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This article in CS

  1. Vol. 49 No. 4, p. 1336-1346
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    Received: Sept 22, 2008


    * Corresponding author(s): hagrama@uark.edu
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doi:10.2135/cropsci2008.06.0551

Genetic Assessment of a Mini-Core Subset Developed from the USDA Rice Genebank

  1. H. A. Agrama *,
  2. WenGui Yan,
  3. Fleet Lee,
  4. Robert Fjellstrom,
  5. Ming-Hsuan Chen,
  6. Melissa Jia and
  7. Anna McClung
  1. Univ. of Arkansas, Rice Research and Extension Center, 2900 Highway 130E, Stuttgart, AR 72160

Abstract

Development of core collections is an effective tool to extensively characterize large germplasm collections, and the use of a mini-core subsampling strategy further increases the effectiveness of genetic diversity analysis at detailed phenotype and molecular levels. We report the formation of a mini-core subset containing 217 entries derived from 1794 core entries representing the genetic diversity found in more than 18,000 accessions of the USDA-ARS rice (Oryza sativa L.) germplasm collection. The mini-core was developed with PowerCore software on the basis of 26 phenotypic traits and 70 molecular markers. The 217 entries in the mini-core had a similar distribution over 15 geographical regions, with 1794 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 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.

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