Genetic structure associated with diversity and geographic distribution in the USDA rice world collection
Hesham A. Agrama, WenGui Yan, Melissa Jia, Robert Fjellstrom, Anna M. McClung
DOI: 10.4236/ns.2010.24036   PDF   HTML     7,581 Downloads   16,481 Views   Citations


Cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, aus, tropical japonica, temperate japonica and aromatic. Genetic characterization of rice germplasm collections will enhance their utilization by the global research community for improvement of rice. The USDA world collection of rice germ-plasm that was initiated in 1904 has resulted in over 18,000 accessions from 116 countries, but their ancestry information is not available. A core subset, including 1,763 accessions repre-senting the collection, was genotyped using 72 genome-wide SSR markers, and analyzed for genetic structure, genetic relationship, global distribution and genetic diversity. Ancestry analysis proportioned this collection to 35% indica, 27% temperate japonica, 24% tropical japonica, 10% aus and 4% aromatic. Graphing model-based ancestry coefficients demon-strated 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 tem-perature. 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, indicated by average alleles and pri-vate alleles per locus. Aromatic has the most polymorphic information content. Indica and aromatic were genetically closer to tropical ja-ponica than temperate japonica. This study of global rice has found significant population stratification generally corresponding to major geographic regions of the world.

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Agrama, H. , Yan, W. , Jia, M. , Fjellstrom, R. and McClung, A. (2010) Genetic structure associated with diversity and geographic distribution in the USDA rice world collection. Natural Science, 2, 247-291. doi: 10.4236/ns.2010.24036.

Conflicts of Interest

The authors declare no conflicts of interest.


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