Using High-Throughput Genotyping to Narrow a Global Germplasm Collection of Rice.

The USDA rice core collection, about 10% of the whole collection including more than 18,000 accessions originated from 116 countries, could be effectively used to assess the whole collection with 88% certainty. Genotyping the 1,794 accessions in the core with 75 SSR markers demonstrated that a great majority of genetic variance was due to within instead of among geographic regions, and within instead of among countries. Germplasm accessions obtained from the Southern Asia, Southeast Asia and Africa were highly diversified, while those from North America, and Western and Eastern Europe had the lowest diversity. Ancestry analysis proportioned the core collection to 35% indica, 27% temperate japonica, 24% tropical japonica, 10% aus and 4% aromatic. A mini-core including 217 entries was formed using PowerCore software based on 26 phenotypic traits and 70 SSRs. The mini-core had a full coverage of the 26 traits and captured all the 962 alleles identified by the 70 markers in the core collection, which maximized allelic richness up to 100%. This core has been phenotyped for 30 traits and partially genotyped using a custom-designed Affymetrix array consisting of 44,100 SNPs. The mini-core has been phenotyped for 40 traits in both Arkansas and Texas, and is under resequencing for genome-wide association study. Each of the core and mini-core accessions is available for global community, free of charge and agreement.