Genome-wide association of drought-related and biomass traits with HapMap SNPs in Medicago truncatula

Yun Kang, Muhammet Sakiroglu, Nicholas Krom, John Stanton-Geddes, Mingyi Wang, Yi Ching Lee, Nevin D. Young, Michael Udvardi

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59 Scopus citations


Improving drought tolerance of crop plants is a major goal of plant breeders. In this study, we characterized biomass and drought-related traits of 220 Medicago truncatulaHapMap accessions. Characterized traits included shoot biomass, maximum leaf size, specific leaf weight, stomatal density, trichome density and shoot carbon-13 isotope discrimination (δ13C) of well-watered M.truncatula plants, and leaf performance in vitro under dehydration stress. Genome-wide association analyses were carried out using the general linear model (GLM), the standard mixed linear model (MLM) and compressed MLM (CMLM) in TASSEL, which revealed significant overestimation of P-values by CMLM. For each trait, candidate genes and chromosome regions containing SNP markers were found that are in significant association with the trait. For plant biomass, a 0.5 Mbp region on chromosome 2 harbouring a plasma membrane intrinsic protein, PIP2, was discovered that could potentially be targeted to increase dry matter yield. A protein disulfide isomerase-like protein was found to be tightly associated with both shoot biomass and leaf size. A glutamate-cysteine ligase and an aldehyde dehydrogenase family protein with Arabidopsis homologs strongly expressed in the guard cells were two of the top genes identified by stomata density genome-wide association studies analysis.

Original languageEnglish (US)
Pages (from-to)1997-2011
Number of pages15
JournalPlant Cell and Environment
Issue number10
StatePublished - Oct 1 2015

Bibliographical note

Publisher Copyright:
& Sons Ltd.


  • Biomass
  • Compressed mixed linear model
  • Drought
  • GWAS
  • Medicago truncatula
  • Single nucleotide polymorphisms


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