms that may be used to determined how similar sequences are to each other. Many algorithms assign different values for gaps in sequences that can affect the overall percent score in a variety of ways. 

Such claims are not often granted these days. Unless examples of related sequences are specified in the patent and furthermore are shown to have similar function, they are not usually allowed. 

For example, the first claim of US Patent No. 6821764:

  1. An isolated nucleic acid fragment encoding a serine O-acetyltransferase comprising: (a) a nucleotide sequence encoding a polypeptide having serine O-acetyltransferase activity, wherein the polypeptide has an amino acid sequence of at least 95% sequence identity, based on the cluster, when compared to SEQ ID NO: 8 or (b) a full complement of the nucleotide sequence of (a).

Amino Acid Substitutions

Some applications include claim language reciting particular amino acid substitutions.   For example, claim 1 from US Patent No. 7057088:

An isolated DNA encoding a protein selected from the group consisting of

(a) a DNA encoding a protein comprising the amino acid sequence set forth in SEQ ID NO: 1,
(b) a DNA comprising the nucleotide sequence from position 54 to 1199 set forth in SEQ ID NO:2, and
(c) a DNA encoding a protein comprising the amino acid sequence set forth in SEQ ID NO:1,

wherein one to 10 amino acid residues are substituted, deleted, added, and/or inserted and wherein said protein:

(i) has gibberellin 2β-hydroxylase activity; and
(ii) conserves amino acids corresponding to His-241, Asp-243 and His-302 in the amino acid sequence set forth in SEQ ID NO:1.

Claiming Any Nucleotide Sequence that Encodes a Specified Amino Acid Sequence

One common way to capture a nucleotide sequence is provide the SEQ ID NO of an amino acid and word the claim such that any nucleotide sequence that encodes that amino acid sequence is claimed. Because the genetic code is degenerate, such a claim encompasses a very large number of nucleic acid sequences.

For example, the first claim of US Patent No. 7268271

A method for increasing LEC1 expression in a plant cell, wherein said increase is measured against a control plant cell, said method comprising introducing an isolated LEC1 nucleic acid into the plant cell to produce a plant cell that exhibits increased LEC1 expression, wherein the isolated LEC1 nucleic acid comprises a member selected from the group consisting of (a) a polynucleotide which encodes a polypeptide of SEQ ID NO: 2;(b) a polynucleotide of SEQ ID NO: 1; and(c) a polynucleotide complementary to a polynucleotide of (a) or (b).

SEQ ID NO:2 is purely an amino acid sequence, and thus all nucleic acids coding for this sequence are covered by this claim.

Cross-Species Patent Coverage

As discussed in Chapter 2 of this landscape, rice has significant homology and synteny with other plant species. This leads to the possibility that composition of matter claims for rice sequences and related sequences (related by a specified percent identity or by hybridization) will encompass similar sequences in other plants. We refer to this as "cross-coverage".

For example, a claim that reads:

An isolated nucleic acid sequence that has at least 80% sequence identity to SEQ ID NO:10.

may “literally” cover more than one species if there are sequences from more than one species that fall within the 80% sequence identity range.

In the U.S., there is a presumption of validity for patent claims, but there are a number of other factors that may actually limit the scope of claims that at first glance appear to literally cover other species. Some of these factors include:

A detailed analysis is necessary to determine if a patent claim to a sequence covers more than one species.

There are a number of ways that the claim language itself may limit the number of species covered. For example:

An isolated nucleic acid sequence that has at least 80% sequence identity to SEQ ID NO:10, wherein the isolated nucleic acid sequence is from maize.

Because this claim specifies maize, it would likely not cover rice.

An isolated nucleic acid sequence that has at least 80% sequence identity to SEQ ID NO:10, wherein the isolated nucleic acid sequence encodes a polypeptide of a monocot.

In this case, a polypeptide that was more than 80% identical that encoded a dicot polypeptide would likely not fall under the scope of the claim.

An isolated nucleic acid sequence that has at least 80% sequence identity to SEQ ID NO:10, wherein the isolated nucleic acid sequence encodes a soluble starch synthase.

With this claim, if there were a sequence that was more than 80% identical that encodes an insoluble starch synthase, it would probably not fall under the scope of the claim.

How many nucleotide sequences can be examined in a patent application?

While it may initially be alarming to find a patent application that claims thousands, or tens of thousands of sequences, it is highly unlikely that the application will be granted with more than one, or possibly a few.  The United States Patent Office currently only examines one claimed sequence in each patent application.  However, it is important to note that policies limit the number of sequences examined, but not the number of sequences in the claim set as initially filed.  The limitation to one sequence occurs in the inital stage of the examination process, which often takes place long after the application (with the initial bulk claim set) has published.

Policy in the U.S. - one sequence per application

According to a notice issued by the USPTO (1316 O.G.13, 27 March 2007), for new applications, an examiner has the option to restrict claims such that only a single nucleotide sequence will be examined per application. The examiner, however, does retain the option to examine more than one sequence if he or she deems it appropriate.  

This notice rescinded a 1996 notice (1192 O.G. 68, 19 November 1996) on the subject. In that notice (see Section 2434 of the MPEP), the USPTO issued a partial waiver of 37 CFR 1.141 to permit examination of up to 10 independent and distinct nucleotide sequences claimed in a single application.  A similar revision was also made for search and examination of applications filed under the PCT, as a partial waiver of 37 CFR 1.475.

Despite the 1996 Notice, PTO examiners usually examined only a single nucleotide sequence.  The 2007 Notice simply eliminated the opportunity for applicants to argue that claims to multiple nucleotide sequences should be examined together.  

While these notices do not specifically mention polypeptide (amino acid) sequences, polypeptide sequences are also generally limited to one sequence per application.

PCT Policy - multiple sequences if sufficiently linked as an inventive concept

For PCT patent applications, the number of sequences examined in an application is limited by Rule 13, Unity of Invention. Rule 13 requires that "the international application shall relate to one invention only or to a group of inventions so linked as to form a single general inventive concept". For applications claiming multiple nucleic acid sequences, "unity of invention will exist when the polynucleotide molecules, as claimed, share a general inventive concept, i.e., share a technical feature which makes a contribution over the prior art." Therefore, for applications filed in the United States through the PCT process, more than one sequence can be examined in an application. 

Is my sequence patented?

It is not always a straightforward task to determine if a sequence of interest is already patented, or is the subject of a pending patent application.   Sequences in claims are referred to by a number designator - e.g., SEQ ID NO: 1.  The sequences themselves are in a separate section called the Sequence Listing.  Unfortunately, in the Sequence Listing, there is usually little annotation of the sequences. Annotation, such as it is, must be teased out of the patent text.

To compare sequences in the Sequence Listing and claims to a selected sequence, there are options.  Free search options include BLAST and CAMBIA's patent sequence search tool, and pay options include a number of proprietary or subscription based services, such as Thompson-Derwent and Genome Quest.

BLAST

BLAST is a program that finds regions of similarity in biological sequences. It can be used to search for similar nucleotide or amino acid sequences, and also allows searches of a translated nucleotide database using both nucleotide and amino acid queries. To search for patent sequences in BLAST, the patent database must be selected. An oft-used patent database is provided by GenBank, and it contains sequences from granted U.S. patents as well as sequences in published PCT applications and Japanese patents. This search collection currently lacks sequences in U.S. applications, however. Searching with BLAST will identify many patents that contain sequences that are similar to a sequence of interest, but does not differentiate between sequences that are in the Sequence Listing from sequences referenced in claims.

CAMBIA's Patent Sequence Search Tool

CAMBIA offers a free patent sequence search tool that uses the BLAST search interface. The search collection includes sequences from granted U.S. patents as well as U.S. patent applications, all of the sequences in the GenBank collection, as well as many more sequences that are provided by the USPTO in a different format, e.g., sequences from bulk sequence applications.  An important feature of our search tool is that it allows users to search for patent sequences that are claimed in patents and patent applications rather than sequences that are simply disclosed in the specification.

Claim Language is Key

Claim language is complex and quite variable, and does not lend itself well to automated analysis via software solutions. If a sequence of interest is recited in a patent claim, it is the claim language that ultimately determines if the sequence is patented or not.

Below is an example where a sequence mentioned in the claims is actually claimed as a composition of matter:

An isolated nucleic acid segment comprising the sequence of SEQ ID NO:2.

Alternatively, here is an example of a claim that recites a sequence, but where that sequence is not claimed: 

A vector construct comprising the sequence of SEQ ID NO:7 operatively linked to a nitrogen-responsive promoter.

The claim states that the sequence of SEQ ID NO:7 must be "operatively linked to a nitrogen-responsive promoter". Therefore, the claimed nucleotide encompasses both SEQ ID NO:7 and the promoter, and if your sequence was linked to a different type of promoter, then the use of your sequence would not infringe upon this patent.

What are some options if a sequence that you are working on is claimed in a patent or patent application?

A granted U.S. Patent gives a patentee the right to exclude others from making, using, selling, or offering to sell the claimed invention in the U.S. In addition, a patentee may exclude others from importing the claimed product or product of a claimed method, even if it is not patented in the originating country.

Patent applications are not the same as granted patents. If there is no granted patent, there is no infringement. If a patent owner has a good faith belief that you are infringing her patent, the patent owner may request that you "cease and desist", demand licensing fees or royalties, or sue you in court.

So, what if you have discovered that a nucleotide or amino acid sequence that you are working on in your laboratory is claimed in a U.S. patent or pending application? Don't panic! There are a number of options available to you.

First, take a careful look at the claim language to see if the sequence that you are concerned about is indeed claimed in a patent or patent application. Remember that a patent in the U.S. only applies to the U.S. If you are in another country, a U.S. patent or patent application does not apply to you (unless you plan to import the patented subject matter into the U.S.). Refer to the last section of the previous page in this landscape paper for examples of sequences that are simply recited in a claim as opposed to claimed as compositions of matter.

Options if it is a patent application in the U.S.:

  1. Submit prior art to the examiner as a "third party submission". If the application is a U.S. application, and if you have evidence that the sequence was published prior to the patent filing date, and the application of interest was published less than two months prior, you (as a third party) may submit patents or publications for consideration in a pending published application, pursuant to 37 CFR 1.99 (rule 99). With these types of submissions, the third party is not allowed to comment or provide explanation as to what they are submitting. See section 1134.01 of the MPEP for more information about this option. The downside to this approach is that the examiner is not obligated to consider your submission.

  2. Submit prior art to the inventor or assignee. You, or a party on your behalf, can submit the publication in which the sequence is published to the applicant. If it is actually prior art, and the applicant hasn't already submitted it to the examiner, applicant then has a duty to disclose it. The downside to this approach is that if you identify yourself in the submission, the patent applicant may be alerted that you are working on the sequence, and if the patent issues, may flag you for royalties or legal action.
  3. Do nothing. If you are at a university or non-profit institution, and if you are not using the sequence for commercial gain, it is unlikely that a patent applicant will take legal action against you when the patent issues. See the article by Nottenburg et al. "Accessing other people's technology for non-profit research" (link is to a PDF) for more details. A downside to this is that if you use the subject matter of a patent application, and the patent later issues, and the claims in the granted patent are substantially identical to the claims in the application, the patentee has the option to collect royalties retroactively to the publication date of the patent. See 35 USC 154 for more details on information about "provisional patent rights".

Options if it is a granted patent in the U.S.:

  1. Negotiate a license. Contact the patent holder and see if they would be willing to provide you with a license to use the sequence. Some companies grant different types of licenses depending on who's seeking it. If you are a researcher at a university or non-profit organization, they may grant you an inexpensive or cost-free non-commercial license. The downsides to this is that the fee for the license may be more than you can afford to pay, or that they may refuse to grant you a license at all.  In addition, you are alerting the patent holder to a potential infringer. 
  2. Initiate a reexamination. If you have evidence that the patent is invalid due to prior art, you can initiate a patent reexamination. There are two types of patent reexamination; an inter partes reexamination, and an ex parte reexamination. For an inter partes reexamination, both the reexamination requester and the patent holder may file briefs with the USPTO. With an ex partes reexamination, only the requester files a brief. If the USPTO finds the claims unpatentable over the new prior, they will cancel them. The downside to this option is that affirmation rates of patents in reexamination proceedings is relatively high.
  3. Invent around the patent. Depending on the scope of the claims, and whether or not broadening language is used, you may be able to make minor substitutions in the nucleotide or amino acid sequence that will allow you to "work around" the patent claim without affecting the function of your sequence. The downsides are that re-engineering DNA or protein constructs can be expensive and time-consuming, and that broadening language may make this difficult or impossible to do.
  4. Do nothing. If you are at a university or non-profit institution, and if you are not using the sequence for commercial gain, it is unlikely that a patent applicant will take legal action against you. See the article by Nottenburg et al. "Accessing other people's technology for non-profit research" (link is to a PDF) for more details. Another important fact to note is that due to 11th amendment to the U.S. Constitution, which deals with each State's sovereign immunity in regards to federal lawsuits, state universities cannot be sued in federal court. The downside is that you may expose yourself to risk of legal action, particularly if you are using the sequence in collaboration with a for-profit company.
  5. Get a legal opinion. A legal opinion will protect you from willful infringement charges if you choose the "do nothing" option. The downside to this option is that legal opinions are generally quite costly and will not protect you from a lawsuit or being judged as an infringer.

Chapter 4: Mapping of Rice Patents and Patent Applications Onto the Rice Genome

rice17-hand

CAMBIA has produced a patent landscape for the Oryza sativa genome. Our analysis included both granted U.S. patents and pending patent applications. In addition to structural genes, our study encompassed non-coding nucleotide sequences such as promoters.

This chapter shows the results of our analysis. In addition to static plots, we have incorporated the Gbrowse genome browser to enable interactive visualization of the patent and patent application sequences relative to the rice genome.

Summary

Surprisingly, only 0.26% of the rice genome is recited in the claims of granted U.S. patents.

This fraction represents the actual, non-redundant coverage of the genome by the sequences that were identified in our analysis. The analysis included all sequences recited in claims, whether they encoded proteins or not. In contrast, the Jensen and Murray analysis reported that around 20% of the coding sequences of the human genome were claimed in granted U.S. patents (Science 310: 239-240). This is a different metric than we used for determining the overall percent coverage. An approximation can be made of the fraction of coding sequences claimed in U.S. patents, however, by estimating the number of claimed coding sequences (213) and dividing by the total number of rice genes (coding sequences) (37,544 according to Nature, 2005, 436: 793-800).  Using this formula,  the percent coverage is roughly 0.57%, but still remains below 1% of the rice genome.

Patent applications show a different picture as to the fraction of the rice genome recited in claims. Due largely to “bulk sequence applications”, roughly 74% of the rice genome is recited in claims of U.S. patent applications. But due to patent examination policies in the U.S., it is unlikely that very many of these sequences will become part of the claims of granted patents.

These numbers are our best estimate based on our chosen methodologies. In some ways, they are an overcount of the number of patents that recite rice sequences in the claims, because a number of these patents and patent applications are directed at plants other than rice. Therefore, the claims may not actually encompass the rice gene. Also, some of the claims that are included in this analysis are method or product claims that don't directly claim a rice sequence as a composition of matter.

On the other hand, the numbers presented here are an undercount because we did not include nucleotide sequences that are claimed based on the amino acid sequences that they encode. A common practice is to claim "any nucleotide sequence that encodes the amino acid sequence of SEQ ID NO:X". This type of claim will not be picked up in our current analysis because it is an amino acid sequence rather than a nucleotide sequence that is recited in the claim. In future revisions of this landscape, we plan to incorporate amino acid claims to provide a more complete picture of the rice genome.

Methods for Rice Genome Landscaping

In this landscape, we have determined the extent to which the rice genome nucleotide sequences are recited in the claims of both issued U.S. patents and U.S. patent applications. Our process entailed a number of informatics steps that are outlined below.

In summary, we compiled a database of patent nucleotide sequences that are recited in the claims of granted U.S. patents and U.S. patent applications, and compared these sequences to the published rice genome using MEGABLAST. We determined which sequences were highly homologous to sequences in the rice genome and mapped these sequences to the corresponding location on the rice chromosome. We only included sequence matches that yielded a BLAST E value of 1e-200 or less, which is highly statistically significant. The results of our analysis are shown in the subsequent pages of this landscape.

It is important to note that the patent and patent application sequences used in this analysis were selected without reference to which genome they are from. For example, if a maize sequence is nearly identical to a rice sequence, then it will be included in our list of results. We have chosen to include such sequences because the inherent similarity of plant genomes makes it possible for patents that claim one species to dominate another. For example, it is possible that a patent claiming a maize sequence can result in exclusionary treatment of the corresponding rice sequence. Chapter 3 discusses this concept in more detail.

1. Compilation of a searchable rice genome database

We started with the most recent rice genome sequences from the TIGR Rice Genome Annotation web site and then used the formatdb program from NCBI to convert the data to a searchable BLAST database.

2. Compilation of sequence databases for granted patents and patent applications

Applications

For patent applications, we acquired the sequences of the bulk sequence applications from the Publication Site for Issued and Published Sequences (PSIPS) web site. This web site provides sequence listings for U.S. patents and patent applications with sequence listings that are longer than 300 pages. We also acquired the sequence listings for the non-bulk sequence listings (fewer than 300 pages in length) that are published by the USPTO as an XML document. For each of the listing types (bulk sequence and non-bulk sequence), there was a separate file for nucleotides and amino acids. Data for U.S. applications are available since 2001, when patent applications began to be published.

The bulk and non-bulk sequence listings were then converted to a common data format (FASTA) and combined to create one database for nucleotide sequences, and one database for amino acid sequences. Additionally, each of these combined databases was converted to a searchable BLAST database for use with CAMBIA's patent sequence search tool.

Granted (Issued) Patents

For granted U.S. Patents, we had a data source that wasn't available for the applications; GenBank at NCBI has a searchable patent database of sequences disclosed in granted patents. To create our granted patents sequence database, we started by acquiring the U.S. patent sequences from GenBank. This required removing all sequences that originated from non-U.S. patents.

We then acquired the sequence listings from the bulk and non-bulk patents in the manner described above in the Applications section. The data from all three sources (GenBank, bulk, and non-bulk) were converted to a common format. We then carried out a filtering step that removed any duplicate sequences in the data provided by GenBank, and the sequences provided by the USPTO (bulk and non-bulk).

The identical process was carried out for nucleotide sequences and amino acid sequences, however, our analysis currently is confined to nucleotide sequences. As with the patent applications, each of these combined databases was converted to a searchable BLAST database for use with CAMBIA's patent sequence search tool.

3. Identification of sequences that are recited in the claims of granted patents and patent applications

A key feature of our analysis is parsing out the sequences that were recited in the claims of patents and patent applications, rather than just disclosed in the specification. The goal is to ultimately identify sequences that are claimed in patents and applications, but normally a review of the claim language by a human being is required to determine whether sequences that are mentioned in claims are actually claimed. To this end, we created four databases that contain only the sequences that are mentioned in the claims of patents and patent applications. These four databases correspond to nucleotide sequences in applications, amino acid sequences in applications, nucleotide sequences in granted patents, and amino acid sequences in granted patents.

We compiled a list of common phrases that are used to identify sequence listings in claims. This step was tricky, as there are many different phrases that patent applicants use to designate sequence listings in claims. Using these phrases, we created a list of sequence ID numbers that are designated in patent claims. Four new databases were then created that contain only the sequences mentioned in the claims of patents and patent applications.

4. MEGABLAST search of rice genome database using the sequences mentioned in claims as input

After compiling a collection of sequences that are mentioned in the claims of patents and applications, we then used those sequences to query the rice genome database (see step 1) using MEGABLAST to identify sequences that have significant homology to sequences in the rice genome. The criteria for matches in the database was that they have a BLAST E value less than 1e-200. We performed this analysis only with the nucleotide sequences mentioned in the claims of patents and patent applications.

5. Plotting the results of the analysis

The sequences with significant homology to sequences in the rice genome were plotted three different ways. 

