Abstract
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.
Highlights
Rice (Oryza sativa L) is one of the earliest domesticated crop species and has become the one of the world’s most widely grown crops
A member of more than 20 wild species in the genus Oryza [4,5], is commonly regarded as the wild progenitor of cultivated rice, O. sativa, which is divided into two sub-species: indica and japonica
Using genotypic information of the core subset generated by 72 genome-wide single sequence repeat (SSR) markers, the objectives of this study were to 1) characterize genetic structure of ancestry population, 2) analyze geographic distribution of each population in rice growing areas of the world, and 3) describe genetic diversity and specialty in each of the populations, including average alleles distinct and private to a population in the USDA rice world collection
Summary
Rice (Oryza sativa L) is one of the earliest domesticated crop species and has become the one of the world’s most widely grown crops. A member of more than 20 wild species in the genus Oryza [4,5], is commonly regarded as the wild progenitor of cultivated rice, O. sativa, which is divided into two sub-species: indica and japonica. A wide compatibility gene is necessary to utilize hybrid vigor between the two sub-species [9], which is greater than the vigor within either sub-species alone. This classification confirms the empirical distinction between them, which the Chinese recognized in literature as early as 100 AD [10] and called ‘Hsian’ for indica and ‘Jing or Geng’ for japonica [11]. The domestication from O. rufipogon to two sub-species of O. sativa is believed to have occurred several times [12], but more recent studies indicate a single domestication [13]
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