Whole-genome resequencing identifies quantitative trait loci associated with mycorrhizal colonization of soybean

  • Michelle L. Pawlowski
  • Tri D. Vuong
  • Babu Valliyodan
  • Henry T. Nguyen
  • Glen L. HartmanEmail author
Original Article


Key message

A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with colonization of soybean by an arbuscular mycorrhizal fungus (Rhizophagus intraradices). Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes.


Arbuscular mycorrhizal fungi (AMF) form associations with over 80% of all terrestrial plant species and assist their host plants by increasing their nutrient uptake, drought tolerance, and resilience against pathogens and pests. Genotypic variation of crop plants to AMF colonization has been identified in crops, including soybean; however, the genetics controlling levels of AMF colonization in soybean are unknown. The overall goal of our study was to identify genomic regions associated with mycorrhizal colonization in soybean using genome-wide association analysis. A diverse panel of 350 exotic soybean genotypes inoculated with Rhizophagus intraradices were microscopically evaluated for root colonization using a modified gridline intersect method. Root colonization differed significantly (P < 0.001) among genotypes and ranged from 11 to 70%. A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with R. intraradices colonization that explained 24% of the phenotypic variance. Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. The results showed there was a significant genetic component to the level of colonization by R. intraradices in soybean. This information may be useful in the development of AMF-sensitive soybean cultivars to enhance nutrient uptake, drought tolerance, and disease resistance in the crop.



Arbuscular mycorrhizal fungi




Genome-wide association study


Linkage disequilibrium


Principal component


Principal component analysis


Quantititatve trait loci


Single nucleotide polymorphisms


Whole-genome resequencing



We thank Amanda Bardeau and Theresa Herman for their help with the greenhouse experiments, T. Herman for assisting with revising the manuscript, and Hao-Xun Chang for his advice on LD analysis and candidate gene selection. We thank Dr. Joseph Morton at the International Culture Collection of Vesicular Mycorrhizal Fungi for his advice on AMF species selection and for providing the isolate used in this study. We thank the United Soybean Board and the USDA-ARS for funding, as well as the University of Illinois Department of Crop Sciences for support via the James B. Sinclair and Fraley-Borlaug Fellowships.

Author Contribution statement

MPL, TDV, and GLH planned, and designed experiments. MPL completed root colonization analysis, LD analysis, and identified candidate genes. TDV performed genome-wide association study, phylogenetic and kinship analyses. BV and HTN selected and sequenced the 350 soybean accessions, MPL, TDV, and GLH wrote the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethic standards

The author state that the experiments comply with the current laws of the country in which they were performed (USA).

Supplementary material

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Fig. S1Phylogenetic relatedness of a diverse panel of 350 soybean accessions in the WGRS-derived 50 K SNP dataset. (PDF 130 kb)
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Authors and Affiliations

  1. 1.Department of Crop ScienceUniversity of IllinoisUrbanaUSA
  2. 2.Department of Plant SciencesUniversity of MissouriColumbiaUSA
  3. 3.USDA, Agricultural Research ServicesUniversity of IllinoisUrbanaUSA

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