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

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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.

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Acknowledgments

Funding for this work was provided by USDA-NIFA grant number 2008-55301-18746 “Association genetics of beta-glucan metabolism to enhance oat germplasm for food and nutritional function”.

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Authors and Affiliations

  1. The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA

    Mark A. Newell

  2. Department of Agronomy, Iowa State University, Ames, IA, 50011, USA

    Franco G. Asoro & William D. Beavis

  3. Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA

    M. Paul Scott

  4. Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, 50011, USA

    Pamela J. White

  5. USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University Department of Plant Breeding and Genetics, 407 Bradfield Hall, Ithaca, NY, 14853, USA

    Jean-Luc Jannink

Authors
  1. Mark A. Newell
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  2. Franco G. Asoro
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  3. M. Paul Scott
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  4. Pamela J. White
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  5. William D. Beavis
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  6. Jean-Luc Jannink
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Corresponding author

Correspondence to Jean-Luc Jannink.

Additional information

Communicated by I. Mackay.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1. Information about all of the lines included in this study including the assigned numbers and data from GRIN for each line.

ESM 2. Final imputed marker data and beta-glucan BLUPs used for analysis with rows representing lines and columns representing markers.

ESM 3. List of rice candidates and significant DArT marker homology with rice including locations, putative functions of rice genes, and genomic regions of all sequences.

Supplementary material 1 (XLS 141 kb)

Supplementary material 2 (XLS 853 kb)

Supplementary material 3 (XLS 42 kb)

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Newell, M.A., Asoro, F.G., Scott, M.P. et al. Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin. Theor Appl Genet 125, 1687–1696 (2012). https://doi.org/10.1007/s00122-012-1945-0

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  • DOI: https://doi.org/10.1007/s00122-012-1945-0

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