Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes

International Rice Research Institute, Metro Manila, The Philippines (K.L.M., R.B., D.M., H.L.); The Institute for Genomic Research, Rockville, Maryland 20850 (C.R.B.); and Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523 (J.E.L.)

The International Rice Functional Genomics Consortium (IRFGC) has initiated a project to provide the rice research community with access to extensive information on genetic variation present within and between diverse rice cultivars and landraces, as well as the genetic resources to exploit that information. Among crop plants, rice is uniquely positioned to achieve this goal due to the release of a high-quality, whole-genome sequence; advances in the use of high-density arrays to compare complex genomes; and the availability of large collections of genetic materials rich in trait variation. In this project, the international rice research community will collaborate with Perlegen Sciences to identify a large fraction of the single nucleotide polymorphisms (SNPs) present in cultivated rice through whole-genome comparisons of 21 rice genomes, including cultivars, germplasm lines, and landraces. The SNP data will be entirely public (www.oryzasnp.org) and can be used to identify a collection of SNPs for undertaking whole-genome scans. Initial funding for this effort has been provided by the International Rice Research Institute (IRRI), the Generation Challenge Program, and the U.S. Department of Agriculture's Cooperative State Research, Education and Extension Service. In this communication, we wish to inform the research community about this project, to mobilize the research community to participate in detailed phenotyping of these lines, and to provide the opportunity to nominate additional candidate lines for a potential extension of this study.

^{Full Article in Plant Physiology.}