  1. Sequence Count. For these plots, the Oryza sativa genome was divided into 300 kbp segments. For patent applications that claim Oryza sativa gene sequences, we plotted the number of sequences that match at least a 150 bp fragment of each 300 kbp genome segment. For each sequence, only the highest-scoring genome match was counted.
  2. Patent Count. As with the Sequence Count plots, the Oryza sativa genome was divided into 300 kbp segments. For patent applications that claim Oryza sativa gene sequences, we plotted the number of patent applications that claim a 150 base pair or longer fragment of each 300 kbp genome segment. For each sequence, only the highest-scoring genome match was counted.
  3. Percent Genome Coverage. For these plots, we plotted the percentage of each genome segment that was recited in the claims of patent applications. Unlike the previous two plot types, there was no requirement that the fragments that matched the rice genome sequences be a minimum length (e.g., 150 base pairs). However, the minimum size for a positive match using MEGABLAST is 26 base pairs, so matches shorter than 26 were not included in the analysis. In addition, if multiple sequences covered the same portion of the genome, that portion of the genome was counted as being covered only once.

The end result of our analysis was a dataset of patents containing rice sequences in their claims, linked to the specific map location of those sequences on the rice genome. The sequences and matched genomic regions are made using highly specific search criteria, resulting in "exact" matching of sequences recited in the claims to their corresponding genomic sequence. No attempt was made to identify homologous sequences within the genome, which may also be claimed by the patent document. Hence the maps obtained are likely to under-represent the actual sequence claims in rice, from patents claiming rice sequences.

Whole Genome View of Nucleotide Sequences from U.S. Patents that are Highly Similar to Rice Genome Sequences

To generate the data for this application, sequences were extracted from both US applications and US granted patents. The extracted sequences were then compared to the genome using MEGABLAST, and are shown here using the Gbrowse genome browser.

Granted U.S. patents are designated by the blue arrow heads, and applications are designated by the grey shading on each of the 12 chromosomes. The darker the shading, the more patent application sequences there are with homology to that particular section of the chromosome*.

The figure below is interactive! Click on a chromosome to see more detail about rice patents and patent applications, and then shift + click to see the region in greater detail.

How to use the genome viewer:

  • click on a chromosome to see a higher resolution view
  • mouse over a feature to see a label
  • shift + click on a chromosome or feature to view segment in the CAMBIA Rice genome browser
  • to print this figure, right-click (or control + click) to bring up Flash controls and select the print option

* Each chromosome is divided into sections 300,000 base pairs in length. It is important to note that it is possible that each 300,000 base pair section encompasses a plurality of different sequences, and therefore a dark shading pattern may indicate that multiple sequences are recited in the claims of patent applications, rather than a single sequence recited in the claims of multiple patent applications.

U.S. Applications that Recite Nucleotide Sequences in Claims

The blue bars in the plot below represent the total number of newly-filed U.S. patent applications per month that recite nucleotide sequences in their claims. The nucleotide sequences can be from any organism.  The applications were plotted by their filing date. In order to be included in the graph, the sequence had to be at least 150 base pairs in length and have a BLAST E value that was less than 1e-200. Note that there is an 18 month delay between when an application is filed and when it is published, so the data for the last 18 months is incomplete.

Summary

This plot indicates that the number of applications that recite nucleotide sequences in the claims appears to be have decreased after peaking in 2002.

U.S. Applications that Recite Oryza sativa Nucleotide Sequences in Claims

The blue bars in the plot below represent the number of US patent applications filed per month that recite at least one Oryza sativa nucleotide sequence in their claims. The applications are plotted by their filing date. In order to be included in the graph, the sequence had to be at least 150 base pairs in length and have a BLAST E value that was less than 1e-200. Note that there is an 18 month delay between when an application is filed and when it is published, so the data for the last 18 months is incomplete.

Summary

Similar to the previous page showing all U.S. applications, this plot indicates that the number of applications that recite Oryza sativa nucleotide sequences in the claims appears to be decreasing. The number of applications reciting rice sequences appears to have peaked in 2003.

Granted US Patents on Oryza sativa

US Patent Applications on Oryza sativa

Granted U.S. Patents: Number of Sequences Oryza sativa Sequences Referenced in Claims per Genome Segment

The blue bars in the plots below represent the number of sequences recited in the claims of U.S. patents that match a given 300 kilobase pair (kbp) segment of the rice genome. By match, we mean that the patent sequence is at least 150 base pairs in length and aligns with a rice genome sequence with a BLAST E value of 1e-200 or less. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that the majority of the 300 kbp segments do not match any sequences that are recited in the claims of granted U.S. patents. For the segments that have one or more matches, there are no more than eight matched sequences per segment. Chromosome 3 has the most sequences matches with 55, and chromosome 9 had the fewest with 13.

See the corresponding plots for the Arabidopsis genome landscape.

Granted US Patents on Oryza sativa

US Patent Applications on Oryza sativa

Granted U.S. Patents: Number of Patents that Claim Oryza sativa Sequences per Genome Segment

The blue bars in the plots below represent the number of granted U.S. patents that recite sequences in claims that match each 300 Kbp segment of the rice genome. By match, we mean that the patent sequence is at least 150 base pairs in length and aligns with a rice genome sequence with a BLAST E value of 1e-200 or less. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that the majority of the 300 kbp segments do not have any patents with recited sequences that match the rice genome. For the segments that have one or more patents, the highest number of patents is six. Chromosome 3 has the most patents with 39.

See the corresponding plots for the Arabidopsis genome landscape.

Granted US Patents on Oryza sativa

US Patent Applications on Oryza sativa

Granted U.S. Patents: Percent Coverage by Oryza sativa Patent Claims per Genome Segment

The blue bars in the plots below represent the percent of coverage of a given 300 kbp segment by granted U.S. patents. For example, if an entire 300 kbp segment matched sequences that were recited in claims US patents, the plot would read 100% for that segment. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that only a small percentage of the rice genome is recited in the claims of granted U.S. patents. The 300 kbp region with the highest percent coverage is chromosome 4, where one segment exhibits 3.55% patent coverage. For the entire rice genome, the percent coverage by granted U.S. patents is just 0.26%.

See the corresponding plots for the Arabidopsis genome landscape.

Granted US Patents on Oryza sativa

US Patent Applications on Oryza sativa

U.S. Patent Applications: Number of Oryza sativa Sequences Referenced in Claims per Genome Segment

The blue bars in the plots below represent the number of sequences recited in the claims of U.S. patent applications that match a given 300 kilobase pair (kbp) segment of the rice genome. By match, we mean that the patent sequence is at least 150 base pairs in length and aligns with a rice genome sequence with a BLAST E value of 1e-200 or less. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

In contrast to the plots for the granted patents, these plots show that every segment of the rice genome matches 100 or more sequences recited in patent applications.

See the corresponding plots for the Arabidopsis genome landscape.

Granted US Patents on Oryza sativa

US Patent Applications on Oryza sativa

U.S. Patent Applications: Number of Patent Applications that Claim Oryza sativa Sequences per Genome Segment

The blue bars in the plots below represent the number of U.S. patent applications that recite sequences in claims that match each 300 Kbp segment of the rice genome. By match, we mean that the patent sequence is at least 150 base pairs in length and aligns with a rice genome sequence with a BLAST E value of 1e-200 or less. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that for every 300 kbp segment of the rice genome, there are four or more patent applications that recite sequences in claims that match the rice genome.

See the corresponding plots for the Arabidopsis genome landscape.

Granted US Patents on Oryza sativa

US Patent Applications on Oryza sativa

U.S. Patent Applications: Percent Coverage by Oryza sativa Patent Claims per Genome Segment

The blue bars in the plots below represent the percent of coverage of a given 300 kbp segment by U.S. patent applications. For example, if an entire 300 kbp segment matched sequences that were recited in claims US patent applications, the plot would read 100% for that segment. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that a large percentage of the rice genome is recited in the claims of granted U.S. patents. Approximately 74% of the rice genome is recited in claims of U.S. patent applications.

See the corresponding plots for the Arabidopsis genome landscape.

Chapter 5: Identification of Granted Patents that Claim Rice Genome Sequences

rice1-closeup

In our analysis, we have used MEGABLAST to compare the rice genome to all of the nucleotide sequences that are mentioned in the claims of granted patents. Using this approach, we have identified a large number granted patents that recite a nucleotide sequence in a claim that has a high degree of similarity to a nucleotide sequence of the rice genome. All of the sequences identified using this approach have a BLAST E value that is less than 1e-200 and are at least 150 nucleotides in length. See our methods page in Chapter 4 for more details about how we compiled the sequences used for the MEGABLAST analysis.

Summary

Using MEGABLAST, we identified a total of 248 matches between rice genome nucleotide sequences and sequences that are recited in the claims of granted U.S. patents. The 248 matches are disclosed in 173 granted patents. Information about the 173 granted patents are provided in this chapter along with links to the pertinent sequences in CAMBIA's patent sequence server.

U.S. Patents Claiming Rice Sequences

The table below lists all of the U.S. granted patents with claims that mention nucleotide sequences that are highly similar to rice genome sequences. The criteria for each sequence were that they had a BLAST E value of e-200 or less when compared with a rice genome sequence and a length of at least 150 nucleotides. The patents are organized alphabetically by assignee. This list is current as of March 2008. Patents that have expired due to non-payment of fees (according to PAIR) are designated by red type.

To view or BLAST the sequences that have homology to rice, click on one of the numbers in the "SEQ ID with homology to rice" column.

Patent No.

Assignee

Title

SEQ ID with homology to rice

Subject of Patent

6376750

Academia Sinica

Plant seedling and embryo promoter

2, 5

plant seedling and embryo promoter

7291768

Academia Sinica

Plant MYB proteins

1

MYB proteins

6995253

Advanced Research &, Technology Institute (Bloomington, IN, US)

Genes for regulating disease resistance in plants

5

Genes for regulating disease resistance in plants

7132587

Agency of Industrial Science and Technology

Non-autonomous transposon gene of rice, transformed plant and method of use

1

Method to detect transposon

6177267

Arch Development Corp.

Acetyl-CoA carboxylase from wheat

9

Acetyl-CoA carboxylase

5801233

Arch Development Corporation

Nucleic acid compositions encoding acetyl-coa carboxylase and uses therefor

9, 30

acetyl-CoA carboxylase

6306636

ARCH Development Corporation

Nucleic acid segments encoding wheat acetyl-CoA carboxylase

6

wheat acetyl-CoA carboxylase

5910626

ARCH Development Corporation

Acetyl-CoA carboxylase compositions and methods of use

9

Acetyl-CoA carboxylase

6787337

Aventis CropScience S.A.

Recording of DNA sequences to enable them to be expressed in yeasts, and the transformed yeasts obtained

1, 7, 8, 9, 10, 14

cytochrome P450

6933111

Bayer BioScience N.V.

Glufosinate tolerant rice

6

Glufosinate tolerant rice (PCR kit)

6403864

BIO-ORIENTED TECHNOLOGY RESEARCH ADVANCEMENT INSTITUTION

Precursor polypeptide of a plant growth factor, a gene encoding a precursor polypeptide of a plant growth factor and a method for promotion of plant growth

2

phytosulfokine (preprophytosulfokine), a growth factor

7119192

Bio-oriented Technology Research Advancement Institution

Stress-induced promoter derived from rice

1

Stress-induced promoter derived from rice

6528701

Board of Supervisors of Louisiana State University and Agricultural and Mechanical College

Rice ubiquitin-derived promoters

3

Rice ubiquitin-derived promoters

6943280

Board of Supervisors of Louisiana State University and Agricultural and Mechanical College

Resistance to acetohydroxycid synthase-inhibiting herbicides

18

Resistance to acetohydroxycid synthase-inhibiting herbicides

7049485

Board of Trustees of Michigan State University

Transgenic plants containing ligninase and cellulase which degrade lignin and cellulose to fermentable sugars

1

Cellulase, lignin peroxidase

6891086

Calgene LLC

Plastid transformation of Brassica

19

Plastid transformation

6515206

Calgene LLC

Plastid transformation of Brassica

19

trnV-rps7/12 intergenic region and primers

6479735

Centre National de la Recherche Scientifique - CNRS (Paris, FR)

Transgenic plants including a transgene consisting of a hybrid nucleic acid sequence, comprising at least one unedited mitochondrial gene fragment from higher plants and process for producing them

3, 8

unedited mitochondrial gene

6933146

Commonwealth Scientific and Industrial Research Corporation (Campbell, AU)

Methods and means for producing efficient silencing construct using recombinational cloning

13, 23, 24, 25, 26

Silencing construct

7001771

Commonwealth Scientific and Industrial Research Organisation (Campbell, AU), Biogemma SAS (Paris, FR), Goodman Fielder PTY Limited (Sydney, AU)

Genes encoding wheat starch synthases and uses thereof

3

starch synthase II

6242221

Commonwealth Scientific and Industrial Research Organization (Campbell, AU)

Genomic polyphenol oxidase gene fragments of plants

41

polyphenol oxidase

5641876

Cornell Research Foundation, Inc.

Rice actin gene and promoter

56

rice actin 1 gene promoter

7053268

Danisco A/S

Promoter

1, 2, 6

Promoters

6429357

Dekalb Genetics Corp. (Mystic, CT), Cornell Research Foundation, Inc.

Rice actin 2 promoter and intron and methods for use thereof

1, 2

actin 2 promoter

6204039

E.I. du Pont de Nemours and Company

Plant isocitrate dehydrogenase homologs

3

isocitrate dehydrogenase homologs

6218169

E.I. du Pont de Nemours and Company

Aromatic amino acid catabolism enzymes

3

Aromatic amino acid catabolism enzymes

6271031

E.I. du Pont de Nemours and Company

Quinolinate metabolism enzymes

5

L-aspartate oxidase

6297055

E.I. du Pont de Nemours and Company

Amino acid decarboxylases

3

lysine decarboxylase

6312954

E.I. du Pont de Nemours and Company

Plant geranylgeranyl transferases

9

geranylgeranyl transferases

6329204

E.I. du Pont de Nemours and Company

Plant caffeic acid 3-0-methyltransferase homologs

9

caffeic acid 3-0-methyltransferase

6346403

E.I. du Pont de Nemours and Company

Methionine metabolic enzymes

3

Methionine metabolic enzymes

6355462

E.I. du Pont de Nemours and Company

Disease resistance factor

1, 3

FAD-linked oxidoreductase 2

6383776

E.I. du Pont de Nemours and Company

Plant sugar transport proteins

5

Plant sugar transport proteins

6436657

E.I. du Pont de Nemours and Company

Polynucleotides encoding aminomethyltransferases

27

aminomethyltransferases

6441274

E.I. du Pont de Nemours and Company

Plant tryptophan synthase beta subunit

1

tryptophan synthase beta subunit

6465229

E.I. du Pont de Nemours and Company

Plant caffeoyl-coa o-methyltransferase

13

caffeoyl-CoA O-methyltransferase

6479731

E.I. du Pont de Nemours and Company

Pi-ta gene conferring fungal disease resistance to plants

1, 68

AVR-Pita gene

6653099

E.I. du Pont de Nemours and Company

Plant UDP-glucose dehydrogenase

7

UDP-glucose dehydrogenase

6664445

E.I. du Pont de Nemours and Company

Plant amino acid biosynthetic enzymes

35

S-adenosyl methionine synthetase

6743969

E.I. du Pont de Nemours and Company

Modification of PI-TA gene conferring fungal disease resistance to plants

57

Modification of PI-TA gene

6756218

E.I. du Pont de Nemours and Company

Sucrose phosphate synthase

23

Sucrose phosphate synthase

6794561

E.I. du Pont de Nemours and Company

Plant protein kinases

3

protein kinase

6821764

E.I. du Pont de Nemours and Company

Genes encoding sulfate assimilation proteins

7

serine O-acetyltransferase

6831206

E.I. du Pont de Nemours and Company

Serine O-acetytransferase

1, 2

Serine O-acetytransferase

6855870

E.I. du Pont de Nemours and Company

Plant cinnamyl-alcohol dehydrogenase homologs

9

cinnamyl-alcohol dehydrogenase

6872872

E.I. du Pont de Nemours and Company

Genes for microsomal delta-12 fatty acid desaturases and related enzymes from plants

7

microsomal delta-12 fatty acid desaturases

6891083

E.I. du Pont de Nemours and Company

Plant aminoacyl-tRNA synthetases

9

Glutamyl-tRNA synthetase

6916971

E.I. du Pont de Nemours and Company

Polynucleotides encoding aminolevulinic acid biosynthetic enzymes

3

Polynucleotides encoding aminolevulinic acid biosynthetic enzymes

6916972

E.I. du Pont de Nemours and Company

Mevalonate synthesis enzymes

19

Mevalonate synthesis enzymes

6919466

E.I. du Pont de Nemours and Company

Genes for microsomal delta-12 fatty acid desaturases and related enzymes from plants

7

microsomal delta-12 fatty acid desaturases

6939710

E.I. du Pont de Nemours and Company

Genes encoding sulfate assimilation proteins

1

Genes encoding sulfate assimilation proteins

7008664

E.I. du Pont de Nemours and Company

Method for improving the carcass quality of an animal

1

delta-9 stearoyl ACP desaturase

7053269

E.I. du Pont de Nemours and Company

Phospholipid:diacylglycerol acyltransferases

21

phospholipid:diacylglycerol acyltransferase

7098379

E.I. du Pont de Nemours and Company

Plant UDP-glucose dehydrogenase

5

UDP-glucose dehydrogenase

7105721

E.I. du Pont de Nemours and Company

Genes for microsomal delta-12 fatty acid desaturases and hydroxylases from plants

7

delta-12 fatty acid desaturases and hydroxylases

7199283

E.I. du Pont de Nemours and Company

Geranylgeranyl pyrophosphate synthases

43

geranylgeranyl diphosphate synthase

6204063

E.I. du Pont de Nemours and Company

Plant glycolysis and respiration enzymes

3

Plant glycolysis and respiration enzymes

6251668

E.I. du Pont de Nemours and Company

Transcription coactivators

3

Transcription coactivators

6271441

E.I. du Pont de Nemours and Company

Plant aminoacyl-tRNA synthetase

3

aminoacyl-tRNA synthetase

6368840

E.I. du Pont de Nemours and Company

Acyl-CoA oxidase homologues

17

acyl CoA oxidase

6372965

E.I. du Pont de Nemours and Company

Genes for microsomal delta-12 fatty acid desaturases and hydroxylases from plants

7

microsomal delta-12 fatty acid desaturases and hydroxylases

7186890

E.I. du Pont de Nemours and Company

Serine O-acetyltransferase

4

Serine O-acetyltransferase

7189531

E.I. du Pont de Nemours and Company

Nucleic acid encoding plant sugar transport proteins

19

sugar transporter

7195887

E.I. du Pont de Nemours and Company

Rice 1-deoxy-D-xylulose 5-phosphate synthase and DNA encoding thereof

25

1-deoxy-D-xylulose 5-phosphate synthase

7217862

E.I. du Pont de Nemours and Company

Geranylgeranyl pyrophosphate synthases

33

Geranylgeranyl pyrophosphate synthases

7282359

E.I. du Pont de Nemours and Company

Plant 1-deoxy-D-xylulose 5-phosphate reductoisomerase

7

1-deoxy-D-xylulose 5-phosphate reductoisomerase

7238512

E.I. du Pont de Nemours and Company

Method to produce para-hydroxybenzoic acid in the stem tissue of green plants by using a tissue-specific promoter

43, 44, 45

Cellulose synthase promoter

7288695

E.I. du Pont de Nemours and Company

Plant genes encoding Dr1 and DRAP1, a global repressor complex of transcription

31

Dr1 and DRAP1

7252966

Evolutionary Genomics LLC (Aurora, CO)

EG307 polynucleotides and uses thereof

5, 91

EG307 polynucleotides

7060873

Greengene Biotech Inc.

Method for producing a plant with a high-growth rate

1

OsHDAC3 histone deacetylase

6958434

Greengene Biotech, Inc.

OsCc1 promoter and methods of transforming monocot plants using the same

1

OsCcl promoter

6423838

Hitachi, Ltd.

Gene for proline transporter in rice

1

proline transporter

6307125

Hoechst Schering AgrEvo, GmbH

Nucleic acid molecules encoding enzymes from wheat which are involved in starch synthesis

5

Wheat starch synthase

6734339

Hoechst Schering AgrEvo, GmbH

Nucleic acid molecules encoding enzymes from wheat which are involved in starch synthesis

5

starch synthesis enzymes

7034139

Incorporated Administrative Agency, National Agriculture and Bio-Oriented Research Organization

Rice gene for controlling tolerance to salt stress

1

gene for controlling tolerance to salt stress

7138277

Incorporated Administrative Agency, National Agriculture and Bio-Oriented Research Organization

Genes encoding plant transcription factors

1

transcription factor OsDREB1A

6673549

Incyte Corporation

Genes expressed in C3A liver cell cultures treated with steroids

730

appears to be a gene chip

6512163

Institute of Molecular Agrobiology

RANK1, an ankyrin-repeat containing peptide from rice associated with disease resistance

8

RANK1, an ankyrin-repeat containing peptide

7238857

Japan Science and Technology Agency

Ethylene-responsive transcription coactivators in plants

2

Ethylene responsive transcription co-activator

5747327

Japan Tobacco Inc.

