Theoretical and Applied Genetics

, Volume 125, Issue 8, pp 1687–1696

Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin

  • Mark A. Newell
  • Franco G. Asoro
  • M. Paul Scott
  • Pamela J. White
  • William D. Beavis
  • Jean-Luc Jannink
Original Paper

DOI: 10.1007/s00122-012-1945-0

Cite this article as:
Newell, M.A., Asoro, F.G., Scott, M.P. et al. Theor Appl Genet (2012) 125: 1687. 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 CslF gene 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.

Supplementary material

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Supplementary material 1 (XLS 141 kb)
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Supplementary material 2 (XLS 853 kb)
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Supplementary material 3 (XLS 42 kb)

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Mark A. Newell
    • 1
  • Franco G. Asoro
    • 2
  • M. Paul Scott
    • 3
  • Pamela J. White
    • 4
  • William D. Beavis
    • 2
  • Jean-Luc Jannink
    • 5
  1. 1.The Samuel Roberts Noble FoundationArdmoreUSA
  2. 2.Department of AgronomyIowa State UniversityAmesUSA
  3. 3.Corn Insects and Crop Genetics Research UnitUSDA-ARSAmesUSA
  4. 4.Department of Food Science and Human NutritionIowa State UniversityAmesUSA
  5. 5.USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University Department of Plant Breeding and GeneticsIthacaUSA