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The Plant Genome Abstract - Original Research

Genome-Wide Association Mapping Reveals Novel QTL for Seedling Leaf Rust Resistance in a Worldwide Collection of Winter Wheat


This article in TPG

  1. Vol. 9 No. 3
    unlockOPEN ACCESS
    Received: June 02, 2016
    Accepted: July 24, 2016
    Published: September 29, 2016

    * Corresponding author(s): xiangyang.xu@ars.usda.gov
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  1. Genqiao Liac,
  2. Xiangyang Xu *a,
  3. Guihua Baib,
  4. Brett F. Carverc,
  5. Robert Hungerd,
  6. J. Michael Bonmane,
  7. James Kolmerf and
  8. Hongxu Dongg
  1. a Wheat, Peanut and Other Field Crops Research Unit, USDA–ARS, Stillwater, OK 74075
    c Plant and Soil Science Dep., Oklahoma State Univ., Stillwater, OK 74078
    b Hard Winter Wheat Genetics Research Unit, USDA–ARS, Manhattan, KS 66506
    d Entomology and Pathology Dep., Oklahoma State Univ., Stillwater, OK 74078
    e Small Grains and Potato Germplasm Research Unit, USDA–ARS, Aberdeen, ID 83210
    f Cereal Disease Laboratory, USDA–ARS, St. Paul, MN 55106
    g Dep. of Crop Sciences & Energy Biosciences Institute, Univ. of Illinois, Urbana, IL 61801
Core Ideas:
  • The association panel used in this study may represent the largest in wheat GWAS
  • Three pathotypes, including a bulked races collected in the field, were used
  • A total of 14 QTL for leaf rust resistance were identified at a FDR of 0.01.
  • Six QTL identified in this study are novel loci in bread wheat
  • Thirty-one additional QTL were significant at a FDR of 0.05.


Leaf rust of wheat (Triticum aestivum L.) is a major disease that causes significant yield losses worldwide. The short-lived nature of leaf rust resistance (Lr) genes necessitates a continuous search for novel sources of resistance. We performed a genome-wide association study (GWAS) on a panel of 1596 wheat accessions. The panel was evaluated for leaf rust reaction by testing with a bulk of Puccinia triticina Eriks. (Pt) isolates collected from multiple fields of Oklahoma in 2013 and two predominant races in the fields of Oklahoma in 2015. The panel was genotyped with a set of 5011 single-nucleotide polymorphism (SNP) markers. A total of 14 quantitative trait loci (QTL) for leaf rust resistance were identified at a false discovery rate (FDR) of 0.01 using the mixed linear model (MLM). Of these, eight QTL reside in the vicinity of known genes or QTL, and more studies are needed to determine their relationship with known loci. QLr.stars-7AL1 is a new QTL to bread wheat but is close to a locus previously identified in durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.]. The other five QTL, including QLr.stars-1BL3, QLr.stars-1DC1, QLr.stars-2BL1, QLr.stars-5BL1, and QLr.stars-7AS1, are likely novel loci for leaf rust resistance. The uneven distribution of the 14 QTL in the six subpopulations of the panel suggests that wheat breeders can enhance leaf rust resistance by selectively introgressing some of these QTL into their breeding materials. In addition, another 31 QTL were significantly associated with leaf rust resistance at a FDR of 0.05.

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