Phospholipase D gene originated from plant

1, 3, 5

Phospholipase D

5912333

Japan Tobacco Inc.

DNA encoding carbonic anhydrase

5

carbonic anhydrase

6462185

Japan Tobacco Inc.

Floral organ-specific gene and its promoter sequence

3

Floral organ-specific gene promoter sequence

6660851

Japan Tobacco Inc.

Floral organ-specific gene and its promoter sequence

1, 7

enhancer

6998477

Japan Tobacco Inc.

Nucleic acid fragment, recombinant vector containing the same and method of promoting the expression of structural genes by using the same

1, 2

promoters

7109321

Japan Tobacco Inc.

DNA fragment directing gene expression predominant in flower organ

3

flower organ promoter

7186821

Japan Tobacco Inc., Syngenta Limited

Rice sucrose transporter gene promoter

1

Rice sucrose transporter gene promoter

6916973

Korea Kumho Petrochemical Co., Ltd.

Nucleic acid molecules encoding hyperactive mutant phytochromes and uses thereof

1

phytochrome A

7045680

Korea Kumho Petrochemical Co., Ltd.

Transgenic zoysiagrass with reduced shade avoidance

1

modified phytochrome A gene

6995302

Kumiai Chemical Industry Co., Ltd. (Tokyo, JP), Kojima (Mineo, Nagano)

Gene regulating plant branching, vector containing the gene, microorganism transformed by the vector, and method for regulating plant branching by using the microorganism

1

rice MADS box gene

 7238864  

Kumiai Chemical Industry Co., Ltd. (Tokyo, JP), Kojima (Mineo, Nagano) AND National Institute of Agrobiological Sciences (Tsukuba-Shi, JP)

Acetolactate synthase gene promoter

1

Acetolactate synthase promoter

7232940

Missouri Board of Curators (Columbia, MO)

Polynucleotide sequences from rice

2

Rice tubulin promoter

6506962

Monsanto Technology LLC

Acquired resistance genes in plants

1

Acquired resistance genes in plants

7132528

Monsanto Technology LLC

Promoter from the rice triosephosphate isomerase gene OsTPI

1, 4, 10, 11

Promoter from the rice triosephosphate isomerase gene OsTPI

7157281

Monsanto Technology LLC

High lysine maize compositions and event LY038 maize plants

7

High lysine maize compositions

6501009

Monsanto Technology LLC (St. Louis, MO)

Expression of Cry3B insecticidal protein in plants

19

Cry3B insecticidal protein

6797860

Nagoya University (Nagoya, JP)

Promoter derived from phytosulfokine precursor gene

1, 2, 3

Promoter

7154028

National Agriculture and Bio-Oriented Research Organization

Gibberellin 2-oxidase gene, functions and uses thereof

3

Gibberellin 2-oxidase gene

7132524

National Agriculture and Bio-oriented Research Organization (Ibaraki, JP), National Institute of Agrobiological Sciences

Plant brassinolide responsive genes and use thereof

3

brassinolide responsive gene and protein

6984727

National Institute of Agrobiological Science, Bio-oriented Technology Research Advancement Institution

Gene involved in brassinosteroid responses

1

polypeptide involved in a signal transduction system for brassinosteroid hormone

7214851

National Institute of Agrobiological Science, Bio-oriented Technology Research Advancement Institution

Bzip type transcription factors regulating the expression of rice storage protein

1, 3

Bzip type transcription factors

6576815

National Institute of Agrobiological Sciences

Promoter sequence expressed in anthers and pollens

1

Promoter sequence expressed in anthers and pollens

6861574

National Institute of Agrobiological Sciences

Sodium/proton antiporter gene

1

Sodium/proton antiporter gene

7132292

National Institute of Agrobiological Sciences

Anther-specific promoter from the rice TUB8 gene and uses thereof

3

Anther-specific promoter from the rice TUB8

7135625

National Institute of Agrobiological Sciences

Gene concerning brassinosteroid-sensitivity of plants and utilization thereof

3

Gene concerning brassinosteroid-sensitivity

7176347

National Institute of Agrobiological Sciences

Vegetative growth specific promoter and transgenic plant obtained with the same

1

Vegetative growth specific promoter (OsGA3ox2 gene promoter)

7189890

National Institute of Agrobiological Sciences

Gene related to regeneration ability of plants and uses thereof

1

NAD-/NADP-dependent oxidoreductase

7192774

National Institute of Agrobiological Sciences

Seed-specific promoter from the rice glutelin GluB-1 gene and uses thereof

1

glutelin GluB-1

6501007

National Institute Of Agrobiological Sciences (Ibaraki, JP)

Method of dwarfing plants

2

Antisense

7329544

National Institute of Agrobiological Sciences

Society for Techno-Innovation of Agriculture, Forestry and Fisheries, Tokyo (JP)

Plant lesion formation suppressing gene, Sp17 and use thereof

1*, 2*

Heat stress transcription factor Sp17

7186888

National Institute of Agrobiological Sciences (Ibaraki, JP), Japan Science and Technology Agency

Cold stress-responsive CRTintP gene and use thereof

1

Cold stress-responsive CRTintP gene

7253339

National Institute of Agrobiological Sciences (Ibaraki, JP) AND Society for Techno-Innovation of Agriculture, Forestry and Fisheries (Tokyo, JP) AND National Agriculture and Bio-Oriented Research Organization (Saitama, JP)

Plant photoperiod sensitivity gene Hd1 and use of the same

2, 4

Plant photoperiod sensitivity gene Hd1

7271003

National Insitute of Agrobiological Sciences (Ibaraki, JP)

Rice-derived high expression polypeptide chain elongation factor promoter and method of using the same

1

OsEF1β1

7049490

National Institute of Agrobiological Sciences, Riken

Gibberellin 3β-hydroxylase genes of rice and uses thereof

4

Gibberellin 3beta-hydroxylase genes

7326827

National Institute of Agrobiological Sciences

Sodium/proton antiporter gene

1*

Sodium/proton antiporter gene

7041484

National Research Council of Canada

Starch branching enzymes

1

starch branching enzyme

7053203

Natl. Institute of Agrobiological Sciences, Bio-Oriented Technology Research Advancement Institution

Gene controlling ethylene synthesis

1

protein capable of controlling ethylene synthesis

6809234

New York University (New York, NY), Pioneer Hi-Bred International, Inc. (Johnston, IA)

Scarecrow gene, promoter and uses thereof

95

Scarecrow gene

5986172

Nissan Chemical Industries, Ltd.

Rice NADH-dependent reductase, gene therefor, and use thereof

1

NADH-dependent reductase

6759526

Nissan Chemical Industries, Ltd.

DNA fragment having promoter function

1, 2, 3

Promoter

6812381

Nissan Chemical Industries, Ltd.

DNA fragment having promoter function

2

Promoter

5859336

Novartis Corporation

Synthetic DNA sequence having enhanced activity in maize

26

calcium-dependent protein kinase gene promoter

5688939

Novartis Finance Corporation

Plant adenylosuccinate synthetase and DNA coding therefor

5

adenylosuccinate synthetase(ADSS) protein

6750380

Pioneer Hi-Bred International , Inc., The Curators of the University of Missouri

Isolated nucleic acid moelcules encoding the Dw3 P-glycoprotein of sorghum and methods of modifying growth in transgenic plants therewith

7, 8

Dw3 P-glycoprotein

6313375

Pioneer Hi-Bred International, Inc.

Maize aquaporins and uses thereof

7, 13, 17

aquaporins

6399859

Pioneer Hi-Bred International, Inc.

Plant uridine diphosphate-glucose dehydrogenase genes, proteins, and uses thereof

1, 3

UDP-glucose dehydrogenase

6559355

Pioneer Hi-Bred International, Inc.

Rad3 orthologues and uses thereof

1

Rad3 orthologues (DNA helicase)

6762348

Pioneer Hi-Bred International, Inc.

Genetic control of plant growth and development

12, 14, 15

Rht polypeptide obtained from Triticum aestivum

7009087

Pioneer Hi-Bred International, Inc.

Compositions and methods for altering the disulfide status of proteins

24

NADPH-thioredoxin reductase

7098381

Pioneer Hi-Bred International, Inc.

Plant uridine diphosphate-glucose dehydrogenase genes, proteins, and uses thereof

1, 3

uridine diphosphate-glucose dehydrogenase genes

7202396

Pioneer Hi-Bred International, Inc.

Rad3 orthologues and uses therof

1

Rad3 protein (DNA helicase)

6194638

Pioneer Hi-Bred International, Inc.

Alteration of hemicellulose concentration in plants

3

Reversibly Glycosylated Protein (RGP)

6441151

Pioneer Hi-Bred International, Inc.

Plant prohibition genes and their use

3, 5

antisense prohibition nucleotides

6573426

Pioneer Hi-Bred International, Inc.

Gene involved in pyrimidine biosynthesis in plants

9

Rad3 orthologues (DNA helicase)

6627797

Pioneer Hi-Bred International, Inc.

Maize lipoxygenase polynucleotide and methods of use

1, 2

lipoxygenase

7041874

Pioneer Hi-Bred International, Inc., The Curators of the University of Missouri

Isolated nucleic acid molecules encoding the Br2 P-glycoprotein of maize and methods of modifying growth in plants transformed therewith

1, 2

Br2 P-glycoprotein of maize

6313376

Pioneer Hi-Bred International, Inc., The Regents of the University of California

Maize aquaporins and uses thereof

3, 5

aquaporins

6930225

Pioneer Hi-Bred Int'l Inc.

Maize cellulose synthases and uses thereof

25, 27, 29

cellulose synthases

7268271

Pioneer Hi-Bred International, Inc. (Johnston, IA)

Methods of use of LEC1 polynucleotides and polypeptides

1

LEC1 polynucleotides and polypeptides

7268272

Pioneer Hi-Bred International, Inc. (Johnston, IA)

Genetic control of plant growth and development

14

Rht gene

7276647

Pioneer Hi-Bred International, Inc. AND The Curators of the University of Missouri

Isolated nucleic acid molecules encoding the Dw3 P-glycoprotein of sorghum and methods of modifying growth in transgenic plants therewith

7, 8

Dw3 P-glycoprotein

5639948

Plant Genetic Systems, N.V.

Stamen-specific promoters from rice

5, 6, 7, 8

Rice promoters

6521816

PlantTec Biotechnologie GmbH Forschung und Entwicklung

Nucleic acid molecules from rice and their use for the production of modified starch

1

starch synthesis enzyme

7307199

POSCO

PCR family genes which confer tolerance to heavy metals

6*

Plant cadmium resistance

5677175

Purdue Research Foundation

Plant pathogen induced proteins

1, 2, 3

pathogen-inducible regulatory element

6541621

Purdue University Research Foundation

Hypoxia inducible promoter

2

hypoxia inducing promoter

5498544

Regents of the University of Minnesota

Method and an acetyl CoA carboxylase gene for conferring herbicide tolerance

1

Zea mays acetyl-coenzyme A carboxylase mRNA

6146867

Regents of the University of Minnesota (Minneapolis, MN), United States of America

Methods for expressing a maize acetyl CoA carboxylase gene in host cells and encoded protein produced thereby

1, 5

acetyl CoA carboxylase

6180363

Rhone-Poulenc Agro

Recoding of DNA sequences permitting expression in yeast and obtained transformed yeast

1, 7, 8, 9, 10, 14

?

6750378

Rhone-Poulenc Agro

Maize H3C4 promoter combined with the first intron of rice actin, chimeric gene comprising it and transformed plant

2, 3

Maize H3C4 promoter combined with the first intron of rice actin

7057088

Riken (Saitama, JP), National Institute of Agro-Biological Sciences

Gibberellin 2β-hydroxylase genes of rice and uses thereof

2

Gibberellin 2beta-hydroxylase genes

7285700

Rutgers, The State University of New Jersey (New Brunswick, NJ)

Plastid directed DNA constructs comprising chimeric plastid targeting regions, vectors containing same and methods of use thereof

4

Vectors for targeting plastid

6274789

Society for Techno-Innovation of Agriculture, Forestry and Fisheries

Rice gene resistant to blast disease

2, 3

PiB protein

6867293

Syngenta Limited

Polynucleotide constructs having at least one transcriptional enhancer and encoding a modified rice EPSPS enzyme

43, 44, 49, 50, 52, 53

Transcriptional enhancers and EPSPS genes

7186887

Syngenta Participations AG

Nucleic acids encoding oryza sativa nuclear cap binding protein 80 and methods of use

1

nuclear cap binding protein 80

6271440

The Australian National University

Plant regulatory proteins III

1, 3

(transcription factors) gibberellin-regulated genes

7094951

The Ohio State University

Cloning and characterization of the broad-spectrum resistance gene Pi2

7

broad-spectrum resistance gene Pi2

5693506

The Regents of the University of California

Process for protein production in plants

2

transcriptional initiation region

5859339

The Regents of the University of California

Nucleic acids, from oryza sativa, which encode leucine-rich repeat polypeptides and enhance xanthomonas resistance in plants

1, 3

leucine-rich repeat polypeptides

5977434

The Regents of the University of California

Procedures and materials for conferring disease resistance in plants

1, 3

RRK polynucleotide sequence

5994628

The Regents of the University of California

Process for protein production in plants

2

alpha-amylase gene

6833493

The Regents of the University of California

Barley gene for thioredoxin and NADP-thioredoxin reductase

10

NADP-thioredoxin reductase

6995306

The Regents of the University of California

Nucleic acid encoding an NPR1 interactor from rice and method of use to produce pathogen-resistant plants

3

NPR1 interactor

5695939

The Salk Institute for Biological Studies

Plant defense genes and plant defense regulatory elements

2

chitinase

7205150

Universidad Publica de Navarra, JCR Pharmaceuticals Co., Ltd.

Transgenic plants over-expressing plant ADP-glucose pyrophosphatase

7

ADP-glucose pyrophosphatase

7250556

University of Georgia Research Foundation, Inc. (Athens, GA) AND Washington University (St. Louis, MO)

Transposable elements in rice and methods of use

1

Transposable rice sequences

6750057

University of Florida

Ubiquitin ligase

1

Ubiquitin ligase

6781044

Ventria Bioscience

Plant selectable marker and plant transformation method

1, 4

glucanase gene (Gns9) promoter

5859326

Washington State University

Gene controlling floral development and apical dominance in plants

1

OsMADS1 MADS-box

5861542

Washington State University Research Foundation

Gene controlling floral development and apical dominance in plants

1

OsMADS1

5990386

Washington State University Research Foundation

Genes controlling floral development and apical dominance in plants

12, 16

Genes controlling floral development and apical dominance (MADS box)

5750873

Yale University

Nucleic acid molecules that encode tassel seed 2(TS2), a protein involved in the control of flower development in plants

1, 2, 9

tassel seed 2 (TS2)

6455688

Zeneca Limited

Plant gene specifying acetyl coenzyme A carboxylase and transformed plants containing same

9

acetyl coenzyme A carboxylase

5854420

Zeneca Limited ; GBX, ICI Australia Operations Proprietary Limited

Maize acetyl CoA carboxylase encoding DNA clones

1

acetyl CoA carboxylase

* Links to sequences for some newly-granted patents are not yet available.  

Grouping Granted U.S. Patents on Rice by Type

There are a number of different ways that nucleic acid sequences may be referenced or recited in a patent claim. Three different possibilities are Composition of Matter claims, Method claims, and Product claims. Composition of Matter claims are claims that directly claim a sequence that is highly similar to a rice sequence. Method claims are claims where a rice sequence (or a sequence highly similar to rice) is used in a method. Product claims encompass all other types of claims wherein a rice nuceotide sequence (or a sequence highly similar to rice) is incorporated into a product, such as a plant or vector, and it is the product that is claimed (as opposed to the sequence). In Method and Product claims, the sequence is not claimed directly. Below are examples of each.

Figure 1: Claim Types

Figure 1 shows the three types of claims in the 173 granted patents that we identified using MEGABLAST. 

Rice Genome Claim Types Pie Graph

Figure 1

Figure 2: Composition of Matter Claim Types

Figure 2 shows a breakdown of the 143 patents that had composition of matter claims, and separates those that had "structural gene" sequences from those that had promoter sequences. For the purposes of this graph, we are defining "structural gene" sequences as those sequences that may be translated into a protein.

Rice Genome Claim Types--Comp of Matter Pie Graph

Figure 2

Granted Rice Patents by Assignee

To generate the graph and table below, we organized the granted patents by assignee. In some cases, subsidiaries of companies are consolidated with their parent company (as designated by the superscript numbers in the table below). E. I. du Pont de Nemours and Company, which includes Pioneer Hi-Bred, has the most granted patents on rice sequences with 62.

Graph of Top Patent Holders

Assignee Name

No. of Patents

E. I. du Pont de Nemours and Company1

62

National Institute of Agro-Biological Sciences (NIAS)

19

National Agriculture and Bio-Oriented Research Organization (NARO)

10

Bayer BioScience N.V.2

8

Syngenta Limited3

8

Japan Tobacco Inc.

7

The Regents of the University of California

7

Monsanto4

7

Arch Development Corp.

4

Commonwealth Scientific and Industrial Research Corporation

3

Nissan Chemical Industries, Ltd.

3

The Curators of the University of Missouri

3

Washington University

3

Academia Sinica

2

Board of Supervisors of Louisiana State University and Agricultural and Mechanical College

2

Cornell Research Foundation, Inc.

2

Greengene Biotech Inc.

2

Incorporated Administrative Agency,

2

Japan Science and Technology Agency

2

Korea Kumho Petrochemical Co., Ltd.

2

Kumiai Chemical Industry Co., Ltd.

2

Purdue Research Foundation

2

Regents of the University of Minnesota

2

Society for Techno-Innovation of Agriculture, Forestry and Fisheries, National Agriculture

2

Advanced Research & Technology Institute

1

Agency of Industrial Science and Technology

1

Auburn University

1

Biogemma SAS

1

Board of Trustees of Michigan State University

1

Centre National de la Recherche Scientifique

1

Goodman Fielder PTY Limited

1

Evolutionary Genomics LLC

1

Hitachi, Ltd.

1

ICI Australia Operations Proprietary Limited

1

Incyte Corporation

1

Institute of Molecular Agrobiology

1

JCR Pharmaceuticals Co., Ltd.

1

Kojima

1

Missouri Board of Curators

1

Nagoya University

1

National Research Council of Canada

1

New York University

1

POSCO

1

RIKEN

1

Rutgers, The State University of New Jersey

1

The Australian National University

1

The Ohio State University

1

The Salk Institute for Biological Studies

1

Universidad Publica de Navarra

1

University of Florida

1

University of Georgia Research Foundation, Inc

1

Ventria Bioscience

1

Yale University

1

Yissum research development co.

1

1E. I. du Pont de Nemours and Company includes Pioneer Hi-Bred
2Bayer includes: Aventis CropScience, Hoechst Schering AgrEvo, Plant Genetic Systems, Plant Tec Biotechnologie and Rhone-Poulenc Agro
3Syngenta includes: Danisco A/S, Novaritis Corp. and Zeneca Limited
4Monsanto includes: Calgene and Dekalb Genetics Corp.

Chapter 6: Patent Applications on Rice

rice18-grains

This chapter shows the results of MEGABLAST analyses of sequences that are recited in the claims of U.S. patent applications. The sequence database used in this analysis contains sequences from all applications, regardless of whether they are abandoned or pending.

Patent applications usually become publicly available 18 months after they are filed, and therefore, our analysis will not include the most recently-filed patent applications. However, we will be updating the tables periodically with new patent data as we acquire it.

Analyses of patent applications differ from those of granted patents because applications often claim many nucleotide and amino acid sequences, in some cases tens or hundreds of thousands, for example, in bulk sequence applications. If granted however, they are likely to claim only one or two of these sequences (read ahead for a description of how many sequences are examined in a U.S. patent application). For this reason, we have not performed a detailed analysis of the sequences mentioned in the claims of pending U.S. patent applications, since most of them will not end up in the claims of a granted patent.

Summary

We identified 313 U.S. patent applications that recite rice sequences in the claims. Of these, 30% are abandoned. We also found that approximately 74% of the rice genome is recited in the claims of U.S. patent applications.

