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The Rice Genome
at Ten

Helping to solve the 9 billion people question

World agriculture got a major boost with the completion of the rice genome sequence in December 2004 and subsequent publication in Nature on August 2005. To date, the map-based sequence of the japonica rice cultivar Nipponbare remains as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives. It has also provided great insights in understanding other major cereal crops such as maize, wheat, barley and sorghum that comprised the food source for the entire human race.

On the agricultural front, the rice genome sequence enhances the characterization of many agronomic traits that allows breeders to incorporate highly desirable traits such as high productivity, biotic/abiotic stress resistance etc., and the successful development of cultivars which could be grown in a wide range of environments. It is highly expected that ongoing efforts on a much deeper analysis of the genome including a wide array of rice germplasm throughout the world will provide the platform for propelling the next green revolution.

This website provides an overview of progress in rice genomics since the completion of the genome sequence focusing on what we have learned so far, what we have accomplished so far, and what we have to achieve in the next ten years and beyond, as we embark on helping to solve the 9 billion people question.

Messages

Dr. Takuji Sasaki
Chairman, International Rice Genome Sequencing Project
Professor, Tokyo University of Agriculture
Tokyo, Japan

Ten years ago, the International Rice Genome Sequencing Project (IRGSP) completed the accurate genome sequence of the japonica rice cultivar Nipponbare (Nature 436, 793-800). The initiative to sequence the genome was conceptualized in 1997 at a Rockefeller-sponsored workshop co-chaired by the late Mike Gale (John Innes Center) and Benjamin Burr (now retired from the Brookhaven National Institute) at the 5th International Congress of Plant Molecular Biology in Singapore. This was followed by a working group meeting in Tsukuba, Japan on February 1998, which led to the charting of the road for sequencing the genome. Looking back into the six long years until the completion of the genome sequence in 2004, the collaboration has been a very rewarding experience despite all the accompanying obstacles that included securing enough funding and the unexpected competition with the private sectors which eventually contributed their efforts to the IRGSP. The most important legacy of this collaboration is the strong desire from participating countries to obtain an accurate map-based sequence on the presumption that nothing more than a high-quality sequence is indispensable for improvement of a crop such as rice which feeds more than half of the world population. And true enough, after 10 years, the Nipponbare genome has become not only a reference sequence for other cereal crops but has also served as a platform that promotes ground breaking researches in rice.

After the completion of the sequence, we proceeded immediately into the task to accurately annotate the genome sequence via the Rice Annotation Project (RAP). Using the Nipponbare full-length cDNA sequence data, evidence-based annotation was carried out which facilitated more efficient utilization of the genome sequence in many areas of rice research such as the cloning of genes corresponding targeted phenotypes, comparative analysis of genome architectures among Oryza species and/or Poaceae, identification of location of many new types of transposable elements etc. As researchers around the world started to use the genome sequence information, another major development was the launching of new journal in 2007 specifically for rice research. Appropriately titled “Rice” (http://www.thericejournal.com), the journal covers a wide range of research ranging from genome analysis, functional genomics, breeding and basic rice biology. It soon became an open access journal allowing researchers direct access to the latest research outputs in rice.

It is interesting to note that the strategy adopted by IRGSP was truly solid relying mainly on clone-by-clone strategy using the Sanger method. The last decade also saw the proliferation of next generation sequencing (NGS) technology that enabled the acceleration of sequencing to more than a thousand fold in comparison to the Sanger method. This development is similar to riding a local train and the high-speed bullet train. The Sanger method like the local train allows the travellers to enjoy the scenery and other details associated with their travel. On the other hand, travellers on a bullet train could easily get to their destination but could get only a bird’s eye view of the sceneries they passed through. Nevertheless, recent advances in sequencing technology facilitated the sequencing of many rice germplasm including wild rice species as part of the Oryza Map Alignment Project (OMAP). It has also paved the way for the ‘3000 Rice Genomes Project’ using rice accessions from 89 countries. With the reference Nipponbare sequence, the sequence of thousands and thousands of rice germplasm around the world will benefit future generations of humanity.

The next challenge is how rice researchers can maximize the huge amount of data generated by advances in sequencing technology. These data must be incorporated to various inter-related information of rice such as genetics, physiology, evolution, breeding and cultivation as well as trade and economy. The next challenge is how the different countries around the world could design viable programs for rice genomics to contribute in improving rice production in their respective regions. We are facing a new era in rice research targeting the 9 billion people question and all efforts should focus on how we can pool our resources in securing food security. A decade from now, where we do see the rice research community in terms of goals and targets? The task ahead is far more gigantic. But as we reflect on the next decade of rice genomics we can savor the bountiful harvest, the tools, the networks, and the know-how that we have gained in the last ten years, let us welcome the next challenge! Here we go!


