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The Plant Genome Abstract - Original Research

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean


This article in TPG

  1. Vol. 9 No. 3
    unlockOPEN ACCESS
    Received: Feb 08, 2016
    Accepted: July 08, 2016
    Published: September 22, 2016

    * Corresponding author(s): samira.mm@gmail.com
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  1. Samira Mafi Moghaddam *a,
  2. Sujan Mamidiab,
  3. Juan M. Osornoc,
  4. Rian Leec,
  5. Mark Brickd,
  6. James Kellye,
  7. Phillip Miklasf,
  8. Carlos Urreag,
  9. Qijian Songh,
  10. Perry Creganh,
  11. Jane Grimwoodi,
  12. Jeremy Schmutzi and
  13. Phillip E. McCleana
  1. a Genomics and Bioinformatics Program and Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND 58105-6050
    b Present address, HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806
    c Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND 58105-6050
    d Dep. of Soil and Crop Sciences, Colorado State Univ., Fort Collins, CO 80523-1170
    e Dep. of Plant, Soil and Microbial Sciences, Michigan State Univ., East Lansing, MI 48824
    f Vegetable and Forage Crops Research Unit, USDA–ARS, Prosser, WA 99350
    g Dep. of Agronomy and Horticulture, Univ. of Nebraska, NE 69361-4939
    h Soybean Genomics and Improvement Lab, USDA–ARS, Beltsville, MD 20705
    i HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806


Common bean (Phaseolus vulgaris L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter- and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango–Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome-wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ∼30 candidate genes based on a priori and candidate gene search strategies centered on the 100-kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.

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