U.S. Patent Applications that Recite Rice Sequences in Claims

The table below lists all of the U.S. patent applications that in the claims, recite nucleotide sequences that are highly similar or identical to rice genome sequences. The criteria for each sequence was that they had a BLAST E value of e-200 or less and were at least 150 nucleotides in length. The status date refers to the last time that we checked the status in PAIR. To view the sequences associated with the claims of an application, click on the number in the "Number of Sequences in Claims" column.

We included applications that were abandoned but that have a pending family member that recites rice sequences in the claims. We also included abandoned applications that have a pending continuation applications that have not yet published. For these non-published continuation applications, we don't know if rice sequences are recited in the claims because the sequences are not yet available.

Summary

As of March 2008, there were 313 pending applications that recite sequences identical to or highly similar to rice.

Application No.

Assignee

Title

Number of Sequences in Claims

Status

Status Date

20050066387

Academica Sinica

Rice glutelin gene promoters

15

Non Final Action Mailed

15 Oct ‘07

20050266558

Agrigenesis BioSciences Limited

Wrightson Seeds Limited

Compositions isolated from forage grasses and methods for their use

40

Non Final Action Mailed

15 Oct ‘07

20070157337

Arcadia BioSciences, Inc.

Promoter sequence obtained from rice and methods of use

1

Docketed New Case - Ready for Examination

12 Dec ‘07

20060137041

Australian National University, The

Method of producing plants having enhanced transpiration efficiency and plants produced therefrom

45

Response to Non-Final Office Action Entered and Forwarded to Examiner

19 Feb ‘08

20020102532

Avalon Pharmaceuticals, Inc.

Cancer gene determination and therapeutic screening using signature
gene sets

658

Abandoned but has pending family member

20080050379

20 March '08

20060099670

BASF Aktiengesellschaft

Method for the genetic modification of organisms of the genus blakeslea,corresponding organisms and the use of the same

25

Docketed New Case - Ready for Examination

15 Oct ‘07

20060234333

BASF Aktiengesellschaft

Method for producing carotenoids or their precursors using geneticallymodified organisms of the blakeslea genus, carotenoids or their precursorsproduced by said method and use thereof

20

Docketed New Case - Ready for Examination

15 Oct ‘07

20070033670

BASF Aktiengesellschaft

Northwest Plant Breeding Company

Wheat Plants having Increased tolerance to imidazolinone herbicides

8

Docketed New Case - Ready for Examination

15 Oct ‘07

20050260754

BASF Plant Science GMBH

Constructs and methods for the regulation of gene expression

47

Non Final Action Mailed

19 Feb ‘08

20060010514

BASF Plant Science GMBH

Polynucleotides encoding mature AHASL proteins for creatingimidazolinone-tolerant Plants

10

Non Final Action Mailed

15 Oct ‘07

20050132439

BASF Plant Science GMBH

Novel nucleic acid sequences and their use in methods for achieving pathogenresistance in Plants

44

Response to Non-Final Office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060137043

BASF Plant Science GmbH

Nucleic acid sequences encoding proteins associated with abiotic stressresponse and Plant cells and Plants with Increased tolerance to environmentalstress

553

Docketed New Case - Ready for Examination

15 Oct ‘07

20070199103

BASF Plant Science GmbH

Nucleic acid molecules encoding wrinkled1-like polypeptides and methods of use in Plants

56

Docketed New Case - Ready for Examination

12 Dec ‘07

20070243543

BASF Plant Science GmbH

Method for Isolation of Transcription Termination Sequences

41

TSS review complete

12 Dec ‘07

20070250946

BASF Plant Science GmbH

Monocot Ahass Sequences and Methods of Use

7

Docketed New Case - Ready for Examination

12 Dec ‘07

20030215950

Battelle Memorial Institute

Isolated polynucleotides and methods of promoting a morphology in a fungus

33

Non final action mailed

15 Oct ‘07

20080034451

Bayer Bioscience

Rice Pollen-Preferential Promoters And Uses Thereof

10

Non Final Action Mailed

20-March '08

20050044593

Biolex, Inc.

Chloroplast transformation of duckweed

4

Notice of Appeal Filed

15 Oct ‘07

20040210962

Board of Regents of the University of Nebraska, The

Implementation of a mitochondrial mutator

42

Non Final Action Mailed

15 Oct ‘07

20050150002

Board of Trustees Operating Michigan State University, The

Novel carotenoid hydroxylases for use in engineering carotenoid metabolism inPlants

48

Non Final Action Mailed

15 Oct ‘07

20070039075

Bayer Cropscience S.A.

Fertile transplastomic leguminous Plants

2

Docketed New Case - Ready for Examination

15 Oct ‘07

20080022421

Bayer Cropscience

Plants With Increased Activity Of A Starch Phosphorylating Enzyme

4

Docketed New Case - Ready for Examination

20-March '08

20060185037

Board of Trustees of Michigan State University

Transgenic Plants containing ligninase and cellulase which degrade lignin andcellulose to fermentable sugars

3

Docketed New Case - Ready for Examination

15 Oct ‘07

20070192900

Board of Trustees of Michigan State University

Production of beta-glucosidase, hemicellulase and ligninase in E1 and FLC-cellulase-transgenic Plants

11

Docketed New Case - Ready for Examination

12 Dec ‘07

20050204437

Carlsberg A/S

Barley for production of flavor-stable beverage

3

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20050081261

Ceres, Inc.

Methods and compositions for altering seed phenotypes

42

Notice of Appeal Filed

19 Feb ‘08

20060112445

Ceres, Inc.

Novel regulatory regions

1

Docketed New Case - Ready for Examination

15 Oct ‘07

20070094750

Ceres, Inc.

Novel ADC polynucleotides and polypeptides, uses thereof Including methodsfor improving seeds

8

Non Final Action Mailed

15 Oct ‘07

20050191723

Chromagenics B.V.

Method for simultaneous production of multiple proteins; vectors and cellsfor use therein

129

Non Final Action Mailed

15 Oct ‘07

20060141577

Chromagenics B.V.

Selection of host cells expressing protein at high levels

66

Docketed New Case - Ready for Examination

15 Oct ‘07

20060172382

Chromagenics B.V.

Selection of host cells expressing protein at high levels

68

Docketed New Case - Ready for Examination

15 Oct ‘07

20060195935

Chromagenics B.V.

Selection of host cells expressing protein at high levels

71

Docketed New Case - Ready for Examination

15 Oct ‘07

20070212755

Chromagenics B.V.

Novel Sequence for Improving Expression of Nucleic Acid

66

TSS review complete

12 Dec ‘07

20070270578

CropDesign N.V

Plants Having Increased Yield and a Method for Making the Same

3

Application Dispatched from Preexam, Not Yet Docketed

20-March '08

20040231016

Commonwealth Scientific and Industrial Researcj Organization

Efficient gene silencing in Plants using short dsRNA sequences

8

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20070136895

Council of Scientific and Industrial Research (New Delhi IN)

Nucleic acids and methods for producing seeds with a full diploid complement of the maternal genome in the embryo

5

Docketed New Case - Ready for Examination

12 Dec ‘07

20040019926

CROP DESIGN N.V.

Novel Plant cyclin-dependent kinase inhibitors

23

Response to Non-Final office Action Entered and Forwarded to Examiner

19 Feb ‘08

20050268358

Cropdesign N.V.

Plants having improved growth characteristics and a method for making thesame

15

Non Final Action Mailed

15 Oct ‘07

20060112442

Cropdesign N.V.

Rice promoters

22

Non Final Action Mailed

15 Oct ‘07

20070107082

Cropdesign N.V.

Transgenic monocotyledonous Plants overexpressing a nhx protein and havingimproved growth characteristics and a method for making the same

1

Non Final Action Mailed

15 Oct ‘07

20070118931

Cropdesign N.V.

Plants having modified growth characteristics and method for making the same

6

Docketed New Case - Ready for Examination

15 Oct ‘07

20070067875

Cropdesign N.V.

Centre National de la Recherche Scientifique (C.N.R.S.)

Plants having improved growth characteristics and a method for making thesame

6

Docketed New Case - Ready for Examination

15 Oct ‘07

20050198705

Croughan, Timothy P

Resistance to acetohydroxyacid synthase-inhibiting herbicides

1

Non Final Action Mailed

15 Oct ‘07

20050164394

Commonwealth Scientific and Industrial Research Corporation

Methods and means for producing efficient silencing construct usingrecombiNational cloning

9

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060035379

Commonwealth and Scientific and Industrial Research Organisation ("CSIRO")

BPC Foods Pty. Limited

Biogemma SAS

Genes encoding wheat starch synthases and uses thereof

4

Non Final Action Mailed

15 Oct ‘07

20050262597

Cropdesign, N.V.

Method for Increasing transgene expression

2

Docketed New Case - Ready for Examination

15 Oct ‘07

20060292572

Department of Veterans Affairs

Regents of the University of California, The

Sidney Kimmel Cancer Center

Ludwig Institute for Cancer Research

Cell-type-specific patterns of gene expression

38826

Non Final Action Mailed

15 Oct ‘07

20050091708

Dow AgroSciences LLC

Dow Chemical Company, The

Nucleic acid compositions conferring altered metabolic characteristics

7554

Non Final Action Mailed

15 Oct ‘07

20020138882

E I du Pont De Nemours and Company

Polynucleotides encoding proteins involved in plant metabolism

193

Abandoned but has pending family member(s)

11/955,827 (not yet published)

31 Jan '08

20020184659

E I du Pont De Nemours and Company

Plant genes encoding Dr1 and DRAP1, a global repressor complex of
transcription

21

Abandoned but has pending family member(s)

11/888,497 (not yet published)

31 Jan '08

20030024007

E I du Pont De Nemours and Company

Plant Myb transcription factor homologs

62

Abandoned but has pending family member(s)

11/960,827 (not yet published)

31 Jan '08

20040053285

EI du Pont De Nemours and Company

Plant transcription factors

29

Abandoned -- Failure to Respond to an office Action

19 Feb ‘08

20030054521

E I du Pont De Nemours and Company

Nucleotide sequences of a new class of diverged delta-9 stearoyl-ACP
desaturase genes

15

Abandoned but has pending family member(s)

20050066390

31 Jan '08

20030077623

E I du Pont De Nemours and Company

Polynucleotides and polypeptides involved in post-transcriptional gene
silencing

18

Abandoned but has pending family member(s)

20050204427

31 Jan '08

20030126645

E I du Pont De Nemours and Company

Alteration of embryo/endosperm size during seed development

69

Abandoned but has pending family member(s)

20060218675

31 Jan '08

20040088759

EI du Pont De Nemours and Company

Plant diacyglycerol acyltransferases

22

Final Rejection Mailed

19 Feb ‘08

20040098760

E I du Pont De Nemours and Company

PIONEER HI-BRED INTERNATIONAL, Inc.

Transcriptional regulatory nucleic acids, polypeptides and methods of use
thereof

40

Abandoned but has pending family member(s)

11/779,552 (not yet published

31 Jan '08

20040181828

EI du Pont De Nemours and Company

Plant genes encoding DR1 and DRAP1, a global repressor complex oftranscription

21

Publications -- Issue Fee Payment Verified

15 Oct ‘07

20050066390

EI du Pont De Nemours and Company

Nucleotide sequences of a new class of diverged delta-9 stearoyl-ACPdesaturase genes

17

Non Final Action Mailed

15 Oct ‘07

20050120405

EI du Pont De Nemours and Company

Plant amino acid biosynthetic enzymes

21

Final Rejection Mailed

15 Oct ‘07

20050204427

EI du Pont De Nemours and Company

Polynucleotides and polypeptides involved in post-transcriptional genesilencing

18

Non Final Action Mailed

15 Oct ‘07

20050282278

EI du Pont De Nemours and Company

Plant sugar transport proteins

28

Notice of Allowance Mailed -- Application Received in office of Publications

15 Oct ‘07

20060010512

E I du Pont De Nemours and Company

Nitrogen transport metabolism

2

Abandoned but has pending family member(s)

20070011763

31 Jan '08

20060185035

EI du Pont De Nemours and Company

Plant cellulose synthases

22

Non Final Action Mailed

15 Oct ‘07

20060218674

EI du Pont De Nemours and Company

Alteration of Plant embryo/endosperm size during development

28

Non Final Action Mailed

15 Oct ‘07

20060218675

EI du Pont De Nemours and Company

Alteration of embryo/endosperm size during seed development

71

Docketed New Case - Ready for Examination

15 Oct ‘07

20070011763

EI du Pont De Nemours and Company

Nitrogen transport metabolism

8

Non Final Action Mailed

15 Oct ‘07

20070186310

E.I. Du Pont de Nemours and Co.

BRITTLE STALK 2 gene family and related methods and uses

37

Response to Non-Final office Action Entered and Forwarded to Examiner

12 Dec ‘07

20070199096

E.I. Du Pont de Nemours and Co.

Compositions and Methods for Altering Alpha- and Beta-Tocotrienol Content

42

Docketed New Case - Ready for Examination

12 Dec ‘07

20060101544

E.I. du Pont de Nemours and Co.

Phospholipid:diacylglycerol acyltransferases

34

Issue Fee Payment Verified

10 Jan ‘08

20050138691

EI du Pont De Nemours and Company

Pioneer Hi-Bred International, Inc.

Auxin transport proteins

46

Non Final Action Mailed

15 Oct ‘07

20050160494

EI du Pont De Nemours and Company

Pioneer Hi-Bred International, Inc.

Alteration of oil traits in Plants

9

Abandoned -- Failure to Respond to an office Action

10 Jan ‘08

20050273881

EI du Pont De Nemours and Company

Pioneer Hi-Bred International, Inc.

Defensin polynucleotides and methods of use

14

Appeal Brief (or Supplemental Brief) Entered and Forwarded to Examiner

19 Feb ‘08

20060123510

EI du Pont De Nemours and Company

Pioneer Hi-Bred International, Inc.

Plant RNA transport and RNA-directed RNA polymerase proteins

12

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060143728

EI du Pont De Nemours and Company

Pioneer Hi-Bred International, Inc.

Maize multidrug resistance-associated protein polynucleotides and methods ofuse

22

Non Final Action Mailed

15 Oct ‘07

20070261135

EI du Pont De Nemours and Company

Disease resistance factors

34

Docketed New Case - Ready for Examination

20-March '08

20080010699

EI du Pont De Nemours and Company

Lysophosphatidic acid acetyltransferases

55

Non Final Action Mailed

20-March '08

20030177526

Eden Bioscience Corporation

Receptors for hypersensitive response elicitors and uses thereof

54

Abandoned but has pending family member(s)

20050246799

31 Jan '08

20050246799

Eden BioScience Corporation

Receptors for hypersensitive response elicitors and uses thereof

54

Notice of Appeal Filed

19 Feb ‘08

20040016026

Evolutionary Genomics LLC

Methods to identify evolutionarily significant changes in polynucleotide andpolypeptide sequences in domesticated Plants and animals

59

Non final action mailed

15 Oct ‘07

20060225153

Evolutionary Genomics LLC

EG1117 and EG307 polynucleotides and uses thereof

79

Docketed New Case - Ready for Examination

15 Oct ‘07

20050147993

Genica Corporation

Methods and compositions for delivering polynucleotides

187

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060179512

Guelph, University of

Nitrogen-regulated sugar sensing gene and protein and modulation thereof

3

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060123507

Honda Motor Co., Ltd.

Gene elevating cereal yield and utilization thereof

3

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20070186302

Honda Motors Co. AND
National University Corporation Nagoya University

Genes that confer regeneration ability to Plants, and uses thereof

3

Docketed New Case - Ready for Examination

12 Dec '07

20050287541

Hisamitsu Pharmaceutical Co., Inc.
NGK Insulators,Ltd.
Chiba-Prefecture

Microarray for predicting the prognosis of neuroblastoma and method forpredicting the prognosis of neuroblastoma

200

Non Final Action Mailed

15 Oct ‘07

20030199684

Incorporated Administrative Agency National Agriculture and Bio-Oriented Research Organization

Novel gene involved in brassinosteroid responses

2

Abandoned -- Failure to Respond to an office Action

19 Feb ‘08

20050223438

Incorporated Administrative Agency National Agriculture and Bio-Oriented Research Organization

Functional Plant, promoter to be used for producing the functional Plant andmethod of using the same

3

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20050089899

Ipsogen

Institut National de la Sante et de la Recherche Medicale-Inserm

Institut Paoli-Calmettes

Identification of an ERBB2 gene expression signature in breast cancers

99

Non Final Action Mailed

15 Oct ‘07

20060107343

Ishihara Sanyo Kaisha, LTD.

Plant cells and Plant bodies with modified cell growth, development anddifferentiation

14

Docketed New Case - Ready for Examination

15 Oct ‘07

20070028318

Instituto Nacional de Technologia Agropecuaria

Rice Plants having Increased tolerance to imidazolinone herbicides

8

Application Undergoing Preexam Processing

15 Oct ‘07

20060230471

InterNational Research Center for Agricultural Sciences

Incorporated Administrative Agenscy, National Agriculture and Bio-orientedResearch Organization

Genes encoding Plant transcription factors

3

Docketed New Case - Ready for Examination

15 Oct '07

20040003434

J.R. Simplot Company

Refined Plant transformation

1

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct '07

20060206966

Japan International Research Center for Agricultural Sciences

Incorporated Administrative Agency, National Agriculture and Bio-Oriented Research Organization

Stress-induced promoter and method of using the same

2

Notice of Allowance Mailed -- Application Received in office of Publications

15 Oct '07

20060212961

Japan Science and Technology Agency

Rice transposon gene

7

Non Final Action Mailed

17 Apr '08

20060277625

Japan Science and Technology Agency

Non-autonomous transposon gene of rice transformed Plant and method of use

1

Non Final Action Mailed

15 Oct ‘07

20060179517

Japan Tobacco Inc.

Syngenta Limited

The rice restorer gene to the rice bt type cytoplasmic male sterility

14

Non Final Action Mailed

15 Oct ‘07

20060253931

Japan Tobacco Inc.

Syngenta Limited

Method of imparting or controlling fertility with the use of fertilityrestoring gene for rice bt-male sterility cytoplasm and method of judging theexistence of fertility restoring gene

5

Non Final Action Mailed

15 Oct ‘07

20060272053

Korea Kumho Petrochemical Co., Ltd.

Transgenic rice line producing high level of flavonoids in the endosperm

3

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20050160498

Korea University

Gene encoding cysteine protease and its promoter which are expressedspecifically in rice anther, a method for producing male sterile rice bysuppressing expression of the gene

3

Non Final Action Mailed

15 Oct ‘07

20040063101

Ludwig Institute for Cancer Research

Human sarcoma-associated antigens

90

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20040128712

Mendel BioTechnology, Inc.

Methods for modifying Plant biomass and abiotic stress

18

Non Final Action Mailed

15 Oct ‘07

20060162006

Mendel BioTechnology, Inc.

Polynucleotides and polypeptides in Plants

2202

Non Final Action Mailed

15 Oct ‘07

20060162018

Mendel BioTechnology, Inc.

Plant transcriptional regulators of disease resistance

8

Non Final Action Mailed

15 Oct ‘07

20070061911

Mendel BioTechnology, Inc.

Polynucleotides and polypeptides in Plants

1854

Issue Fee Payment Verified

21 Feb ‘08

20040045049

Mendel BioTechnology, Inc.