Dr. Robert Zeigler
Director General
International Rice Research Institute

At the 12th International Rice Functional Genomics Consortium meeting, it is fitting to reflect on an important milestone in the history of Plant Biology. This year, we celebrate the 10th anniversary of the International Rice Genome Sequencing Project’s completion of the world’s first rice sequence. The release of a high quality, map-based Nipponbare genome sequence created the “gold standard” that has anchored most subsequent rice sequencing and genomics work.

Several re-sequencing projects have been launched that depend upon this reference sequence to understand the function of many important rice genes, such as how the plant adapts to the very wide range of environments in which it grows. The most exciting among these initiatives, in my biased view, is the release of 3,000 genome sequences into the public domain in May 2014, by the joint efforts of the Chinese Academy of Agricultural Sciences, the Beijing Genomics Institute, and the International Rice Research Institute.

It is hard to imagine that only 10 years ago, the sequencing of one rice genome was the stuff of international headlines and the result of many millions of dollars of investment. Today, it feels almost routine to announce the sequencing of 3,000 rice genomes.

Access to 3,000 genomes of rice sequence data will tremendously accelerate the ability of breeding programs to help overcome key hurdles that mankind faces today and in future. This collaborative project adds an immense amount of knowledge to rice genetics, and enables detailed analysis by the global research community to ultimately benefit the poorest farmers who grow rice under the most difficult conditions.

The accelerating speed of scientific advancement and the understanding that this brings is cause for great optimism that the world can solve the many serious problems related to food and nutrition security, in the context of a changing climate. We now have the means to sytematically access the incredible array of genetic diversity available in the world’s great rice gene banks. Rice scientists now have within their grasp the ability to develop rice varieties adapted to a range of abiotic stresses previuosly thought to be intractable. Pests and pathogens that defied reliable control via inherent plant resistance can now be approached using a much richer and more sophisticated genetic arsenal. And, the potential is not limited to the diversity offered by O. sativa. Wild releatives in the broader Oryza genus may now be used almost routinely in breeding programs.

I congratulate all who were involved in this pioneering effort and welcome the next generation of rice scientists who will use this knowledge to move us forward.


Dr. Gurdev S. Khush
Adjunct Professor
University of California
Davis, California, USA

Completion of rice genome sequence 10 years ago was the landmark in the history of crop genetics and breeding. It spurred a bustle of interest in sequencing the genomes of many other crop plants. However, map based sequence of rice remains as the only monocot genome that has been sequenced to a high quality level. It was the excellent example of international collaboration as well as public and private collaboration. Availability of rice genome sequence has added many innovations to plant breeder’s toolbox. It has;

  • Helped enhance the understanding of diversity of rice germplasm.
  • Facilitated cloning of genes corresponding to rice phenotypes.
  • Helped identify markers related to the genes of agronomic importance for molecular marker assisted selection (MAS).
  • Helped identify new types of transposable elements.
  • Allowed comparative analysis of genome architecture of Oryza species.
  • Provided insights into the understanding of genomes of other major cereals such as maize, wheat and barley that along with rice provide 50% of the calories consumed by the world population.
  • Allowed the sequencing of numerous other rice varieties using Nipponbare sequence as the reference.

World’s population is expected to increase to more than 9 billion people by 2050. Most of this increase will occur in developing countries of Asia and Africa. It is estimated that we will have to produce 50% more rice by that year. Moreover, this increase must be achieved through sustainable and environmentally friendly practices. This challenge can be met through producing high yielding and nutritious rice varieties. Present yield potential of rice is about 11 tons per hectare. This potential must be raised to about 13 tons. Moreover, average world rice yield is 4.5 tons/hectare. Thus there is a wide gap between potential and actual yields. This yield gap must be narrowed. By raising the average yield to 6 tons per hectare, more rice can be produced from existing land area planted to rice. For this purpose, we need rice varieties with durable resistance to diseases, insects and tolerance to abiotic stresses such as drought, submergence tolerance, salinity and other adverse growing conditions. Rice scientists now have plethora of new genomic tools that were not available to meet such challenges during the first green revolution. Thus, advances in rice genomics will benefit humanity by helping produce more and nutritious food.

9B People Question

The world’s population is expected to grow more than 9 billion in around 2050. The bulk of this population will be concentrated in Asia and Africa where rice is the major staple food. How can farmers grow enough food to feed this population in a more sustainable and environmentally friendly way? Research is now underway to create the next generation of green revolution crops - the so called “green super crops” where “super” means a doubling or tripling of yields, and “green” means a reduction in the use of water, fertilizer, and pesticides etc. The 9 billion people question (9BPQ) is one of the world’s most pressing issues of our time. Our society must realistically solve this question within the next 25 years if we are to be able to supply farmers with the seeds required to feed the future. The challenge now is to explore the many facets of research in genomics and breeding to develop a sustainable strategy and solution to help solve the 9BPQ.

