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Using near-isogenic barley lines to validate deoxynivalenol (DON) QTL previously identified through association analysis

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Abstract

Fusarium head blight (FHB) and its associated mycotoxin, deoxynivalenol (DON), are the major biotic factors limiting cereal production in many parts of the world. A recent association mapping (AM) study of US six-row spring barley identified several modest effect quantitative trait loci (QTL) for DON and FHB. To date, few studies have attempted to verify the results of association analyses, particularly for complex traits such as DON and FHB resistance in barley. While AM methods use measures to control for the effects of population structure and multiple testing, false positive associations may still occur. A previous AM study used elite breeding germplasm to identify QTL for FHB and DON. To verify the results of that study, we evaluated the effects of the nine DON QTL using near-isogenic lines (NILs). We created families of contrasting homozygous haplotypes from lines in the original AM populations that were heterozygous for the DON QTL. Seventeen NIL families were evaluated for FHB and DON in three field experiments. Significant differences between contrasting NIL haplotypes were detected for three QTL across environments and/or genetic backgrounds, thereby confirming QTL from the original AM study. Several explanations for those QTL that were not confirmed are discussed, including the effect of genetic background and incomplete sampling of relevant haplotypes.

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Acknowledgments

We thank Ed Schiefelbein, Guillermo Velasquez, Karen Beaubien, Celeste Falcon, Leticia Kumar, Vikas Vikram, Ahmad Sallam, Richard Horsley, the University of Minnesota—Crookston field crews, and the University of Minnesota Small Grains Pathology lab for their contributions to phenotyping and field logistics. In addition, we thank Shiaoman Chao for SNP genotyping, Yanhong Dong for toxin analysis, and an anonymous reviewer for constructive suggestions on a prior version of this manuscript. Funding for this work was supported by grants from the National Institute of Food and Agriculture U.S. Dept. of Agriculture Agreement No. 2006-55606-16722 “Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement”; the U.S. Wheat and Barley Scab Initiative U.S. Dept. of Agriculture ARS Agreement No. 59-0206-9-072, and the Rahr Foundation. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture.

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  1. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA

    Stephanie Navara & Kevin P. Smith

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  1. Stephanie Navara
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Correspondence to Kevin P. Smith.

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Communicated by M. J. Sillanpaa.

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Navara, S., Smith, K.P. Using near-isogenic barley lines to validate deoxynivalenol (DON) QTL previously identified through association analysis. Theor Appl Genet 127, 633–645 (2014). https://doi.org/10.1007/s00122-013-2247-x

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