Polynucleotides and polypeptides in Plants

1739

Issue Fee Payment Verified

10 Jan ‘08

20060218659

Metanomics GMBH

Preparation of organisms with faster growth and/or higher yield

48

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060085872

Missouri System, University of, The

Increased Plant seed yield

31

Non Final Action Mailed

15 Oct ‘07

20030233670

Monsanto Company

Gene sequences and uses thereof in Plants

736

Examiner's answer to appeal brief mailed

15 Oct ‘07

20040045054

Monsanto Technology

Cotton event pv-ghbk04(531) and compositions and methods for detection
thereof

25

Abandoned but has pending family member(s)

11/801,118 (not yet published)

31 Jan '08

20040116682

Monsanto

Nucleic acid molecules and other molecules associated with the carbon
assimilation pathway

7341

Abandoned but has pending family member(s)

20060195932

31 Jan '08

20040216190

Monsanto Company

Nucleic acid molecules and other molecules associated with Plants and usesthereof for Plant improvement

11088

Notice of Appeal Filed

15 Oct ‘07

20050160500

Monsanto Company

Transgenic Plants with Increased glycine-betaine

36

Non Final Action Mailed

15 Oct ‘07

20060021087

Monsanto Technology LLC

Compositions and methods for control of insect infestations in Plants

16

Non Final Action Mailed

15 Oct ‘07

20060162010

Monsanto Technology LLC

Actin regulatory elements for use in Plants

7

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060168693

Monsanto Technology LLC

Method of Increasing Plant organ and seed size in a Plant

60

Notice of Allowance Mailed -- Application Received in office of Publications

15 Oct ‘07

20060179516

Monsanto Technology LLC

Promoter molecules for use in Plants

1

Response after Final Action Forwarded to Examiner

19 Feb ‘08

20040031072

Monsanto

Soy nucleic acid molecules and other molecules associated with transcriptionPlants and uses thereof for Plant improvement

146

Non final action mailed

15 Oct ‘07

20060272045

Monsanto Technology LLC

Brittle-2 regulatory elements for use in Plants

36

Non Final Action Mailed

15 Oct ‘07

20070020621

Monsanto Technology LLC

Genomic Plant sequences and uses thereof

57467

Awaiting TC Resp, Issue Fee Payment Verified

15 Oct ‘07

20030188332

Monsanto Technology LLC

Amino acid transporters

67

Issue fee payment verified: No. 7220586

15 Oct ‘07

20040123340

Monsanto

Nucleic acid molecules and other molecules associated with plants

17880

Abandoned but has pending family member(s)

20060195941

20070061916

4 Feb '08

20040172684

Monsanto Technology LLC

Nucleic acid molecules and other molecules associated with Plants and usesthereof for Plant improvement

63128

Notice of Appeal Filed

15 Oct ‘07

20040221335

Monsanto Technology LLC

Method for Increasing Total Oil Levels in Plants

12

Abandoned -- Failure to Respond to an office Action

19 Feb ‘08

20050235377

Monsanto Technology

Stress tolerant Plants and methods thereof

49

Non Final Action Mailed

15 Oct ‘07

20050235382

Monsanto Technology

Plant regulatory sequences for selective control of gene expression

6

Appeal Brief (or Supplemental Brief) Entered and Forwarded to Examiner

15 Oct ‘07

20060112447

Monsanto Technology

Nucleotide sequences encoding cry1bb proteins for enhanced expression inPlants

11

Non Final Action Mailed

15 Oct ‘07

20050273882

Monsanto

Expression of Cry3B insecticidal protein in Plants

2

Response to Non-Final office Action Entered and Forwarded to Examiner

19 Feb ‘08

20060236419

Monsanto

Nucleic acid molecules and other molecules associated with Plants and usesthereof for Plant improvement

3549

Non Final Action Mailed

15 Oct ‘07

2007130633

Monsanto UK LTD.

Rice regulatory sequences for gene expression in defined wheat tissue

3

Non Final Action Mailed

12 Dec ‘07

20050155114

Monsanto Company

Stress-inducible Plant promoters

6

Non Final Action Mailed

15 Oct ‘07

20040214272

Monsanto

Nucleic acid molecules and other molecules associated with Plants

369326

Response to Non-Final office Action Entered and Forwarded to Examiner

10 Jan ‘08

20070061916

Monsanto Company

Nucleic acid molecules and other molecules associated with Plants and usesthereof for Plant improvement

117596

Non Final Action Mailed

10 Jan ‘08

20050223435

Monsanto

Methyl-D-erythritol phosphate pathway genes

50

Non Final Action Mailed

15 Oct ‘07

20070039076

Monsanto Technology

Plant Genome sequence and uses thereof

69652

TSS review complete

15 Oct ‘07

20060195941

Monsanto Technology

Nucleic acid molecules and other molecules associated with Plants

17880

Non Final Action Mailed

15 Oct ‘07

20070016974

Monsanto

Nucleic acid molecules and other molecules associated with Plants

43701

Non Final Action Mailed

15 Oct ‘07

20080038366

Monsanto

Actin regulatory elements for use in plants

7

TSS review complete

20-March '08

20080039323

Monsanto

Actin regulatory elements for use in plants

7

Docketed New Case - Ready for Examination

20-March '08

20080039324

Monsanto

Actin regulatory elements for use in plants

7

Docketed New Case - Ready for Examination

20-March '08

20080028482

Monsanto

Corn Plant Mon88017 and Compositions and Methods for Detection Thereof

10

Docketed New Case - Ready for Examination

20-March '08

20050257292

National Institute of Agrobiological Sciences

Ehd1gene promoting Plant flowering, and utlization thereof

9

Non Final Action Mailed

15 Oct ‘07

20060130177

National Institute of Agrobiological Sciences

Methods for enhancing Plant resistance to pathogens

3

Docketed New Case - Ready for Examination

15 Oct ‘07

20040060079

National Institute of Agrobiological Sciences

Bio-Oriented Technology Research Advancement Institution

Method of controlling character of monocotyledon by modification and/oroverexpression of cytochrome P450 monooxygenase gene involved in brassinosteroidbiosynthesis and monocotyledon modified by the gene

22

Non final action mailed

15 Oct ‘07

20060191044

National Institute of Agrobiological Sciences

Seed-specific gene promoters and uses thereof

7

Response to Non-Final Office Action Entered and Forwarded to Examiner

13-Mar-08

20060230470

National Institute of Agrobiological Sciences

Promoter expressing foreign gene in root and shoot apex

3

Non Final Action Mailed

15 Oct ‘07

20070118933

National Institute of Agrobiological Sciences

Seed-specific gene promoters and uses thereof

6

Non Final Action Mailed

15 Oct ‘07

20050032112

National Institute of Agrobiological Sciences

Sodium/proton antiporter gene

2

Patented; Patent No. 7,326,827

21 Feb ‘08

20070275464

National Institute of Agrobiological Sciences

Chitin Oligosaccharide Elicitor-Binding Proteins

4

Docketed New Case - Ready for Examination

20-March '08

20070033677

National Taiwan University

Plant sHSP gene bidirectional promoter and uses thereof

1

Non Final Action Mailed

15 Oct ‘07

20050097639

Nguyen Henry T; Kreps Joel A

Nucleic acid molecules from rice controlling abiotic stress tolerance

196

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20020170087

Pioneer Hi-Bred International, Inc.

Transcriptional regulator nucleic acids, polypeptides and methods of usethereof

40

Abandoned but has pending family member(s)

20040098760

1 Feb '08

20030221224

Pioneer Hi-Bred International, Inc.

Enhanced silk exsertion under stress

14

Notice of Allowance Mailed

20 Feb ‘08

20050066394

Pioneer Hi-Bred International, Inc.

Floral development genes

63

Abandoned but has pending family member(s)

20070157341

1 Feb '08

20070231905

Pioneer Hi-Bred International, Inc.

Methods for Improving Seed Characteristics

2

Docketed New Case - Ready for Examination

12 Dec ‘07

20070234443

Pioneer Hi-Bred International, Inc.

Maize Genes For Controlling Plant Growth and Organ Size and Their Use in Improving Crop Plants

69

Docketed New Case - Ready for Examination

12 Dec ‘07

20070192901

Pioneer Hi-Bred International, Inc. and The Regents of the University of California

Engineering single-gene-controlled staygreen potential into Plants

10

Response to Non-Final office Action Entered and Forwarded to Examiner

12 Dec ‘07

20050081265

Pioneer Hi-Bred International, Inc.

Maize chloroplast protein synthesis elongation factors and methods of use forsame

6

Non Final Action Mailed

15 Oct ‘07

20050257289

Pioneer Hi-Bred International, Inc.

AP2 domain transcription factor ODP2 (ovule development protein 2) andmethods of use

7

Response to Non-Final office Action Entered and Forwarded to Examiner

19 Feb ‘08

20050278803

Pioneer Hi-Bred International, Inc.

Compositions and methods for altering the disulfide status of proteins

2

Docketed New Case - Ready for Examination

15 Oct ‘07

20060015968

Pioneer Hi-Bred International, Inc.

Nucleotide sequences mediating male fertility and method of using same

12

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060064786

Pioneer Hi-Bred International, Inc.

Isopentenyl transferase sequences and methods of use

64

Docketed New Case - Ready for Examination

15 Oct ‘07

20060137033

Pioneer Hi-Bred International, Inc.

Cytokinin-sensing histidine kinases and methods of use

22

Docketed New Case - Ready for Examination

15 Oct ‘07

20060281910

Pioneer Hi-Bred International, Inc.

Alternative splicing factors polynucleotides, polypeptides and uses thereof

3

Non Final Action Mailed

15 Oct ‘07

20060288440

Pioneer Hi-Bred International, Inc.

Nucleotide sequences mediating male fertility and method of using same

12

Docketed New Case - Ready for Examination

15 Oct ‘07

20060288453

Pioneer Hi-Bred International, Inc.

Manipulation of Plant polysaccharide synthases

28

Docketed New Case - Ready for Examination

15 Oct ‘07

2005001097

Pioneer Hi-Bred International, Inc.

The Arizona Board of Regents acting on Behalf of The University of Arizona

Cell cycle nucleic acids, polypeptides and uses thereof

2

Non Final Action Mailed

15 Oct ‘07

20070079397

Pioneer Hi-Bred International, Inc.

The Curators of the University of Missouri

Isolated nucleic acid molecules encoding the Br2 P-glycoprotein of maize andmethods of modifying growth in Plants transformed therewith

3

Docketed New Case - Ready for Examination

15 Oct ‘07

20070157341

Pioneer Hi-Bred Int. and
E.I. Du Pont de Nemours & Co.

Floral Development Genews

62

Docketed New Case - Ready for Examination

12 Dec ‘07

20080028492

Pioneer Hi-Bred

Maize Cellulose Synthases and Uses Thereof

20

Response to Non-Final Office Action Entered and Forwarded to Examiner

20-March '08

20060035227

Plant Genome Cener Co., Ltd.

Methods for distinguishing rice varities

28

Non Final Action Mailed

15 Oct ‘07

20060107344

POSCO

POSTECH Foundation

Organ preferential genes identified by T-DNA insertional mutagenesis of rice

51

Final Rejection Mailed

19 Feb ‘08

20050066389

Regents of the University of California

Genes which produce staygreen characteristics in maize and their uses

18

Response to Non-Final office Action Entered and Forwarded to Examiner

19 Feb ‘08

20030213010

Renessen LLC

Transgenic high tryptophan Plants

69

Non final action mailed

15 Oct ‘07

20060105376

Research Association for Biotechnology

Novel full-length cDNA

4886

Docketed New Case - Ready for Examination

15 Oct ‘07

20060059586

Samuel Roberts Noble Foundation, The

Plants with delayed flowering

15

Docketed New Case - Ready for Examination

15 Oct ‘07

20050044594

SCHMULLING THOMAS; WERNER TOMAS

Method for modifying Plant morphology, biochemistry and physiology

29

Non Final Action Mailed

15 Oct ‘07

20040019927

SHERMAN BRADLEY K; RIECHMANN JOSE LUIS; JIANG CAI-ZHONG; HEARD JACQUELINE E;HAAKE VOLKER; CREELMAN ROBERT A; RATCLIFFE OLIVER; ADAM LUC J; REUBER T. LYNNE;KEDDIE JAMES; BROUN PIERRE E; PILGRIM MARSHA L; DUBELL ARNOLD N; PINEDA OMAIRA;YU GUO-LIANG

Polynucleotides and polypeptides in Plants

2076

Non final action mailed

15 Oct ‘07

20060107352

Sungene GMBH & CO. KGAA

Transgenic expression cassettes for expression of nucleic acids in the Plantblooms

23

Non Final Action Mailed

15 Oct ‘07

20060130182

Sungene GMBH & CO. KGAA

Expression cassette for nucleic acids in Plant tissue containing starch

40

Docketed New Case - Ready for Examination

15 Oct ‘07

20040016025

Syngenta Participations AG

Rice promoters for regulation of plant expression

2731

Abandoned but has pending family member(s)

20070056055

1 Feb '08

20050032156

Syngenta Participations AG (US)

Identification and characterization of phosphate transporter genes

46

Non Final Action Mailed

15 Oct ‘07

20050177901

Syngenta Participations AG

Identification and characterization of Plant genes

474

Non Final Action Mailed

15 Oct ‘07

20060253917

Syngenta Participations AG

Cell proliferation-related polypeptides and uses therefor

98

Non Final Action Mailed

15 Oct ‘07

20060260011

Syngenta Participations AG

Methods and genetic constructs for modification of lignin composition of corncobs

3

Docketed New Case - Ready for Examination

15 Oct ‘07

20070089180

Syngenta Participations AG

Transcription factors of cereals

826

Docketed New Case - Ready for Examination

15 Oct ‘07

20060288450

Samuel Roberts Noble Foundation

Plant N-acylethanolamine binding proteins

29

Non Final Action Mailed

20 Feb ‘08

20070015249

Seikagaku Corporation

Chondroitin polymerase and DNA encoding the same

3

Docketed New Case - Ready for Examination

15 Oct ‘07

20070006344

Syngenta Participations AG

Regulatory sequences for expressing gene products in Plant reproductivetissue

68

Non Final Action Mailed

15 Oct ‘07

20060075523

Syngenta

Abiotic stress responsive polynucleotides and polypeptides

8

Docketed New Case - Ready for Examination

15 Oct ‘07

20060235215

Syngenta

Stress-related polypeptides and uses therefor

153

Docketed New Case - Ready for Examination

15 Oct ‘07

20060248613

THE Board of Regents of THE University of NEBRASKA

Implementation of a mitochondrial mutator

41

Non Final Action Mailed

15 Oct ‘07

20060183137

The Scripps Research Institute

Syngenta Participations AG

Stress-regulated genes of Plants, transgenic Plants containing same, andmethods of use

5339

Non Final Action Mailed

15 Oct ‘07

20060143734

Temasek Life Sciences Laboatory Limited

Nucleic acids from rice conferring resistance to bacterial blight diseasecaused by xanthomonas spp

9

Issue Fee Payment Received

19 Feb ‘08

20060228751

The Ohio State University

Cloning and characterization of the broad-spectrum resistance gene P12

2

Docketed New Case - Ready for Examination

15 Oct ‘07

20040209325

University of Arkansas

Mitogen-activated protein kinase and method of use to enhance biotic and abiotic stress tolerance in Plants

4

Issue Fee Payment Verified

21 Feb ‘08

20060218677

University of DELHI

Department of Biotechnology

Novel gene osisap1 of rice confers tolerance to stresses and a method thereof

2

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20070250956

University of Guelph

Nitrogen-Regulated Sugar Sensing Gene and Protein and Modulation Thereof

6

Non Final Action Mailed

12 Dec ‘07

20060185036

The University of Michigan

Transgenic Plants containing ligninase and cellulase which degrade lignin andcellulose to fermentable sugars

5

Non Final Action Mailed

15 Oct ‘07

20060179513

The University of Michigan

Transgenic Plants containing ligninase and cellulase which degrade lignin andcellulose to fermentable sugars

6

Notice of Allowance Mailed

21 Feb ‘08

20040237134

University of Sasketchewan

Wheat Plants having Increased resistance to imidazoline herbicides

4

Non Final Action Mailed

15 Oct ‘07

20060242739

Universidad Publica De Navarra

Niigata University

Plant nucleotide-sugar pyrophosphatase/phosphodiesterase (nppase), method ofobtaining same and use of same in the production of assay devices and in theproduction of transgenic Plants

24

Docketed New Case - Ready for Examination

15 Oct ‘07

20060218676

University of Washington

Compositions and method for modulation of Plant cell division

14

Docketed New Case - Ready for Examination

15 Oct ‘07

20030056244

Ventria Bioscience

Feed additive compositions and methods

45

Non Final Action Mailed

19 Feb ‘08

20030172403

Ventria Bioscience

Plant transcription factors and enhanced gene expression

5

Abandoned but has pending family member(s)

20030056244

20030074700

20040111766

20050229273

4 Feb '08

20040111766

Ventria Bioscience

Expression of human milk proteins in transgenic Plants

10

Non Final Action Mailed

15 Oct ‘07

20050118625

Wyeth

Nucleic acid arrays for detecting gene expression associated with humanosteoarthritis and human proteases

5235

Non Final Action Mailed

15 Oct ‘07

20050287570

Wyeth

Probe arrays for expression profiling of rat genes

8192

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060160121

Wyeth

Probe arrays for detecting multiple strains of different species

18598

Docketed New Case - Ready for Examination

15 Oct ‘07

20040123343

unknown

Rice nucleic acid molecules and other molecules associated with Plants anduses thereof for Plant improvement

204966

Appeal Brief (or Supplemental Brief) Entered and Forwarded to Examiner

15 Oct ‘07

20040204579

unknown

Nucleic acid molecules encoding enzymes from wheat which are involved instarch synthesis

4

Notice of Allowance Mailed -- Application Received in office of Publications

15 Oct ‘07

20050223429

unknown

Method for modifying Plant morphology, biochemistry and physiology

49

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20060031967

unknown

Compositions and methods for modulation of Plant cell division

43

Non Final Action Mailed

15 Oct ‘07

20060112446

unknown

Transposon genes of rice, transformed Plant and method of use

3

Non Final Action Mailed

15 Oct ‘07

20060130174

unknown

Transposon and transposase genes of rice, transposase, transformant andmethod of use

3

Non Final Action Mailed

15 Oct ‘07

20060195932

unknown

Nucleic acid molecules and other molecules associated with the carbonassimilation pathway

7341

Response to Non-Final office Action Entered and Forwarded to Examiner

15 Oct ‘07

20070243533

unknown

Products and Methods of Organism Identification in Nutritional Supplements

208

Non Final Action Mailed

12 Dec ‘07

20050064454

unknown

Cancer gene determination and therapeutic screening using signature gene sets

8447

Abandoned but has pending family member(s)

20080050379

4 Feb '08

Abandoned Rice Patent Applications

Many applications never make it to becoming actual patents, but are rather abandoned during the examination process. When this occurs, the inventions disclosed in the patent application become available for public to use, as long as they are not the subject of another granted patent. For U.S. applications reciting rice sequences in the claims, we found that roughly 30% are abandoned (Figure 1). The table below shows the applications that recite rice sequences (or sequences highly similar to rice) in the claims that are abandoned, and that did not have any pending continuations as of March 2008.

Figure 1: Pending vs. Abandoned U.S. Rice Patent Applications

Pending vs. Abandoned Rice Applications

Application No.

Assignee

Title

No. of Sequences in Claims

Status Date

20050150008

Agrigenesis Biosciences Limited

Wrightson Seeds Limited

Compositions isolated from forage grasses and methods of use

190

30 Jan '08

20030237108

Agrigenesis Biosciences Limited

Compositions isolated from forage grasses and methods for their use

88

20 March '08

20070054278

Applera Corporation

Polymorphisms in nucleic acid molecules encoding human enzyme proteins,methods of detection and uses thereof

558824

30 Jan '08

20010036654

ARCH Development Corporation

Canola acetyl-CoA carboxylase compositions and methods of use

14

30 Jan '08

20020115085

Avalon Pharmaceuticals

Cancer gene determination and therapeutic screening using signature
gene sets

318

20 March '08

20040023395

Bionox, Inc.

Transgenic tetraploid plants and methods of production

46

31 Jan '08

20020092041

California, The Regents of the University of

PROCEDURES AND MATERIALS FOR CONFERRING DISEASE RESISTANCE
IN PLANTS

12

31 Jan '08

20040221332

Cropdesign N.V.