How to solve 9 billion people question

Gurdev S. Khush
University of California
Davis, CA 95616
USA

According to various estimates, we will have to produce 50% more food than the present level by 2050 for the following reasons:

  1. There will be two billion more mouths to feed.
  2. Living standards are improving all over the world, particularly in the developing countries resulting in demand for high value foods such as milk, meat and eggs, indirectly increasing demand for food grains as livestock feed.
  3. At present, one billion people go to bed hungry every night. They are so poor that they cannot purchase adequate amounts of food. Once poverty alleviation programs succeed, their purchasing power will increase and so will the demand for food.

The increased food demand has to be met from less land, less chemicals, less water and from less labor under hazards of climate change. Two main strategies to meet this challenge are:

  1. Increasing the yield potential of crops
    Conventional breeding methods to increase crop productivity include ideotype breeding, hybrid breeding and wide hybridization. Genetic approaches include molecular markers and genetic engineering. Available genomic sequences have facilitated the identification and cloning of genes and QTL for yield traits. For example, rice yield is determined by source and sink size. Three sink size components are number of panicles per unit area, number of spikelets per panicle and grain weight. Genomic approaches have allowed the identification and cloning of genes for these sink traits. These are FC1 and htd1 for tillering, Gn1a and OsSPL14 for panicle architecture, and GS3, GW2 and tgw6 for grain weight. Development, identification and validation of functional SNP markers for target genes will facilitate pyramiding of these genes into elite germplasm through molecular marker aided selection. Information on source size is available but measurements of large segregating populations are still problematic. Recombinant technology for introduction of transgenic traits for yield enhancement is being tried. Ongoing project on enhancement of photosynthesis in rice is a good example.
  2. Closing the yield gap
    Present yield potential of rice is 10-11 tons per hectare. However world average yield is 4.5 tons per hectare. By raising the average yield to 5-6 tons, more rice can be produced. For this purpose, rice varieties with more durable resistance to diseases and insects and abiotic stresses are being developed. Various genomic and genetic engineering approaches are being applied for this purpose.

Genome Overview

The sequencing was accomplished by a consortium of publicly funded laboratories from10 countries and regions, which comprise the International Rice Genome Sequencing Project (IRGSP). Japan through the Rice Genome Research Program (RGP), a joint collaboration of the National Institute of Agrobiological Sciences (NIAS) and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), was in-charge of sequencing chromosomes 1, 2, 6, 7, 8 and 9, which correspond to almost half of the genome. The US groups, which comprise of the ACWW Consortium representing the University of Arizona, Cold Spring Harbor Laboratory, Washington University and the University of Wisconsin-Madison, The Institute for Genome Research (TIGR) and Plant Genome Center at Rutgers (PGIR), were in-charge of sequencing chromosomes 3, 10 and 11. China through the National Center for Gene Research of the Chinese Academy of Sciences was in-charge of chromosome 4. Taiwan is in-charge of chromosome 5 through the Academia Sinica Plant Genome Center. France through Genoscope was in-charge of chromosome 12 and a duplicated region in chromosome 11. Other participating groups include the Korea Rice Genome Research Program (KRGRP), the Indian Initiative for Rice Genome Sequencing (IIRGS), the National Center for Genetic Engineering and Biotechnology (BIOTEC) in Thailand, the Brazilian Rice Genome Initiative (BRIGI) and the John Innes Center in UK. These groups were involved in sequencing specific regions in chromosomes 1, 2, 9 and 11. Originally planned as a 10-year project, the sequence was completed in six years based on the principles of sharing materials, data, and technology. The contribution of two private companies namely, Monsanto and Syngenta also facilitated the early completion of the sequence.

The rice genome assembly is now referred to as Os-Nipponbare-Reference-IRGSP-1.0 after integration of the RAP-DB/IRGSP pseudomolecules with the MSU Rice Genome Annotation Project pseudomolecules. The original Nipponbare genome assembly was revised using the optical map of rice to validate the minimal tiling path and sequence data obtained by re-sequencing two Nipponbare lines using the Illumina Genome Analyzer II/IIx and Roche 454 platforms. The gene loci, gene models and other features of the genome in RAP and MSU databases are now based on the same genome assembly. A paper describing the unified pseudomolecules has been published in Rice journal.

