Genetic assessment of a mini-core subset developed from the USDA rice genebank

H. A. Agrama, WenGui Yan, Fleet Lee, Fjellstrom Robert, Ming Hsuan Chen, Melissa Jia, Anna McClung

Research output: Contribution to journalArticle

64 Citations (Scopus)

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 identifi ed 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.

Original languageEnglish
Pages (from-to)1336-1346
Number of pages11
JournalCrop Science
Volume49
Issue number4
DOIs
Publication statusPublished - Jul 2009

Fingerprint

USDA
Agricultural Research Service
germplasm conservation
rice
genetic variation
Oryza sativa
germplasm
alleles
phenotype
genetic markers

Keywords

  • Alkali spreading value
  • ASV
  • Coincidence rate
  • CR%
  • MD%
  • Mean difference
  • PCR
  • Polymerase chain reaction
  • QTL
  • Quantitative trait loci
  • Simple sequence repeat
  • Single nucleotide polymorphism
  • SNP
  • SSR
  • Variable rate
  • Variance difference
  • VD%
  • VR%

ASJC Scopus subject areas

  • Agronomy and Crop Science

Cite this

Agrama, H. A., Yan, W., Lee, F., Robert, F., Chen, M. H., Jia, M., & McClung, A. (2009). Genetic assessment of a mini-core subset developed from the USDA rice genebank. Crop Science, 49(4), 1336-1346. https://doi.org/10.2135/cropsci2008.06.0551

Genetic assessment of a mini-core subset developed from the USDA rice genebank. / Agrama, H. A.; Yan, WenGui; Lee, Fleet; Robert, Fjellstrom; Chen, Ming Hsuan; Jia, Melissa; McClung, Anna.

In: Crop Science, Vol. 49, No. 4, 07.2009, p. 1336-1346.

Research output: Contribution to journalArticle

Agrama, HA, Yan, W, Lee, F, Robert, F, Chen, MH, Jia, M & McClung, A 2009, 'Genetic assessment of a mini-core subset developed from the USDA rice genebank', Crop Science, vol. 49, no. 4, pp. 1336-1346. https://doi.org/10.2135/cropsci2008.06.0551
Agrama, H. A. ; Yan, WenGui ; Lee, Fleet ; Robert, Fjellstrom ; Chen, Ming Hsuan ; Jia, Melissa ; McClung, Anna. / Genetic assessment of a mini-core subset developed from the USDA rice genebank. In: Crop Science. 2009 ; Vol. 49, No. 4. pp. 1336-1346.
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