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The Plant Genome Abstract - Original Research

Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean


This article in TPG

  1. Vol. 9 No. 2
    unlockOPEN ACCESS
    Received: Sept 29, 2015
    Accepted: Feb 22, 2016
    Published: May 6, 2016

    * Corresponding author(s): phillip.mcclean@ndsu.edu
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  1. Sujan Mamidia,
  2. Phillip N. Miklasb,
  3. Jennifer Trappb,
  4. Erin Felicettib,
  5. Jane Grimwoodc,
  6. Jeremy Schmutzc,
  7. Rian Leed and
  8. Phillip E. McClean *e
  1. a Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND 58108-6050
    b USDA–ARS, Grain Legume Genetics and Physiology Research Unit, 24106 N. Bunn Rd, Prosser, WA 99350
    c HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
    d Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND 58108-6050
    e Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND 58108-6050 and Genomics and Bioinformatics Program, North Dakota State Univ., Fargo, ND 58108-6050
Core Ideas:
  • Sequenced-based introgression mapping rapidly maps QTL to a physical location
  • A highly polymorphic candidate gene associated with apoptosis maps in the WM7.1 QTL
  • A highly polymorphic gene associated with effector recognition maps in the WM8.3 QTL


White mold, caused by the necrotrophic fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease of common bean (Phaseolus vulgaris L.). WM7.1 and WM8.3 are two quantitative trait loci (QTL) with major effects on tolerance to the pathogen. Advanced backcross populations segregating individually for either of the two QTL, and a recombinant inbred (RI) population segregating for both QTL were used to fine map and confirm the genetic location of the QTL. The QTL intervals were physically mapped using the reference common bean genome sequence, and the physical intervals for each QTL were further confirmed by sequence-based introgression mapping. Using whole-genome sequence data from susceptible and tolerant DNA pools, introgressed regions were identified as those with significantly higher numbers of single-nucleotide polymorphisms (SNPs) relative to the whole genome. By combining the QTL and SNP data, WM7.1 was located to a 660-kb region that contained 41 gene models on the proximal end of chromosome Pv07, while the WM8.3 introgression was narrowed to a 1.36-Mb region containing 70 gene models. The most polymorphic candidate gene in the WM7.1 region encodes a BEACH-domain protein associated with apoptosis. Within the WM8.3 interval, a receptor-like protein with the potential to recognize pathogen effectors was the most polymorphic gene. The use of gene and sequence-based mapping identified two candidate genes whose putative functions are consistent with the current model of Sclerotinia pathogenicity.

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