Rice genome-enabled insights into plant biology and agriculture

Jan E. Leach
Colorado State University
Fort Collins, CO 80537-1177
USA

Meeting the near-future global demands for production of food, feed and fiber is a major challenge for agricultural scientists. At its inception, the rice genome sequencing effort was justified based on the promise that a high quality genome sequence would help to meet these needs by accelerating not only rice crop improvement, but also the improvement of other cereal crops. Has the rice genome sequence lived up to these promises? Using rice genome sequence-enabled approaches, such as sequence-based mapping, functional genomics etc., many genes relevant to agriculture have been cloned, and their functions in traits such as flowering time, biotic and abiotic stresses, and plant architecture have been validated. Markers for these genes are being used to introduce corresponding useful traits into rice. Discovery of sequence variation in diverse rice by comparison of draft sequences to the high-quality genome sequence has provided insights into rice evolution and adaptation. Beyond rice, comparative genomics approaches, have facilitated gene discovery and improvement of other cereal crops with larger, more complex genomes, such as wheat and barley. These and other examples demonstrate the value of the high-quality rice genome sequence in advancing agricultural productivity.

A Decade of Rice Genomics

map-base m-usa m-india m-korea m-brazil m-taiwan m-japan m-france m-china m-thailand m-uk

Contribution of the participating countries/region in the International Rice Genome Sequencing Project (IRGSP) to the genome sequencing effort. Click the flag for an overview of progress in rice genomics in each country.

Rice 2020 and Beyond

Rice 2020: A Call For an International Coordinated Effort in Rice Functional Genomics

In 2008 Qifa Zhang et al. from China proposed the Rice 2020: A Call For an International Coordinated Effort in Rice Functional Genomics (Molecular Plant 1: 715-719) to coordinate research activities aimed at functionally characterizing the rice genome with the eventual goal of creating the so-called “green super rice” varieties. The major themes and specific scientific objectives for each theme are as follows:

  1. Development of enabling tools and genetic resources for an international community of scientists to conduct functional genomics research in rice including insertion mutant collections, full-length cDNA collections, and artificial micro-RNA (amiRNA) collections.
  2. Assignment of biological functions to every annotated gene to facilitate systematic phenotyping and characterization of the mutants, and systematic characterization of gene families.
  3. Systems-wide epigenomes, gene expression profiles and regulatory networks to achieve (1) comprehensive cell- or tissue-specific epigenomes and transcriptomes for selected developmental stages, abiotic and/or biotic conditions; (2) identification of regulatory elements based on the epigenetic profiles and transcriptomes; (3) systematic characterization of regulatory hierarchy of genome expression, its relationship to epigenomes during development and responses to various environmental changes, and their effects on growth and development; and (4) perform global analyses of the proteome and protein–protein interactions.
  4. Global analyses of the proteome and protein–protein interactions. This objective is proposed to achieve (1) tissue-specific proteomes of selected developmental stages and under selected defense and stress conditions; and (2) an experimentally defining comprehensive protein–protein interaction network.
  5. Understand and exploit natural variation of O. sativa and its relatives. This objective is proposed to achieve (1) sequencing a core set of O. sativa strains and its AA-genome relatives; and (2) develop a comprehensive platform for SNP association study to determine the relationship between phenotype and genotype and to identify functional diversity of agriculturally useful genes.
  6. Bioinformatics, data management, and exchange and sharing of information.
  7. Establishment of the toolkit for high-throughput knowledge-based rice breeding.

Events

International Symposium for Rice Functional Genomics

Tucson, Arizona

November 16-19, 2014

PAGXXIII (Rice Functional Genomics Workshop)

San Diego, California

January 10-14, 2015

The Pioneers

Takuji Sasaki

Professor
NODAI Research Institute
Tokyo University of Agriculture
Japan

Yue-ie Caroline Hsing

Institute of Plant and Molecular Biology
Academia Sinica
Taiwan

Rod Wing

Director
Arizona Genomics Institute
USA

Bin Han

Director National Center for Gene Research
Chinese Academy of Sciences
China

Richard McCombie

Professor
Stanley Institute for Cognitive
Genomics
Cold Spring Harbor Laboratory
USA

Akhilesh Tyagi

Director
National Institute of Plant Genome
New Delhi, India

Joachim Messing

Director
Waksman Institute of Microbiology
USA

Antonio Costa de Oliveira

Associate Professor
Universidade Federal de Pelotas
Brazil

Robin Buell

Professor
Department of Plant Biology
Michigan State University
USA

Apichart Vanavichit

Associate Professor
Kasetsart University
Thailand

Francis Quetier

Professor
University of Evry
France

Ben Burr

Served as co-chairman of IRGSP
Retired from Brookhaven National Laboratory
Lives in Bellport, NY