Submitted to: Natural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/26/2010
Publication Date: 4/1/2010
Citation: Agrama, H.A., Yan, W., Jia, M.H., Fjellstrom, R.G., McClung, A.M. 2010 Genetic structure associated with diversity and geographic distribution in the USDA rice world collection. Natural Science. 2(4):247-291.
Interpretive Summary: Asian cultivated rice, Oryza sativa L, provides about 20% of the world’s caloric consumption. This species constitutes five genetic groups, indica, AUS, tropical japonica, temperate japonica and aromatic. Analyses of genetic structure and relationships based on genetic differentiation in rice help design breeding strategy, and overcome the sexual barrier for utilizing inter-subspecies heterosis. This subject has attracted numerous studies, but all the studies were based on certain groups of materials instead of a complete worldwide collection. To understand the genetic differentiation, geographic distribution and genetic diversity of rice worldwide, we have systematically sampled 1,785 cultivars from everywhere rice is grown in the world, genotyped these samples using 72 genome-wide molecular markers and analyzed genetic structure using various computer programs. The information generated in this study could help design genetic strategy for gene transfer and utilization of hybrid vigor in rice.
Technical Abstract: Asian cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, AUS, tropical japonica, temperate japonica and aromatic. Genetic characterization of a global rice collection could help better serve the global research community. Collecting worldwide rice germplasm started in 1866 has resulted in a collection of over 18,000 accessions from 115 countries. A core collection, including 1,785 accessions representing the collection, was genotyped using 72 SSR markers, and analyzed for genetic structure, global distribution, AMOVA, genetic diversity and distinct and private alleles. This collection contains 35% indica, 27% temperate japonica, 24% tropical japonica, 10% AUS and 4% aromatic. Graphing model-based ancestry coefficients demonstrated that tropical japonica showed up mainly in the American continents and part of the South Pacific and Oceania, and temperate japonica in Europe and the North Pacific far from the equator, which matched the responses to temperature. Indica is adapted to the warm areas of Southern Asia, South China, Southeast Asia, South Pacific and Central Africa and around the equator while AUS and aromatic are special types of rice that concentrates in Bangladesh and India. Indica and AUS were highly diversified while temperate and tropical japonicas had low diversity. AUS had the most alleles distinct and private from any others. Indica and aromatic were genetically closer to tropical japonica than temperate japonica.