ARS | Publication request: Genetic assessment of a mini-core subset developed from the USDA rice genebank

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 22, 2008
Publication Date: June 30, 2009
Citation: Agrama, H.A., Yan, W., Lee, F.N., Fjellstrom, R.G., Chen, M., Jia, M.H., McClung, A.M. 2009. Genetic assessment of a mini-core subset developed from the USDA rice genebank. Crop Science. 49:1336-1346.

Interpretive Summary: Core collection is a subset sampled from a large germplasm collection and mini-core subset derives from further sampling from the core collection. Core collection improves efficiency of extensive and accurate characterization of germplasm and mini-core subset further improves the efficiency. The present study reports the formation of a mini-core subset containing 217 entries derived from a previously developed rice core collection, comprised of 1,794 entries representing the genetic diversity found in more than the 18,000 accessions of the USDA-ARS rice genebank. Data of 26 phenotypic traits, 69 simple sequence repeat markers and one indel marker were analyzed using PowerCore software to develop the mini-core. The 217 entries in the mini-core had a similar distribution of origins from 15 geographical regions to the core collection. The resultant mini-core had 6.3% of mean difference (MD%), 16.5% of variance difference (VD%), 102.7% of variable rate (VR%) and 97.5% of coincidence rate (CR%) with the core collection, which resulted in full coverage of 26 traits. All 962 alleles identified by the 70 markers in the core collection were captured in the mini-core, which maximized allelic richness up to 100% and resulted in an average genetic diversity (Nei index) of 0.76. As a result, the mini-core presented in this study is a highly suitable and representative subset of the USDA rice core collection as well as the entire USDA-ARS rice germplasm holdings.

Technical Abstract: Development of core collections is an effective tool to extensively characterize large germplasm collections, and the utilization of a mini-core sub-sampling strategy further increases the effectiveness of genetic diversity analysis at detailed phenotype and molecular levels. We report the formation of a mini-core containing 217 entries derived from 1,794 core entries representing the genetic diversity found in more than 18,000 accessions of the USDA-ARS rice germplasm collection. The mini-core was developed with PowerCore software based on 26 phenotypic traits and 70 molecular markers. The 217 entries in the mini-core had a similar distribution over 15 geographical regions with 1,794 entries in the original core collection. The resultant mini-core had 6.3% of mean difference (MD%), 16.5% of variance difference (VD%), 102.7% of variable rate (VR%) and 97.5% of coincidence rate (CR%) with the core collection, which brought about full coverage of 26 traits. All 962 alleles identified by the 70 markers in the core collection were captured in the mini-core, which maximized allelic richness up to 100% and resulted in an average genetic diversity (Nei index) of 0.76, ranging from 0.37 to 0.97 among the markers. In conclusion, the developed mini-core is a highly suitable and representative of the USDA rice core collection as well as the entire USDA-ARS rice germplasm holdings.