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The Plant Genome Abstract - Original Research

Genome-Wide Association Analysis Identifies Candidate Genes Associated with Iron Deficiency Chlorosis in Soybean


This article in TPG

  1. Vol. 4 No. 3, p. 154-164
    unlockOPEN ACCESS
    Received: Apr 22, 2011

    * Corresponding author(s): phillip.mcclean@ndsu.edu
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  1. Sujan Mamidi,
  2. Shireen Chikara,
  3. R. Jay Goos,
  4. David L. Hyten,
  5. Deepti Annam,
  6. Samira Mafi Moghaddam,
  7. Rian K. Lee,
  8. Perry B. Cregan and
  9. Phillip E. McClean 
  1. S. Mamidi, S. Chikara, S.M. Moghaddam, R.K. Lee, and P.E. McClean, Genomics and Bioinformatics Program, North Dakota State Univ., Fargo, ND 58102; S. Mamidi, S. Chikara, S.M. Moghaddam, R.K. Lee, and P.E. McClean, Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND 58102; R.J. Goos, School of Natural Resources, North Dakota State Univ., Fargo, ND 58102; D.L. Hyten and P.B. Cregan, USDA-ARS, Soybean Genomics and Improvement Lab., Beltsville, MD 20705; D. Annam, Dep. of Statistics, North Dakota State Univ., Fargo, ND 58102; Sujan Mamidi and Shireen Chikara contributed equally to this manuscript


Iron deficiency chlorosis (IDC) is a significant yield-limiting problem in several major soybean [Glycine max (L.) Merr.] production regions in the United States. Soybean plants display a variety of symptoms that range from a slight yellowing of the leaf to interveinal chlorosis, to stunted growth that reduces yield. The objective of this analysis was to employ single nucleotide polymorphism (SNP)-based genome-wide association mapping to uncover genomic regions associated with IDC tolerance. Two populations [2005 (n = 143) and 2006 (n = 141)] were evaluated in replicated, multilocation IDC trials. After controlling for population structure and individual relatedness, and selecting statistical models that minimized false positives, 42 and 88 loci, with minor allele frequency >10%, were significant in 2005 and 2006, respectively. The loci accounted for 74.5% of the phenotypic variation in IDC in2005 and 93.8% of the variation in 2006. Nine loci from seven genomic locations were significant in both years. These loci accounted for 43.7% of the variation in 2005 and 47.6% in 2006. A number of the loci discovered here mapped at or near previously discovered IDC quantitative trait loci (QTL). A total of 15 genes known to be involved in iron metabolism mapped in the vicinity (<500 kb) of significant markers in one or both populations.

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