Human/rice genome project

Rice (Oryza sativa) is one of the most important crops in the world. Rice, wheat, and maize together account for about half of the world's food production, and rice itself is the principal food of half of the world's population (Sasaki and Burr, 2000). Rice is the obvious choice for the first whole genome sequencing of a cereal crop. The rice genome is well mapped and well characterized, and it is the smallest of the major cereal crop genomes at an estimated 400 to 430 Mb. The next largest genome of an important cereal crop is that of sorghum, at 750 to 770 Mb, and the wheat genome is ∼37 times the size of the rice genome at close to 16,000 Mb (Arumuganathan and Earle, 1991). Grass genomes, including those of rice, wheat, maize, barley, rye, and sorghum, share a large degree of synteny, making rice an excellent model cereal (Gale and Devos, 1998). Rice is also the easiest of the cereal plants to transform genetically. A genome size of 430 Mb nonetheless represents a daunting task for whole genome sequencing. The rice genome is 3.5 times the size of the Arabidopsis genome and the third largest public genome project undertaken to date, behind the human and mouse genomes. The International Rice Genome Sequencing Project (IRGSP) began in September 1997, at a workshop held in conjunction with the International Symposium on Plant Molecular Biology in Singapore. Scientists from many nations attended the workshop and agreed to an international collaboration to sequence the rice genome. As a result, representatives from Japan, Korea, China, the United Kingdom, and the United States met six months later in Tsukuba to establish the guidelines. The participants agreed to share materials and to the timely release of physical maps and annotated DNA se-quence to public databases. The IRGSP has evolved to include 11 nations, and the IRGSP Working Group, composed of a representative from each participating nation, formulates IRGSP policies and finishing standards. The recent interim IRGSP meeting at Clemson University (September 19 and 20, 2000) in South Carolina was the largest rice genome meeting to date and was attended by more than 70 scientists and administrators from Japan, Taiwan, Thailand, Korea, China, India, Brazil, France, Canada, and the United States. The meeting was organized by Rod Wing, U.S. IRGSP Representative (Clem-son University), and chaired by Ben Burr, IRGSP Coordinator (Brookhaven National Laboratory, New York), and Takuji Sasaki, Program Director of the Rice Genome Research Program (RGP) in Japan. Major players in the project include the RGP; the CCW, a collaboration between the Clemson University Genomics Institute (CUGI), Cold Spring Harbor Laboratory, and the Washington University Genome Sequencing Center; the Institute for Genome Research (TIGR) in Rockville, MD; and the Plant Genome Initiative at Rutgers University (PGIR). Various additions and/or changes in IRGSP members were noted at the meeting. Brazil became the newest member and was represented by Antonio Costa de Oliveira of the Universidad Federal de Pelotas, who proposed to work on chromosome 12. Canada representative Thomas Bureau of McGill University proposed switching from work on chromosome 2 to coordinating activities on chromosome 9 with Thailand. India, previously an unfunded member of the IRGSP, has a new Rice Genome Program (represented by Akhilesh Tyagi of the University of Delhi and Nagendra Singh of the Indian Agricultural Research Institute) and will begin work on chromosome 11. A full list of participating countries and institutions, including URLs of sites offering information relevant to the IRGSP, is provided in Table 1. Table 1. Table 1. Rice Sequencing Participants and Chromosome Assignments Rice genome sequencing is being conducted along the same lines as numerous other large-scale genome sequencing projects. Large insert genomic libraries, used as the primary sequencing templates, are constructed in bacterial artificial chromosomes (BACs) or P1-derived artificial chromosomes (PACs). Sequencing of the rice genome is being performed mainly from genomic BAC or PAC libraries created from the Nipponbare variety, which was chosen as the common template throughout the IRGSP; China, working on the sequencing of chromosome 4, is the only IRGSP member to use a different variety, indica Guang Lu Ai 4 (Sasaki and Burr, 2000). Budiman (1999), in a report accessible through the CUGI website, presents a complete description of the preparation of two deep-coverage rice BAC libraries (25-fold genome coverage) used by the IRGSP.