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Article
Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin
Theoretical and Applied Genetics
  • Mark A. Newell, The Samuel Roberts Noble Foundation
  • Franco G. Asoro, Iowa State University
  • M. Paul Scott, United States Department of Agriculture
  • Pamela J. White, Iowa State University
  • William D. Beavis, Iowa State University
  • Jean-Luc Jannink, United States Department of Agriculture
Document Type
Article
Publication Date
12-1-2012
DOI
10.1007/s00122-012-1945-0
Abstract
Detection of quantitative trait loci (QTL) controlling complex traits followed by selection has become a common approach for selection in crop plants. The QTL are most often identified by linkage mapping using experimental F2, backcross, advanced inbred, or doubled haploid families. An alternative approach for QTL detection are genome-wide association studies (GWAS) that use pre-existing lines such as those found in breeding programs. We explored the implementation of GWAS in oat (Avena sativa L.) to identify QTL affecting β-glucan concentration, a soluble dietary fiber with several human health benefits when consumed as a whole grain. A total of 431 lines of worldwide origin were tested over 2 years and genotyped using Diversity Array Technology (DArT) markers. A mixed model approach was used where both population structure fixed effects and pair-wise kinship random effects were included. Various mixed models that differed with respect to population structure and kinship were tested for their ability to control for false positives. As expected, given the level of population structure previously described in oat, population structure did not play a large role in controlling for false positives. Three independent markers were significantly associated with β-glucan concentration. Significant marker sequences were compared with rice and one of the three showed sequence homology to genes localized on rice chromosome seven adjacent to the CslFgene family, known to have β-glucan synthase function. Results indicate that GWAS in oat can be a successful option for QTL detection, more so with future development of higher-density markers.
Rights
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.
Language
en
File Format
application/pdf
Citation Information
Mark A. Newell, Franco G. Asoro, M. Paul Scott, Pamela J. White, et al.. "Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin" Theoretical and Applied Genetics Vol. 125 Iss. 8 (2012) p. 1687 - 1696
Available at: http://works.bepress.com/pamela_white/15/