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A genome-wide association study of malting quality across eight U.S. barley breeding programs

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Abstract

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We report malt quality QTLs relevant to breeding with greater precision than previous mapping studies. The distribution of favorable alleles suggests strategies for marker-assisted breeding and germplasm exchange.

Abstract

This study leverages the breeding data of 1,862 barley breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The mapping panel consisted of six-row and two-row advanced breeding lines from eight breeding populations established at six public breeding programs across the United States. A total of 4,976 grain samples were subjected to micro-malting analysis and mapping of nine quality traits was conducted with 3,072 SNP markers distributed throughout the genome. Association mapping was performed for individual breeding populations and for combined six-row and two-row populations. Only 16 % of the QTL we report here had been detected in prior bi-parental mapping studies. Comparison of the analyses of the combined two-row and six-row panels identified only two QTL regions that were common to both. In total, 108 and 107 significant marker-trait associations were identified in all six-row and all two-row breeding programs, respectively. A total of 102 and 65 marker-trait associations were specific to individual six-row and two-row breeding programs, respectively indicating that most marker-trait associations were breeding population specific. Combining datasets from different breeding program resulted in both the loss of some QTL that were apparent in the analyses of individual programs and the discovery of new QTL not identified in individual programs. This suggests that simply increasing sample size by pooling samples with different breeding history does not necessarily increase the power to detect associations. The genetic architecture of malting quality and the distribution of favorable alleles suggest strategies for marker-assisted selection and germplasm exchange.

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Acknowledgments

This research was supported by United States Department of Agriculture-NIFA Grant No. 2009-85606-05701, “Barley Coordinated Agricultural Project” and United States Department of Agriculture-NIFA Grant No. 2011-68002-30029, “Triticeae Coordinated Agricultural Project” and the American Malting Barley Association.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108-6026, USA

    Mohsen Mohammadi & Kevin P. Smith

  2. Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA

    Thomas K. Blake

  3. USA Cereal Crop Research Unit, USDA-ARS, 502 Walnut St., Madison, WI, 53726, USA

    Allen D. Budde

  4. USDA-ARS-BRL, 1605 Albrecht Blvd. N, Fargo, ND, 58102, USA

    Shiaoman Chao

  5. Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA

    Patrick M. Hayes

  6. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA

    Richard D. Horsley

  7. Limagrain Cereal Seeds, 2040 SE Frontage Road, Fort Collins, CO, 80525, USA

    Donald E. Obert

  8. Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA

    Steven E. Ullrich

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  1. Mohsen Mohammadi
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  2. Thomas K. Blake
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  3. Allen D. Budde
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Correspondence to Kevin P. Smith.

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Communicated by P. Langridge.

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Mohammadi, M., Blake, T.K., Budde, A.D. et al. A genome-wide association study of malting quality across eight U.S. barley breeding programs. Theor Appl Genet 128, 705–721 (2015). https://doi.org/10.1007/s00122-015-2465-5

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