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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #233232
Title: Genetic assessment of a mini-core subset developed from the USDA rice genebank

Author
item AGRAMA, HESHAM
item Yan, Wengui
item LEE, FLEET
item Fjellstrom, Robert
item Chen, Ming Hsuan
item Jia, Melissa
item McClung, Anna

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/22/2008
Publication Date: 6/30/2009
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.