Geographic Diversity Assessed by Molecular Markers in the USDA Rice World Collection.

Knowledge of genetic diversity and relationship in the USDA rice world collection can help utilize, conserve and manage this collection for more efficient service to national and international scientists. The USDA rice core collection including 1,794 accessions originating from 114 countries in 14 geographic regions was genotyped with 71 SSR and one indel markers. The 72 markers revealed 1,005 alleles averaging 14 alleles per locus. Sixty markers were highly (PIC>0.5), 10 reasonably (0.5>PIC>0.25) and 2 slightly informative.  Great majority of genetic variance was due to within instead of among geographic regions, and within instead of among countries. The regions and countries were highly and significantly differentiated using these markers. Germplasm accessions originating in Subcontinent, Southeast Asia and Africa were highly diversified, while those in North America, and West and East Europe had the lowest diversity. Different measurements of genetic diversity, average number of alleles per locus, PIC, Nei index and average number of private alleles per locus, uniformly reached this conclusion. Three main clusters were revealed by the UPGMA using Nei genetic similarity for the 14 regions. Germplasm accessions originating from Myanmar, Indonesia, Cambodia, Malaysia and Nepal were highly diversified, but those from France, Spain, Romania, Italy and the U.S. poorly diversified. Seventy-eight countries from which five or more accessions were sampled in the core collection were differentiated into five main clusters. Rice germplasm in this world collection including its core collection is nationally and internationally available in the USDA National Plant Germplasm System, free of charge or restrictions.