Plant growth regulating genes, proteins and uses thereof

104

31 Jan '08

20010010931

E I du Pont De Nemours and Company

Plant glycolysis and respiration enzymes

20

31 Jan '08

20020001843

E I du Pont De Nemours and Company

Starch biosynthetic enzymes

20

20 March '08

20020009801

E I du Pont De Nemours and Company

Amino acid decarboxylases

20

31 Jan '08

20020066120

E I du Pont De Nemours and Company

PLANT MYB-RELATED TRANSCRIPTION FACTORS

50

20 March '08

20020119546

E I du Pont De Nemours and Company

Squalene synthesis enzymes

16

31 Jan '08

20020152497

E I du Pont De Nemours and Company

Nucleic acid fragments encoding proteins involved in stress response

104

20 March '08

20020182704

E I du Pont De Nemours and Company

Plant proteinases

56

20 March '08

20020187539

E I du Pont De Nemours and Company

Plant myb-related transcription factors

50

31 Jan '08

20030003471

E I du Pont De Nemours and Company

cDNAs encoding polypeptides

106

20 March '08

20030017978

E I du Pont De Nemours and Company

Spf1-related transcription factors

12

31 Jan '08

20030066102

E I du Pont De Nemours and Company

Plant gene for p-hydroxyphenylpyruvate dioxygenase

9

31 Jan '08

20030082787

E I du Pont De Nemours and Company

Plant histidine biosynthetic enzymes

7

31 Jan '08

20030084475

E I du Pont De Nemours and Company

Nucleic acid fragments and proteins affecting storage organelle formation and
methods of use

14

31 Jan '08

20030088083

E I du Pont De Nemours and Company

Metal-binding proteins

14

31 Jan '08

20030088882

E I du Pont De Nemours and Company

Fructokinase

12

31 Jan '08

20030104593

E I du Pont De Nemours and Company

Plant sorbitol biosynthetic

22

20 March '08

20030119165

E I du Pont De Nemours and Company

Plant transcription factors

43

31 Jan '08

20030140372

E I du Pont De Nemours and Company

Genes for desaturases to alter lipid profiles in corn

19

31 Jan '08

20030167508

E I du Pont De Nemours and Company

Novel plant tryptophan synthase beta subunit

10

31 Jan '08

20030167509

E I du Pont De Nemours and Company

Plant histidine biosynthetic enzymes

2

31 Jan '08

20030177522

E I du Pont De Nemours and Company

Plant folate biosynthetic genes

2

31 Jan '08

20030186362

E I du Pont De Nemours and Company

Plant cell cycle regulatory proteins

18

31 Jan '08

20030217384

E I du Pont De Nemours and Company

Obtusifoliol 14a-demethylase

4

31 Jan '08

20040064848

E I du Pont De Nemours and Company

Chorismate biosynthesis enzymes

28

31 Jan '08

20040214216

E I du Pont De Nemours and Company

Plant amino acyl-tRNA synthetase

6

31 Jan '08

20060005277

E I du Pont De Nemours and Company

cDNAs encoding polypeptides

106

31 Jan '08

20030172411

E I du Pont De Nemours and Company
PIONEER HI-BRED INTERNATIONAL, Inc.

Disease resistance factors

16

20 March '08

20050074862

E I du Pont De Nemours and Company

PIONEER HI-BRED INTERNATIONAL, Inc.

Polynucleotides encoding defense responde proteins

2

31 Jan '08

20020045592

ELITRA PHARMACEUTICALS, Inc

Genes identified as required for proliferation in escherichia coli

397

31 Jan '08

20030177524

FALCO SAVERIO CARL; RAFALSKI J. ANTONI; WENG ZUDE

Gene involved in pyrimidine biosynthesis in plants

8

31 Jan '08

20030188334

Famodu Omolayo O; Maxwell Carl A

Magnesium chelatase

2

31 Jan '08

20030170845

Famodu Omolayo O; Orozco Emil M

Tetrahydrofolate metabolic enzymes

70

31 Jan '08

20030177532

Gemstar (Cambridge) Limited

Manipulation of starch granule size and number

24

31 Jan '08

20030200564

Gemstar (Cambridge) Limited

Starch modification

35

31 Jan '08

20050144667

Horticulture and Food Research Institute of New Zealand Limited, The

Plant polypeptides and polynucleotides encoding same

12

31 Jan '08

20040048253

Incyte Corporation

Molecules for diagnostics and therapeutics

422

31 Jan '08

20030134283

Incyte Genomics, Inc.

Genes regulated in dendritic cell differentiation

260

31 Jan '08

20030106106

Japan Tobacco, Inc.

Flower organ-specific gene and its promoter sequence

1

31 Jan '08

20020194646

Large Scale Biology Corporation

Methods of creating dwarf phenotypes in plants

122

31 Jan '08

20030162291

McGill University

Clk-2, cex-7 and coq-4 genes, and uses thereof

50

20 March '08

20030181408

Merck & Co., Inc.

Genes essential for microbial proliferation and antisense thereto

469

31 Jan '08

20040029129

Merck & Co., Inc.

Identification of essential genes in microorganisms

78581

31 Jan '08

20020170089

Millennium Pharmaceuticals

Nucleic acids encoding defense inducible proteins and uses thereof

22

31 Jan '08

20020192813

Monsanto Technology

PLANT EXPRESSION VECTORS

6

31 Jan '08

20030165947

Monsanto Technology

Plant regulatory sequences for selective control of gene expression

28

31 Jan '08

20040093638

Nara Institute of Science and Technology

Method for promoting fatty acid synthesis in a plant

2

31 Jan '08

20040091860

National Institute of Agrobiological Sciences

Rice peroxidases with various characteristics

21

31 Jan '08

20050034189

National Institute of Agrobiological Sciences

Chitin oligosaccharide elicitor- and gibberellin-responsive genes in plants,
and uses thereof

4

31 Jan '08

20040229233

NGK Insulators, Ltd.

Human housekeeping genes and human-tissue specific genes

200

31 Jan '08

20050196754

Nuvelo, Inc.

Novel nucleic acids and polypeptides

60736

31 Jan '08

20060123505

National Institute of Agrobiological Sciences

RIKEN

Foundation for Advancement of InterNational Science

Full-length plant cDNA and uses thereof

56791

31 Jan '08

20030203372

Oxford Biomedica (UK) Ltd.

Analysis method

497

31 Jan '08

20020142319

Paradigm Genetics Inc.

Expressed sequences of Arabidopsis thaliana

900

31 Jan '08

20030115639

Paradigm Genetics Inc.

Expressed sequences of arabidopsis thaliana

999

31 Jan '08

20020023281

Paradigm Genetics Inc.

Expressed sequences of arabidopsis thaliana

999

31 Jan '08

20030167505

Pioneer Hi-Bred International, Inc.

Cell cycle nucleic acids, polypeptides and uses thereof

2

20 March '08

20040068767

Pioneer Hi-Bred International, Inc.

Maize cellulose synthases and uses thereof

6

1 Feb '08

20040078844

Plant Bioscience Limited

Morphochem AG

Methods and means for gene silencing

3

1 Feb '08

20020108140

Purdue Research Foundation

COMPOSITIONS and METHODS FOR ENHANCING DISEASE RESISTANCE IN PLANTS

35

20 March '08

20020076775

Pioneer Hi-Bred International, Inc.

WRKY transcription factors and methods of use

36

1 Feb '08

20050055748

Pioneer Hi-Bred International, Inc.

Stress-responsive genes, regulatory elements, and methods of use for same

14

1 Feb '08

20040019931

Pioneer Hi-Bred International, Inc

Methods and compositions for modifying oil and protein content in plants

6

1 Feb '08

20070020637

Research Association for Biotechnology

Full-length cDNA

4990

1 Feb '08

20040010815

Syngenta Biotechnology, Inc.

Identification and characterization of plant genes

414

1 Feb '08

20030049814

Syngenta Limited

Herbicide resistant plants

4

1 Feb '08

20030079246

Syngenta Limited

Herbicide resistant plants

4

1 Feb '08

20030135888

Syngenta Participations AG

Genes that are modulated by posttranscriptional gene silencing

649

1 Feb '08

20030145347

Syngenta Participations AG

Grain processing method and transgenic plants useful therein

9

1 Feb '08

20040060084

Syngenta Participations AG

DNA comprising rice anther-specific gene and transgenic plant transformed
therewith

6

1 Feb '08

20050132438

Syngenta Participations AG

Novel monocotylednous plant genes and uses thereof

20

1 Feb '08

20070016976

Syngenta Participations AG

Plant genes involved in defense against pathogens

19

1 Feb '08

20010051713

Syngenta

DNA comprising rice anther-specific gene and transgenic plant transformed
therewith

6

20 March '08

20040219675

Syngenta

Nucleic acid molecules from rice encoding proteins for abiotic stresstolerance,
enhanced yeild, disease resistance and altered nutritional qualityand uses thereof

64

1 Feb '08

20070089201

The Dow Chemical Company

DFB Biotech, Inc.

Plant production of immunoglobulins with reduced fucosylation

12

1 Feb '08

20040083501

United States of America, as Represented by the Secretary of Agriculture

Plant genes that confer resistance to strains of Magnaporthe grisea having
AVR CO39 cultivar specificity gene

5

4 Feb '08

20040103453

Universitat Zurich

Syngenta Participations AG

Lipoxygenase genes, promoters, transit peptides and proteins thereof

10

4 Feb '08

20030217389

Washington State University Research Foundation

Novel peptides and methods of use

34

4 Feb '08

20030165870

Wisconsin Alumni Research Foundation

Novel sequences of E. coli CFT073

252

4 Feb '08

20020137139

unknown

Nucleic acid and other molecules associated with lactation and muscle
and fat deposition

15122

4 Feb '08

20030166241

unknown

Plant amino acyl-tRNA synthetase

22

20 March '08

20040006788

unknown

Procedures and materials for conferring disease resistance in plants

12

4 Feb '08

20040060081

unknown

Plant genes that confer resistance to strains of magnaporthe grisea havingavri
co39 cultivar specificity gene

8

20 March '08

20040096875

unknown

Novel gene for controlling leaf shapes

2

4 Feb '08

20040199944

unknown

Maize H3C4 promoter combined with the first intron of rice actin, chimericgene
comprising it and transformed plant

3

5 Feb '08

20060026704

unknown

Vector for the production of transplastomic angiosperm plants

5

20 March '08

20060026721

unknown

Plant cellulose synthases

22

20 March '08

20070060743

unknown

Novel nucleic acids and polypeptides

8051

4 Feb '08

Submarine Applications

Submarine patent applications are applications that pend secretly for an extended amount of time before becoming disclosed to the public by publication. "Classic" submarine patent applications, which were kept pending for years or even decades by filing multiple continuation applications, are generally no longer possible due to the implementation of a publication policy at the USPTO. In addition, the USPTO has changed its policy regarding the term of a patent. Formerly the term of a patent was 17 years calculated from the issue date. Now, applications filed on or after 8 June 1995 have a term that is 20 years from the earliest filing date. This makes the submarine patent applications less likely to have major impact because the extended length of pendency decreases the number of years that the granted patent is enforceable.

In general, U.S. applications filed on or after 29 November 2000 are published 18 months after the priority date, unless a non-publication request is filed. Non-publication is only allowed for applications that have not been filed in a jurisdiction that publishes applications.  This means that most, if not all, unpublished applications have been filed only in the U.S., because essentially all other countries publish patent applications.  Despite the publication rule, some applications can fail to publish in a timely manner. In other cases, the disclosure was made initially in a parent application that was filed before 29 November 2000, but did not publish until 18 months after a continuation was filed. In still other cases, the application was filed with a non-publication request, which was later rescinded.

The following eight applications, all assigned to Monsanto, might be considered "submarine" applications because the subject matter disclosed in the application pended in the patent office for extended periods of time before being published.

Patent Publication No. 20060236419

Length of pendency before publication: approximately 6 years 5 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information

20060236419

  • Earliest priority - 6 May 1999
  • Filed - 2 Jul 2003
  • Publication - 19 Oct 06

Title - Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

Claim 1

A recombinant DNA construct comprising a polynucleotide selected from the group consisting of a polynucleotide comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1-3549.

Claim 2

A recombinant DNA construct comprising a polynucleotide selected from the group consisting of a polynucleotide encoding a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 3550-7098.

Claim 3

A method of producing a plant having an improved property, wherein said method comprises transforming a plant with a recombinant construct comprising a promoter region functional in a plant cell operably joined to a polynucleotide comprising coding sequence for a polypeptide associated with said property, and growing said transformed plant, wherein said polypeptide is selected from the group consisting of: a) a polypeptide useful for improving plant cold tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; b) a polypeptide useful for manipulating growth rate in plant cells by modification of the cell cycle pathway, wherein said polypeptide comprises a sequence identified as such in Table 1; c) a polypeptide useful for improving plant drought tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; d) a polypeptide useful for providing increased resistance to plant disease, wherein said polypeptide comprises a sequence identified as such in Table 1; e) a polypeptide useful for galactomannan production, wherein said polynucleotide comprises a sequence identified as such in Table 1; f) a polypeptide useful for production of plant growth regulators, wherein said polypeptide comprises a sequence identified as such in Table 1; g) a polypeptide useful for improving plant heat tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; h) a polypeptide useful for improving plant tolerance to herbicides, wherein said polypeptide comprises a sequence identified as such in Table 1; i) a polypeptide useful for increasing the rate of homologous recombination in plants, wherein said polypeptide comprises a sequence identified as such in Table 1; j) a polypeptide useful for lignin production, wherein said polypeptide comprises a sequence identified as such in Table 1; k) a polypeptide useful for improving plant tolerance to extreme osmotic conditions, wherein said polypeptide comprises a sequence identified as such in Table 1; l) a polypeptide useful for improving plant tolerance to pathogens or pests, wherein said polypeptide comprises a sequence identified as such in Table 1; m) a polypeptide useful for yield improvement by modification of photosynthesis, wherein said polynucleotide comprises a sequence identified as such in Table 1; n) a polypeptide useful for modifying seed oil yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; o) a polypeptide useful for modifying seed protein yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; p) a polypeptide encoding a plant transcription factor, wherein said polypeptide comprises a sequence identified as such in Table 1; q) a polypeptide useful for yield improvement by modification of carbohydrate use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; r) a polypeptide useful for yield improvement by modification of nitrogen use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; s) a polypeptide useful for yield improvement by modification of phosphorus use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; and t) a polypeptide useful for yield improvement by providing improved plant growth and development under at least one stress condition, wherein said polypeptide comprises a sequence identified as such in Table 1.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070016974

Length of pendency before publication: approximately 7 years 4 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information

20070016974 A1

  • Earliest priority - 30 Sep 1999
  • Filed - 15 Sep 2006
  • Publication - 18 Jan 07

Title - Nucleic acid molecules and other molecules associated with plants

Claim 1

A substantially purified nucleic acid molecule that encodes a plant protein or fragment thereof comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO:43701.

Claim 3

A substantially purified rice protein or fragment thereof, wherein said rice protein is encoded by a nucleic acid molecule that comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO:43701.

Claim 4

A transformed plant having a nucleic acid molecule which comprises: (a) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; (b) a structural nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 43701 or complements thereof; (c) a 3′ non-translated sequence that functions in said plant cell to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of said mRNA molecule.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070020621

Length of pendency before publication: approximately 6 years 5 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information

20070020621

  • Earliest priority - 19 Jul 2000
  • Filed - 23 Mar 2001
  • Publication - 25 Jan 07

Title - Genomic plant sequences and uses thereof

Claim 1

A substantially purified nucleic acid molecule comprising a nucleic acid sequence wherein the nucleic acid sequence: i) hybridizes under stringent conditions with a sequence selected from the group consisting of SEQ ID NO:1 through 57,467, and the complements thereof; or ii) exhibits an 85% or greater identity to a sequence selected from the group consisting of SEQ ID NO:1 through 57,467.

Claim 18

A transgenic plant containing a nucleic acid molecule that comprises in the 5′ to 3′ direction: a nucleic acid sequence that: i) hybridizes under stringent conditions with a sequence selected from the group consisting of SEQ ID NO:1 through 57,467, and the complements thereof; or ii) exhibits an 85% or greater identity to a sequence selected from the group consisting of SEQ ID NO:1 through 57,467; operably linked to a structural nucleic acid sequence; wherein the nucleic acid sequence is heterologous with respect to the structural nucleic acid sequence.

Claim 36

A method of transforming a host cell comprising: a) providing a nucleic acid molecule that comprises in the 5′ to 3′ direction: a nucleic acid sequence that: i) hybridizes under stringent conditions with a sequence selected from the group consisting of SEQ ID NO:1 through 57,467, and the complements thereof; or ii) exhibits an 85% or greater identity to a sequence selected from the group consisting of SEQ ID NO:1 through 57,467; operably linked to a structural nucleic acid sequence; and b) transforming said plant with the nucleic acid molecule.

Monsanto

Remarks

This application was filed on 23 March 2001, but did not publish until 25 January 2007. In this case, it appears that the applicants initially filed a non-publication request, but later rescinded it in March of 2004. Theoretically, it should have pubished shortly after that, but it didn't actually publish until January 2007. To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070039076

Length of pendency before publication: approximately 7 years 7 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information

20070039076

  • Earliest priority - 20 Jul 1999
  • Filed - 24 Jul 2006
  • Publication - 15 Feb 07

Title - Plant genome sequence and uses thereof

Claim 1

A substantially purified nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 69652 or complements thereof.

Claim 2

A substantially purified nucleic acid molecule, said nucleic acid molecule capable of specifically hybridizing to a second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 69652 or complements thereof.

Claim 5

A substantially purified nucleic acid molecule encoding a protein or fragment thereof, wherein said protein or fragment thereof is selected from the group consisting of a rice protein or fragment thereof from Table 1.

Claim 10

A transformed plant having a nucleic acid molecule which comprises: (A) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; which is linked to (B) a structural nucleic acid molecule, wherein said structural nucleic acid molecule encodes a protein or fragment thereof selected from the group consisting of a rice protein homologue or fragment thereof in Table 1; which is linked to (C) a 3′ non-translated sequence that functions in a plant cell to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of said mRNA molecule.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070044171

Length of pendency before publication: approximately 7 years 2 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information

20070044171

  • Earliest priority - 14 Dec 2000
  • Filed - 6 Nov 2003
  • Publication - 22 Feb 07

Title - Nucleic acid molecules and other molecules associated with plants

Claim 1

A recombinant polynucleotide selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 105,582.

Claim 2

A recombinant polypeptide selected from the group consisting of SEQ ID NO: 105,583 through SEQ ID NO: 211,164.

Claim 3

A method of producing a plant having an improved property, wherein said method comprises transforming a plant with a recombinant construct comprising a promoter region functional in a plant cell operably joined to a polynucleotide comprising a coding sequence for a polypeptide associated with said property, and growing said transformed plant, wherein said polypeptide is selected from the group consisting of: a) a polypeptide useful for improving plant cold tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; b) a polypeptide useful for manipulating growth rate in plant cells by modification of the cell cycle pathway, wherein said polypeptide comprises a sequence identified as such in Table 1; c) a polypeptide useful for improving plant drought tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; d) a polypeptide useful for providing increased resistance to plant disease, wherein said polypeptide comprises a sequence identified as such in Table 1; e) a polypeptide useful for galactomannan production, wherein said polynucleotide comprises a sequence identified as such in Table 1; f) a polypeptide useful for production of plant growth regulators, wherein said polypeptide comprises a sequence identified as such in Table 1; g) a polypeptide useful for improving plant heat tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; h) a polypeptide useful for improving plant tolerance to herbicides, wherein said polypeptide comprises a sequence identified as such in Table 1; i) a polypeptide useful for increasing the rate of homologous recombination in plants, wherein said polypeptide comprises a sequence identified as such in Table 1; j) a polypeptide useful for lignin production, wherein said polypeptide comprises a sequence identified as such in Table 1; k) a polypeptide useful for improving plant tolerance to extreme osmotic conditions, wherein said polypeptide comprises a sequence identified as such in Table 1; l) a polypeptide useful for improving plant tolerance to pathogens or pests, wherein said polypeptide comprises a sequence identified as such in Table 1; m) a polypeptide useful for yield improvement by modification of photosynthesis, wherein said polynucleotide comprises a sequence identified as such in Table 1; n) a polypeptide useful for modifying seed oil yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; o) a polypeptide useful for modifying seed protein yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; p) a polypeptide encoding a plant transcription factor, wherein said polypeptide comprises a sequence identified as such in Table 1; q) a polypeptide useful for yield improvement by modification of carbohydrate use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; r) a polypeptide useful for yield improvement by modification of nitrogen use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; s) a polypeptide useful for yield improvement by modification of phosphorus use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; and t) a polypeptide useful for yield improvement by providing improved plant growth and development under at least one stress condition, wherein said polypeptide comprises a sequence identified as such in Table 1.

Monsanto

Remarks

The corresponding patent (US 7214786) has been issued, which has two claims left that are drawn to two sequences: a recombinant polynucleotide of SEQ ID NO: 28,864 and a recombinant polypeptide of SEQ ID NO: 134,446. We have no information that a corresponding patent application has been filed in any other country besides the USA.

Patent Publication No. 200700661916

Length of pendency before publication: approximately 5 years 9 Months

 Publication No.

Title, Independent Claims and Summary

Assignee and licensing information

20070061916

  • Earliest priority - 7 May 2001
  • Filed - 14 Jul 2006
  • Publication - 15 Mar 07

Title -Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

Claim 1

A recombinant polynucleotide selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 58,798.

