Genetic Structural Analysis for Germplasm Accessions in the USDA Rice World Collection.

Rice is grouped into five genetic structures including indica, aus, aromatic, temperate japonica, and tropical japonica. A core collection having 1,785 accessions from 114 countries has been developed that is representative of the USDA rice world collection which includes over 18,000 accessions. The core accessions plus 14 reference cultivars were genotyped with 72 microsatellite markers evenly distributed over the entire genome. Analysis indicated that the 14 references cultivars were classified among the five groups as in previous studies. Based upon these reference cultivars, the core accessions were divided to five sub-structures, indica (623), aus (180), aromatic (80), temperate japonica (481), and tropical japonica(421). Indica had the most alleles per locus, followed by aus, tropical japonica, aromatic and temperate japonica. Aus contained the most private alleles (unique to this sub-group) per locus, followed by indica, aromatic, tropical japonica and temperate japonica. Aromatic had the highest polymorphic information content, followed by indica, aus, tropical japonica and temperate japonica. Principle coordinate analysis demonstrated that tropical japonica was close to temperate japonica and indica close to aus while aromatic was located between these latter two sub-structures. Structural description of the USDA rice core collection will improve global utilization of the germplasm, help identify poorly represented genepools, and will identify diverse germplasm useful further genetic studies and breeding.