Claim 2

A recombinant polypeptide selected from the group consisting of SEQ ID NO: 58,799 through SEQ ID NO: 117,596.

Claim 3

A method of producing a plant having an improved property, wherein said method comprises transforming a plant with a recombinant construct comprising a promoter region functional in a plant cell operably joined to a polynucleotide comprising a coding sequence for a polypeptide associated with said property, and growing said transformed plant, wherein said polypeptide is selected from the group consisting of: a) a polypeptide useful for improving plant cold tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; b) a polypeptide useful for manipulating growth rate in plant cells by modification of the cell cycle pathway, wherein said polypeptide comprises a sequence identified as such in Table 1; c) a polypeptide useful for improving plant drought tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; d) a polypeptide useful for providing increased resistance to plant disease, wherein said polypeptide comprises a sequence identified as such in Table 1; e) a polypeptide useful for galactomannan production, wherein said polynucleotide comprises a sequence identified as such in Table 1; f) a polypeptide useful for production of plant growth regulators, wherein said polypeptide comprises a sequence identified as such in Table 1; g) a polypeptide useful for improving plant heat tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; h) a polypeptide useful for improving plant tolerance to herbicides, wherein said polypeptide comprises a sequence identified as such in Table 1; i) a polypeptide useful for increasing the rate of homologous recombination in plants, wherein said polypeptide comprises a sequence identified as such in Table 1; j) a polypeptide useful for lignin production, wherein said polypeptide comprises a sequence identified as such in Table 1; k) a polypeptide useful for improving plant tolerance to extreme osmotic conditions, wherein said polypeptide comprises a sequence identified as such in Table 1; l) a polypeptide useful for improving plant tolerance to pathogens or pests, wherein said polypeptide comprises a sequence identified as such in Table 1; m) a polypeptide useful for yield improvement by modification of photosynthesis, wherein said polynucleotide comprises a sequence identified as such in Table 1; n) a polypeptide useful for modifying seed oil yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; o) a polypeptide useful for modifying seed protein yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; p) a polypeptide encoding a plant transcription factor, wherein said polypeptide comprises a sequence identified as such in Table 1; q) a polypeptide useful for yield improvement by modification of carbohydrate use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; r) a polypeptide useful for yield improvement by modification of nitrogen use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; s) a polypeptide useful for yield improvement by modification of phosphorus use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; and t) a polypeptide useful for yield improvement by providing improved plant growth and development under at least one stress condition, wherein said polypeptide comprises a sequence identified as such in Table 1.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070067865

Length of pendency before publication: approximately 6 years 10 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information

20070067865

  • Earliest priority - 5 Sep 2000
  • Filed - 14 Aug 2006
  • Publication - 22 Jul 07

Title - Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

Claim 1

A substantially purified nucleic acid molecule comprising a nucleic sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 463,173 or complements thereof or fragments of either.

Claim 2

A substantially purified first nucleic acid molecule, wherein the first nucleic molecule specifically hybridizes to a second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 463,173 complements thereof.

Claim 3

A substantially purified protein or fragment thereof encoded by a first nucleic acid molecule which specifically hybridizes to a second nucleic acid molecule, the second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of a complement of SEQ ID NO: 1 through SEQ ID NO: 463,173.

Claim 5

A purified antibody or fragment thereof which is capable of specifically binding to a protein or fragment thereof, wherein the protein or fragment thereof is encoded by a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting SEQ ID NO: 1 through SEQ ID NO: 463,173.

Claim 6

A transformed plant having a nucleic acid molecule which comprises: (A) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; (B) a structural nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 463,173; and (C) a 3′ non-translated sequence that functions in the plant cell to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of the mRNA molecule.

Claim 8

A transformed plant having a nucleic acid molecule which comprises: (A) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; which is linked to (B) a transcribed nucleic acid molecule with a transcribed strand and a non-transcribed strand, wherein the transcribed strand is complementary to a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 463,173 or fragment thereof; which is linked to (C) a 3′ non-translated sequence that functions in plant cells to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of the mRNA molecule.

Claim 10

A method for determining a level or pattern of a protein in a plant cell or plant tissue under evaluation which comprises assaying the concentration of a molecule, whose concentration is dependent upon the expression of a gene, the gene specifically hybridizes to a nucleic acid molecule having a nucleic acid sequence selected from the group consisting of a complement of SEQ ID NO: 1 through SEQ ID NO: 463,173, in comparison to the concentration of that molecule present in a reference plant cell or a reference plant tissue with a known level or pattern of the protein, wherein the assayed concentration of the molecule is compared to the assayed concentration of the molecule in the reference plant cell or reference plant tissue with the known level or pattern of the protein.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one. This application is a continuation of US Patent Application 09/654,617, which was filed on 5 September 2000, and subsequently abandoned. The parent application was never published. In effect, the subject matter of Application No. US 2007/67865 A1 pended in secret for more than 6.5 years before it was published.

Patent Publication No. 20070083945

Length of pendency before publication: approximately 7 years 1 Month

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information

20070083945

  • Earliest priority - 10 Mar 2000
  • Filed - 2 Aug 2006
  • Publication - 12 Apr 07

Title - Nucleic acid molecules and other molecules associated with plants

Claim 1

A substantially purified nucleic acid molecule, said nucleic acid molecule capable of specifically hybridizing to a second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 304905 or complement or fragment thereof.

Claim 8

A substantially purified nucleic acid molecule comprising a nucleic acid molecule or fragment thereof having a pair of defined ends, wherein said pair of defined ends are selected from the defined ends in Table A.

Claim 11

A substantially purified protein or fragment thereof encoded by a first nucleic acid molecule which specifically hybridizes to a second nucleic acid molecule, said second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO:1 through SEQ ID NO:304905 or complements thereof.

Claim 12

A transformed plant having a nucleic acid molecule which comprises: (A) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; which is linked to (B) a structural nucleic acid molecule, wherein said structural nucleic acid molecule is selected from the group consisting of SEQ ID NO:1 through SEQ ID NO:304905 or complements thereof or fragment of either; which is linked to (C) a 3′ non-translated sequence that functions in a plant cell to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of said mRNA molecule.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Chapter 7: Bulk Sequence Applications

rice19-ricesky

Our analysis has uncovered a number of bulk sequence applications. For the purposes of this landscape, we are defining bulk sequence applications as those that claim more than 1,000 sequences. Bulk sequence applications do not generally result in bulk sequence patents; usually only a few sequences remain by the time the patent issues. While the application is pending however, it requires monitoring communications at the USPTO (via PAIR) to discern which sequences will be claimed by an issued patent. While bulk sequence applications and the possibility of provisional patent rights emanating from publication may create fear, uncertainty, and doubt for researchers working in the area, tools provided by Patent Lens can be used to assist the monitoring process.

U.S. Bulk Sequence Applications that Recite Rice Sequences in Claims

A number of patent applications have been filed in the U.S. that claim more than 1,000 nucleotide and/or amino acid sequences. These applications are referred to as "bulk sequence applications".

Below we have listed 12 bulk sequence applications. In all of the currently pending (i.e., not abandoned) applications below where the applicant has submitted a response to an office action, there is only a single nucleotide SEQ ID NO claimed per application.

It is likely that the large proportion of the rice genome that is claimed in patent applications may be attributable to these bulk sequence applications.

Application No.

Assignee

Title

No. of Sequences Recited in Published Claim Set

Status

Status Date

20040031072

Monsanto

Soy nucleic acid molecules and other molecules associated with transcription plants and uses thereof for plant improvement

285,684

Response to Non-Final Office Action Entered and Forwarded to Examiner

13-Mar-08

20040123343

Monsanto

Rice nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

204,966

Examiner's Answer to Appeal Brief Mailed

25-Mar-08

20040214272

Monsanto

Nucleic acid molecules and other molecules associated with plants

369,326

Response to Non-Final Office Action Entered and Forwarded to Examiner

13-Mar-08

20040216190

Monsanto

Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

11,088

Abandoned -- Failure to Respond to an Office Action

13-Nov-07

20060195932

Monsanto

Nucleic acid molecules and other molecules associated with the carbon assimilation pathway

7,341

Notice of Appeal Filed

13-Mar-08

20060236419

Monsanto

Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

7,098

Non Final Action Mailed

25-Mar-08

20070016974

Monsanto

Nucleic acid molecules and other molecules associated with plants

43,701

Abandoned -- Failure to Respond to an Office Action

29-Feb-08

20070020621

Monsanto

Genomic plant sequences and uses thereof

57,467

Publications -- Issue Fee Payment Verified

13-Mar-08

20070039076

Monsanto

Plant genome sequence and uses thereof

69,652

Non Final Action Mailed

13-Mar-08

20070067865

Monsanto

Annotated plant genes

463,173

Response to Non-Final Office Action Entered and Forwarded to Examiner

13-Mar-08

20040016025

Syngenta

Rice promoters for regulation of plant expression

2,731

Abandoned -- Failure to Respond to an Office Action

12-Dec-05

20070089180

Syngenta

Transcription factors of cereals

1,394

Docketed New Case - Ready for Examination

13-Mar-08

The Good News About Bulk Sequence Applications

The good news about bulk sequence applications is that every sequence that is disclosed in the application becomes part of the public domain when the bulk sequence application publishes. This means that all of the sequences, whether they are claimed or simply disclosed in the specification, can no longer be patented by anyone else in that particular jurisdiction, unless they are already the subject of an earlier filed patent.

Another factor to consider is that for each bulk sequence application, the applicant may file a number of divisional applications in order to claim additional nucleotide sequences. Although, this strategy is likely to be cost prohibitive to most patent seekers. Therefore, a patent family stemming from a bulk sequence application is most likely to result in only a handful of claimed nucleotide sequences.

Chapter 8: Rice Genome Patents in Non-U.S. Jurisdictions

rice4-ricemap

In our analysis, we have chosen to primarily focus on the U.S. patent patents and applications. We recognize that a complete picture of rice genome patenting will require analysis of the patents in key rice-growing jurisdictions outside of the U.S., however, access to patent data in many countries is difficult to obtain. In fact, most patent jurisdictions in developing countries, even those with very substantial innovation and commercialization capability, do not have readily searchable patents, not to mention sequences claimed in patents. For example, the full text of Indian patents cannot be searched either domestically or internationally.

It is one of CAMBIA's long term goals to provide access to patent data from some of the key jurisdictions, and our patent landscapes will continue to evolve as new information becomes available.

In this chapter, we provide information about the availability of patent data in key rice-growing jurisdictions, as well as a table containing all of the U.S. rice patents and patent applications that have counterparts in China.

Status of Patent Searching in the Top Ten Rice-Growing Jurisdictions

Jurisdictional issues play a huge role in determining the freedom to operate in rice innovation. However, the rules regarding gene patenting and the availability of patent data in key rice-growing countries is variable.

China

The front page information (title, inventors, applicants, abstract, priority documents, etc) of Chinese patent documents is searchable in both Chinese and English. Full-text searching of entire patent documents is not currently available, however it is possible to download a copy of the full Chinese patent documents in PDF. China allows patenting of nucleotide and amino acid sequences, but effectively limits bulk sequence applications by limiting each application to one "function". Also, China does not allow patenting of transgenic plants or animals. More information...

India

India allows patenting of nucleotide and amino acid sequences, but does not allow patenting of transgenic plants or animals. It is not possible at this time to search the full text of Indian patent applications, front page information is available from several sources. More information...

Indonesia

Indonesian patent document front page information is full-text searchable, in Indonesian. While it is not possible to conduct a full-text search of entire Indonesian patent documents, it is possible to download a PDF of the documents from the Indonesian IP office website. More information...

Vietnam

It is possible to search the front page information of Vietnamese patent documents, in Vietnamese. English titles of a small subset of Vietnamese patent documents are also searchable. It is not currently possible to obtain full Vietnamese patent documents online. More information...

Thailand

Thai patent document front page information is searchable. It is not currently possible to conduct a full-text search on the full patent documents. More information...

Brazil

Front page information of Brazilian patent documents is searchable in Portuguese. While it is not currently possible to search the full-text of Brazilian patent documents, it is possible to obtain PDF copies from the EPO. More information...

Japan

It is possible to search Japan patent document front page information, in English. The EPO provides PDF copies of the patent documents. NEF-NET (Japan Invention Information Corp.) is a fee-based online Japanese search engine that provides full-text search options for published patent and utility model documents (applications from 1993, registered patents and utility models from 1994). Searches are in Japanese only. More information...

Rice Patent Filings in China

The table below shows granted U.S. patents claiming rice sequences that have corresponding filings in China.

The information related to the filings in China of the following granted U.S. patents was obtained from INPADOC. If a related PCT application was filed, the PCT application number was also used to search for its possible Chinese filing. The legal status of each Chinese patent or patent application was acquired by searching SIPO's patent leagal status database (in Chinese).

Patent No.

Assignee

Title

Name of Gene/Protein Claimed

Filing in China

Status in China

Status  checked

7132587

Agency of Industrial Science and Technology

Non-autonomous transposon gene of rice, transformed plant and method of use

Method to detect transposon

CN02822088 CN200610095860 CN200610095865

Granted
Pending
Pending

25/9/07
31/1/08
31/1/08

6933111

Bayer BioScience N.V.

Glufosinate tolerant rice

Glufosinate tolerant rice (PCR kit)

CN99814584

Pending

31/1/08

7119192

Bio-oriented Technology Research Advancement Institution

Stress-induced promoter derived from rice

Stress-induced promoter derived from rice

CN03123301 CN200610089957

Granted
Pending

31/1/08
31/1/08

7053268

Danisco A/S

Promoter

Promoters

CN00809092

Granted

26/9/07

6479731

E.I. du Pont de Nemours and Company

Pi-ta gene conferring fungal disease resistance to plants

AVR-Pita gene

CN99811644

Withdrawn

26/9/07

6664445

E.I. du Pont de Nemours and Company

Plant amino acid biosynthetic enzymes

S-adenosyl methionine synthetase

CN98805878

Withdrawn

26/9/07

7008664

E.I. du Pont de Nemours and Company

Method for improving the carcass quality of an animal

delta-9 stearoyl ACP desaturase

CN99807225

Withdrawn

26/9/07

6423838

Hitachi, Ltd.

Gene for proline transporter in rice

proline transporter

CN00124140

Withdrawn

26/9/07

6307125

Hoechst Schering AgrEvo, GmbH

Nucleic acid molecules encoding enzymes from wheat which are involved in starch synthesis

Wheat starch synthase

CN97195004
CN200610074327

Granted Pending

26/9/07 31/1/08

6734339

Hoechst Schering AgrEvo, GmbH

Nucleic acid molecules encoding enzymes from wheat which are involved in starch synthesis

starch synthesis enzymes

CN97195004 CN200610074327

Granted
Pending

26/9/07
31/1/08

7034139

Incorporated Administrative Agency, National Agriculture and Bio-Oriented Research Organization

Rice gene for controlling tolerance to salt stress

gene for controlling tolerance to salt stress

CN02802604

Withdrawn

26/9/07

7138277

Incorporated Administrative Agency, National Agriculture and Bio-Oriented Research Organization

Genes encoding plant transcription factors

transcription factor OsDREB1A

CN02154281

Pending

31/1/08

6462185

Japan Tobacco Inc.

Floral organ-specific gene and its promoter sequence

Floral organ-specific gene promoter sequence

CN97194151

Granted

26/9/07

6660851

Japan Tobacco Inc.

Floral organ-specific gene and its promoter sequence

enhancer

CN00802276

Granted

26/9/07

6998477

Japan Tobacco Inc.

Nucleic acid fragment, recombinant vector containing the same and method of promoting the expression of structural genes by using the same

promoters

CN00802035

Granted

26/9/07

7109321

Japan Tobacco Inc.

DNA fragment directing gene expression predominant in flower organ

flower organ promoter

CN99800621

Withdrawn

26/9/07

7186821

Japan Tobacco Inc., Syngenta Limited

Rice sucrose transporter gene promoter

Rice sucrose transporter gene promoter

CN02805219

Granted

26/9/07

6995302

Kumiai Chemical Industry Co., Ltd. (Tokyo, JP), Kojima (Mineo, Nagano)

Gene regulating plant branching, vector containing the gene, microorganism transformed by the vector, and method for regulating plant branching by using the microorganism

rice MADS box gene

CN00813062

Pending

31/1/08

6506962

Monsanto Technology LLC

Acquired resistance genes in plants

Acquired resistance genes in plants

CN00807358

Withdrawn

26/9/07

7157281

Monsanto Technology LLC

High lysine maize compositions and event LY038 maize plants

High lysine maize compositions

CN200480036889

Pending

31/1/08

7214851

National Institute of Agrobiological Science, Bio-oriented Technology Research Advancement Institution

Bzip type transcription factors regulating the expression of rice storage protein

Bzip type transcription factors

CN01804789

Withdrawn

26/9/07

6576815

National Institute of Agrobiological Sciences

Promoter sequence expressed in anthers and pollens

Promoter sequence expressed in anthers and pollens

CN99808484

Withdrawn

26/9/07

6861574

National Institute of Agrobiological Sciences

Sodium/proton antiporter gene

Sodium/proton antiporter gene

CN99816068

Granted

26/9/07

7135625

National Institute of Agrobiological Sciences

Gene concerning brassinosteroid-sensitivity of plants and utilization thereof

Gene concerning brassinosteroid-sensitivity

CN01809828

Pending

31/1/08

7176347

National Institute of Agrobiological Sciences

Vegetative growth specific promoter and transgenic plant obtained with the same

Vegetative growth specific promoter (OsGA3ox2 gene promoter)

CN01823070

Withdrawn

26/9/07

6501007

National Institute Of Agrobiological Sciences (Ibaraki, JP)

Method of dwarfing plants

Antisense

CN99110944

Withdrawn

26/9/07

7049490

National Institute of Agrobiological Sciences, Riken

Gibberellin 3β-hydroxylase genes of rice and uses thereof

Gibberellin 3beta-hydroxylase genes

CN00818906

Withdrawn

26/9/07

6762348

Pioneer Hi-Bred International, Inc.

Genetic control of plant growth and development

Rht polypeptide obtained from Triticum aestivum

CN98809929

Granted

26/9/07

6521816

PlantTec Biotechnologie GmbH Forschung und Entwicklung

Nucleic acid molecules from rice and their use for the production of modified starch

starch synthesis enzyme

CN99812674

Pending

31/1/08

6750378

Rhone-Poulenc Agro

Maize H3C4 promoter combined with the first intron of rice actin, chimeric gene comprising it and transformed plant

Maize H3C4 promoter combined with the first intron of rice actin

CN98813783

Granted

26/9/07

7057088

Riken (Saitama, JP), National Institute of Agro-Biological Sciences

Gibberellin 2β-hydroxylase genes of rice and uses thereof

Gibberellin 2beta-hydroxylase genes

CN00818652

Rejected

26/9/07

6274789

Society for Techno-Innovation of Agriculture, Forestry and Fisheries

Rice gene resistant to blast disease

PiB protein

CN99111004

Withdrawn

26/9/07

6867293

Syngenta Limited

Polynucleotide constructs having at least one transcriptional enhancer and encoding a modified rice EPSPS enzyme

Transcriptional enhancers and EPSPS genes

CN00809796

Withdrawn

26/9/07

7094951

The Ohio State University

Cloning and characterization of the broad-spectrum resistance gene Pi2

broad-spectrum resistance gene Pi2

CN03824033

Pending

31/1/08

5977434

The Regents of the University of California

Procedures and materials for conferring disease resistance in plants

RRK polynucleotide sequence

CN96191493

Granted but lapsed

26/9/07

6781044

Ventria Bioscience

Plant selectable marker and plant transformation method

glucanase gene (Gns9) promoter

CN99807782

Granted

26/9/07

Chapter 9: Key Players in Rice Genome Patenting

rice10-pile

Our analysis has identified several key players in the area of rice genome patenting. DuPont, which includes Pioneer Hi-Bred, has the largest number of granted patents that claim rice sequences, or sequences highly similar to rice. For the applications, Monsanto stands out because of the significant number of bulk sequence applications that they have filed.

This chapter provides some background information about the key players and discusses some of their gene patenting strategies.

Genome Coverage in Applications and Patents by For-Profit Companies

A number of companies have claimed rice genes sequences in U.S. patent applications and issued patents. Here we present graphs showing the percentage of each chromosome that is claimed in patent applications and patents assigned to seven different companies.

For the plots below, the percent coverage for each chromosome is shown. For example, if the entire sequence of a particular rice chromosome were claimed in patents or applications, the plot would read 100% for that chromosome. The Y axes show the percent coverage, and the X-axes show the chromosome of the rice genome. Note: the scales of the Y axes have been adjusted to reflect the data for each company.

Monsanto (includes Calgene, Delta Pine, Seminis, Agracetus, Dekalb, Emergent, Produsem, Mahendra, Stoneville, and Pharmacia)

Applications

Granted Patents

Syngenta (includes Torrey Mesa, Zeneca, Ciba Geigy, Novartis, Advanta, Garst, Agripro, and Danisco)

Applications

Granted Patents

DuPont (includes Pioneer)

Applications

Granted Patents

BASF (includes American Cyanamid)

Applications

Bayer (includes Aventis, Rhone-Poulenc, Plant Genetic Systems, Hoechst, Proagro, Agrevo, Biogentic, Planttec, Sementes, Nunza, Agrinomics, and Rorer)

Applications

Granted Patents

Key Player: DuPont

E. I. du Pont de Nemours and Company (DuPont) has the highest number of granted US patents, currently 62, that claim rice sequences.

DuPont is a well known as a chemical company that was founded in 1802. Over the years, it has undergone restructuring such that its business now includes coatings, crop protection chemicals, genetically modified seeds, electronic materials, polymers, resins, and safety and security materials. With the full acquisition of Pioneer Hi-Bred International in 1999 (acquiring 20% in 1997, and the remaining 80% in 1999), the company has shown that it is focusing more and more on agricultural biotechnology.

In terms of their patent strategy, DuPont focuses mainly on individual genes coding for key enzymes involved in metabolic pathways. 

Key Player: Monsanto

Monsanto, which was founded in St. Louis Missouri in 1901, is an agricultural company that is well-known in the area of plant gene patenting. Monsanto is a key member of an expansive web of business relationships that are shown in a chart on the next page.

To date, Monsanto (inculding Calgene and Dekalb Genetics Corp.) have only seven granted patents on rice sequences. However, Monsanto is a key player in this landscape because of the large number of "bulk sequence applications" that they have filed. To date, Monsanto has 10 pending applications that each recited more than 7,000 sequences in the claims as originally filed. One of these, U.S. Application No. 20040214272, recites 369,326 sequences. The plot below shows the percent coverage of the rice genome by Monsanto patent applications:

Monsanto was the first private company to announce that it completed a working draft of genetic map of rice. According to a 2002 Monsanto Press Release:

‘"Monsanto shared its draft rice genome data with the global scientific community because we understand the importance of rice as both a major global food source and as a model crop for agriculture and plant research," said Robb Fraley, Ph.D., Chief Technology Officer of Monsanto.  In addition to sharing its data with IRGSP, Monsanto established a rice genome database at www.rice-research.org, which makes the data available at no charge to publicly funded researchers. Since the database was established, more than 760 researchers, many located in developing countries, have obtained access to Monsanto's rice genome sequence data."

The following excerpt was reported in Nature Biotechnology (Nature Biotechnology  18, 484, 2000). No mention was made of the patent applications. Patent applications are generally not published for 18 months after their initial filing, but due to non-publication requests by Monsanto, some of these were not published for many years, as late as 2007 (see the page on Submarine Applications).

“On April 4, Monsanto (St. Louis, MO) announced it has completed a "working draft" genetic map of the rice genome and that it will share the information freely with academic researchers. Although most praise the decision, the first time a large multinational corporation has agreed to disclose so much information about an important crop to the academic world, some question the availability of the data and the eventual cost of using it. The map, which was compiled under contract by the laboratory of Leroy Hood of the University of Washington (Seattle), covers locations on all 12 rice chromosomes of the Oryza sativa (japonica variety) rice genome...”

While Monsanto made the sequencing data available to the public, they simultaneously pursued patent coverage for the sequences. Research results published after the filing of the patent applications by anyone working with these sequences would not invalidate the patent applications, but could actually strengthen Monsanto's claims in continuation patent applications. This is a testament to the fact that information that is publicly available, even at no charge or with contribution from public funds, is not necessarily available for public use.

Press Releases

Monsanto Relationships

Monsanto Business Relationships Verdana (image)
Click to enlarge

Key Player: National Institute of Agrobiological Sciences

The National Institute of Agrobiological Sciences (NIAS) is a Japanese government research institute located in Ibaraki, Japan. Their primary focus is on creating industries that increase agricultural productivity and demands for agricultural products. NIAS is the assignee of 19 granted patents that recite rice sequences in claims; second only to DuPont in number of patents. At the time that this landscape was completed, NIAS is also the assignee on eight pending patent applications that recite rice sequences in the claims.

NIAS also played a role in the sequencing of the rice genome.

Key Player: Syngenta

While Syngenta (which includes Danisco A/S, Novaritis Corp. and Zeneca Limited) only has eight granted patents that recite rice sequences in their claims, we consider them to be a key player because of their involvement in the sequencing of the rice genome.

Syngenta has formed a number of business relationships with a wide array of biotech and agricultural companies as shown in the diagram on the next page.

Syngenta Business Relationships

Syngenta Business Relationships_spelling corrected

Chapter 10: Conclusions and Implications of Rice Genome Patenting

rice15-sunset

Our analysis has demonstrated that only 0.26% of the rice genome is recited in the claims of granted U.S. patents. This fraction is based on the actual, non-redundant coverage of the genome by the sequences that we identified . In determining this percentage, we included all sequences recited in claims, regardless of whether they encoded proteins. In contrast, the analysis by Jensen and Murray found that around 20% of the coding sequences of the human genome were claimed in granted U.S. patents (Science 310:239-240). Because the difference between the rice and human might be accounted by use of different metrics, we recalculated the fraction of rice genome in claims according to the Jensen and Murray formula.  For this calculation, the number of coding sequences in claims (213) was divided by the number of rice coding sequences in the genome (37,544 according to Nature, 2005, 436:793-800).  Even using this formula, the percent coverage is roughly 0.57%, which is still substantially smaller than found for human. 

The patent applications tell a different story: roughly 74% of the rice genome is recited in the claims of U.S. patent applications. The high fraction is at least partially due to bulk sequence applications, which claim hundreds or thousands of nucleotide sequences. It is unlikely however, that many of these sequences will actually be claimed in a granted patent.  Under current U.S. patent law, a granted patent rarely issues with more than one sequence. While it is possible that continuations of these applications will be filed, but they will likely only issue with one sequence as well. Furthermore, changes proposed to U.S. patent law include a limit on the number of continuations that may be filed from a given patent application. Therefore, it is unlikely that the percent of the rice genome that is encompassed by patent claims in the U.S. will ever approach the 20% figure published by Jensen and Murray for coding sequences. Thus, the majority of the rice genome is in the public domain and won't be patentable as compositions of matter in the future.

These conclusions, however, are confined to the United States.  As such, the need remains to plot a rice landscape in other jurisdictions; particularly in countries that are the primary producers or consumers of rice.  Difficulties in determining landscapes for these countries include, the dearth of patent information in key jurisdictions and unknown case law. As Patent Lens adds new patent data, transparency will be increased - to everyone's benefit. 

Appendix

rice5-farmer

The appendix includes patent law tutorials and reference material.

What You Need to Know About Patents

Below are some important patent law concepts that are important for understanding the Rice Genome Landscape:

  1. The claims define the scope of protection of a patent.

  2. A patent application is not the same as a patent.

  3. There is no such thing as an international patent.

  4. The entity that has the patent rights may not be the owner listed on the patent document.

  5. Individual patents have a limited lifetime.

What are Claims?

The claims are the most important part of a patent. The goal of the claims is to particularly point out and distinctly claim the subject matter which the applicant regards as his or her invention. There must be at least one claim in a patent, and the reasoning is that possible infringers must be able to understand what is and is not protected based on the claims.

Parts of a Claim

A claim is generally presented in three parts, the preamble, a transitional phrase (or word), and the body.

Preamble

The preamble is an introductory statement that names the invention that is to be claimed. For example, "A method for making a genetically modified plant."

Transitional Phrase

The transitional phrase (or word) specifies whether the claim is limited to only the elements listed, or whether the claim may cover items or processes that have additional elements.  Commonly used transitional phrases include "comprising"and "consisting of". See also Transitional Language in Patent Claims for a more in-depth description of transitional phrases.

Body

The body of a claim lists the elements (also referred to as "limitations") or steps of the named invention.

Claims may be independent or dependent.

Independent Claims

An independent claim defines an operative, complete invention by itself, without referring to, or including limitations of other claims.  The intention of independent claims is to broadly cover all embodiments of the invention without reading on prior art.

Dependent Claims

Dependent claims refer back to and further defines an invention recited in another claim.  In doing so, a dependent claim includes all of the limitations of the claim to which it refers. Dependent claims are often used to define the scope of the elements in an independent claim, and are written to protect specific embodiments of an invention.  Should a court find that the main independent claim was wrongly granted, a dependent claim may still be valid, and is used as a "fallback position". Dependent claims also make it easier for a jury to determine whether infringement as occurred, if the infringing activity is clearly spelled out in a claim rather than just inferred.

Types of Claims

There are a number of different types of claims that are designed for claiming different types of inventions, including:

Composition of Matter Claims

Composition of matter claims list the constituents of a new material, as well as the amount of each constituent, if applicable. Nucleic acids and amino acid sequences are often claimed as compositions of matter.

Apparatus  or Device Claims

Apparatus, or device claims are claims to an apparatus or device.

Method (or Process) Claims

Method or process claims describe a novel method or process used to achieve a particular goal.

Product-By-Process Claims

In a product-by-process claims, a product is defined by the method used to manufacture it.

Markush-Type Claims

Markush-type claims have a list of functionally-equivalent elements. Components not on the list are excluded from the claim.

Importation and Patent Infringement

A patent provides a patent owner with the right to exclude others from utilizing the invention claimed in the patent. In the United States, infringement is governed by Statute 35 U.S.C. 271. it is widely understood that making, using, or selling an invention claimed in a patent without permission of the patent owner is considered to be patent infringement. However, it is also true that importation of an invention claimed in a U.S. patent, even if it is made in a country where there is no patent coverage, qualifies as infringement. In addition, products that are made in another country by a process that is patented in the U.S., may infringe on U.S. patents when the products are imported into the U.S.

Excerpt from 35 U.S.C. 271(f):

"Whoever without authority imports into the United States or offers to sell, sells, or uses within the United States a product which is made by a process patented in the United States shall be liable as an infringer, if the importation, offer to sell, sale, or use of the product occurs during the term of such process patent..."

Similar laws are in force in other countries which belong to the World Trade Organization and thus have ratified the TRIPs Agreement (Trade-Related Aspects of Intellectual Property). 

How does this apply to rice genome patents?

The importation feature of patent infringement laws has the effect of increasing the "reach" of U.S. patents and patent applications.  Although sequences, genes, transgenic organisms, and products such as fruits, seeds, and fibers derived from them are more difficult to patent in other countries, the fact that they can be patented in the U.S. means that investors might be discouraged from investing in non-U.S. countries to create products based on or embodying rice sequences in patents, because they might not be able to enter the large and lucrative U.S. market.

Continuation Applications and Their Affect on the Public Availability of Material Disclosed (But Not Claimed) in Patents

It is generally assumed that inventions claimed in a patent application are available to the public if a patent application is abandoned, after the patent expires, or if a patent lapses due to the applicant's failure to pay maintenance fees. In addition, it is assumed that subject matter disclosed but not claimed in a patent application has been "dedicated to the public" and is therefore available for public use.

In some circumstances however, an expired (or abandoned) patent does not mean that the material claimed in the patent is available for public use. Similarly, when a patent application claims only a subset of the subject matter disclosed in the specification, it does not necessarily mean that the unclaimed subject matter is available for public use.

Why?

A continuing patent application, (also called a “continuation” or “continuation application”) may have been filed that has overlapping claims with the expired or lapsed patent, or that claims subject matter left unclaimed in the parent. (See What is a continuation application? for a description of the different types of continuations.) Alternatively, there may be a pending foreign-filed application that claims the same material as the expired or abandoned patent.

Due to the widespread use of continuation applications in the U.S. and to a lesser extent in other countries, it is important to determine if there are any pending continuation applications before assuming that subject matter claimed in an expired or abandoned patent is available for public use. If the application has been published in the U.S., you can check to see if there are any continuation applications by visiting PAIR at the USPTO.  See also How to View Continuity Data in PAIR.

What is a bulk sequence application?

Bulk sequence applications are patent applications that disclose an inordinately large number of nucleotide or amino acid sequences--many more sequences than can be properly examined. In some cases, large numbers of sequences are included in the application to provide enablement for the invention, but are not actually claimed. However, there has been a recent trend towards filing applications that disclose large groups of nucleic acid sequences from genome sequencing initiatives and sequencing of EST libraries. These applications often disclose and claim (at least initially) large numbers of sequences; in some cases more than 100,000!

How does the USPTO define bulk sequence applications?

The USPTO defines bulk sequence applications only in terms of the sequence listing length, not on the basis of the number of sequences that are claimed. Applications with sequence listings longer than 300 printed pages are termed "lengthy sequence listings". Such sequences are only published in electronic form and are not included with the paper patent publication. Lengthy sequences may be searched at the Publication Site for Issued and Published Sequences (PSIPS). Currently the USPTO publishes about half a dozen such filings every two weeks.

Section 2434 of the MPEP outlines the policy in the U.S. for examination of patent applications claiming large numbers of nucleotide sequences.

Do bulk sequence applications result in bulk sequence patents?

Generally, no. In many jurisdictions, restriction or unity of invention practice limit the number of sequences that are examined in a single application, so the majority of granted patents claim fewer than 20 sequences. In addition, many examiners limit their analysis to sequences that are correlated with an established biological function.

What are some of the reasons that bulk sequence applications are filed?

Patent applicants generally seek to have the broadest possible coverage for their invention. As such, it is often advantageous for an applicant to initially claim a large number of sequences, even though the resulting patent is likely to claim only a handful of sequences. Bulk sequence applications may be used to scare off potential infringers, or used as leverage in licensing negotiations (See Provisional rights associated with pending patent applications), even though the final claim scope may be unknown when the application publishes. These activities can have downstream effects that last longer than the patent term itself. On the positive side, sequences that are disclosed but not claimed in patents as issued are considered to be "dedicated to the public". Therefore, the thousands of sequences that are not claimed in the granted version of the patent are in the public domain, and are precluded from being patented as compositions of matter by anyone else (as long as they are not the subject of another pending application).

Bulk sequence applications can lead to uncertainty as to which sequences are available for public use.

Patents are intended to be a trade of sorts. In exchange for disclosing the details of an invention, the inventor gets a 20 year legal monopoly for his or her invention. An 18 month publication rule has been implemented in most jurisdictions that facilitates this trade by alerting the public about the contents of pending patent applications. Bulk sequence make it difficult for researchers take advantage of the "trade", since they are unable to determine if their work is free of patent claims until after the patent issues.

In addition to creating uncertainty for other researchers in the area of the bulk sequence patent application, such applications put a large amount of information into the public domain, creating a body of prior art that precludes others from patenting the disclosed sequences.

The Basis for Hybridisation Language

DNA is a biological polymer consisting of "simple" repeated subunits, or bases.  It is within the sequence of these bases that genetic information is stored. Although DNA can exist as a single strand in solution, it is generally found within living systems together with its complementary strand (see the figure below).  If we consider a simple representational diagram of a DNA molecule, consisting of a sequence of bases: A, G, C, and T. We can see that some of the bases interact with one another in the figure below.

image3

The bases A,T,G, and C form hydrogen bonds with their respective bases T, A, C and G, in the complementary strand.  These bonds provide a stability to the double strand DNA (dsDNA), under normal circumstances, preventing it from dissociating into single strand DNA (ssDNA).  Significantly, dsDNA can be "melted" to produce ssDNA under certain physical circumstances and can be influenced by many factors such as temperature, salt concentration, inorganic solvents, sequence composition, and (importantly) the degree of sequence similarity or missmatch between ssDNA molecules.

The Concept of Melting Temperature (Tm)

Mathematical relationships between the various physical parameters listed above and the melting point of DNA have been established.  Historically, the point at which 50% of the DNA molecule is ssDNA is referred to as the melting temperature or Tm.

The Tm for a DNA sequence in solution can be estimated via the commonly-used calculation:

Hybridisation Formula

Where     Tm         = melting temperature in oC
               [Na+]     = Molar concentration of sodium ions in
            %[G+C]    = percent of G+C bases in DNA sequence
                 n         = length of DNA sequence in bases
                 P         = temperature correction for % mismatched base pairs (~1oC per 1% mismatch)
                 F         = correction for formamide concentration (= 0.63oC per 1% [formamide])

Note:  A particular DNA sequence will have different Tm values under different conditions. This calculation is sometimes referred to as the effective Tm.

The fact that ssDNA can re-anneal to form dsDNA is used in the process called hybridisation. 

NOTE that the Tm refers to the temperature at which 50% of the DNA is hybridized!

A typical hybridisation experiment consists of a number of steps:

  1. Binding of target ssDNA to a solid support (often a thin nitrocellulose, nylon, or polymer membrane), referred to here as a "blot".
  2. Blocking any remaining free binding sites for DNA on the blot.
  3. Labeling of the "query" ssDNA or probe.
  4. Creation of a hybridisation solution containing the probe at a known concentration of salt, formamide, and other additives.
  5. Incubating the "blot" with the hybridisation solution at a defined temperature (for a specified length of time).
  6. Washing the unhybridised probe off the blot using a specific wash protocol;  the wash conditions are actually more important than the hybridisation conditions for determining what will remain hybridised, but are less often specified in patent applications!
  7. Detecting the bound probe by some means.

If the probe (or query DNA) is similar enough to the target ssDNA (on the blot) then the probe will remain bound to it after the wash step.

"Stringency", which is often use to determine the scope of the claims, refers to the concentrations and temperatures in steps 4-6 above. Strictly speaking, this should refer to the "stringency" of the wash step required remove unbound probe from the target sequences that are covered by the claims. The "query" is often a sequence mentioned in the claims section (as in the example given above).

Although the table below is not legally binding and indeed patent applications may use their own definitions of stringency levels, the typical usage is roughly:

Stringency

[NaCl] (Molar)

Range from Tm (oC)

Description

High

0.0165 - 0.0330

5 to 10oC below Tm

Only highly similar sequences will bind under these conditions (typically >95%)

Medium/Moderate

0.165 - 0.330

20 to 29oC below Tm

Those sequences above and less homologous ones (typically >80%)

Low

0.330 - 0.825

40 to 48oC below Tm

Sequences with lower homology will bind under these conditions (>50%?)

1. Note that the values here are for the purpose of discussion.  Actual values and conditions must be acquired from the patent document specifications.
2. The "Range from Tm" is the temperature of the wash solution required to achieve the level of stringency and is dependent on the factors described above.
3. Values in Column 2 are typical only!
4. Values in column 3 were obtained from US 2006/0057724 A1
5. Values in Column 4 are typical only and sourced from the web.  Refer to patent specifications for your details!
6. Definition of stringency levels may vary between patents (BEWARE). Stringency conditions are usually defined in the patent document!

Sometimes the patent examiner will require the applicant to stipulate the stringency conditions: high/medium/or low stringency, or specifying the [NaCl] and temperature of the wash conditions.  Few bother to give a reference with respect to Tm (a value that can be calculated). It is possible that the conditions defined as stringent in one patent document may not be as stringent as those defined in another!

The Applicant or the Assignee of a Patent May Not Be the Actual Holder of the Patent Rights

The legal owner of a patent is designated as the "Assignee" on United States patents and as the "Applicant" on patents in the rest of the world. However, the rights of a patent holder is like a bundle of sticks, and one of these sticks is legal ownership.

These rights are tradeable. The typical form of trade is a license, in which some or all of the rights may be transferred. For example, the patent owner may license only some of the claims in a patent, all of the claims but only in a particular field of research, all of the rights but only in certain countries, or the right to make and use but not the right to sell. Other types of licenses may also be granted. Unlike the ownership of a patent, which is a matter of public record, licenses can be private. Unless the parties to a license choose to reveal the relationship, it is impossible to know about it. 

The information contained in this page was believed to be correct at the time it was collated. New patents and patent applications, altered status of patents, and case law may have resulted in changes in the landscape. CAMBIA makes no warranty that it is correct or up to date at this time and accepts no liability for any use that might be made of it. Corrections or updates to the information are welcome, please send an email to info@bios.net.