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

Authors: PAWLOWSKI, MICHELLE - University Of Illinois; VUONG, TRI - University Of Missouri; VALLIYODAN, BOSLO - University Of Missouri; NGUYEN, HENRY - University Of Missouri; Hartman, Glen

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2019
Publication Date: 11/9/2019
Citation: Pawlowski, M.L., Vuong, T., Valliyodan, B., Nguyen, H.T., Hartman, G.L. 2019. Whole-genome resequencing identifies quantitative trait loci associated with mycorrhizal colonization of soybean. Theoretical and Applied Genetics. 133:409-417. https://doi.org/10.1007/s00122-019-03471-5.
DOI: https://doi.org/10.1007/s00122-019-03471-5

Interpretive Summary: Arbuscular mycorrhizal fungi (AMF) form associations with over 80% of all terrestrial plant species and assist them by increasing their nutrient uptake, drought tolerance, and resilience against pathogens and pests. Genotypic variation of crop plants to AMF colonization has been identified, including soybean; however, the genetics controlling levels of AMF colonization in soybean are unknown. The overall goal was to identify genomic regions associated with mycorrhizal colonization in soybean. A diverse panel of 350 exotic soybean accessions inoculated by AMF (Rhizophagus intraradices) were microscopically evaluated for root colonization. Colonization of roots by R. intraradices differed significantly among soybean accessions. Genome-wide association analysis identified six chromosomal regions significantly associated with the extent of R. intraradices colonization. The results showed there was a substantial genetic component in soybean to the level of colonization by R. intraradices. This information could be applied to develop AMF-sensitive soybean cultivars that may enhance nutrient uptake, drought tolerance, and disease resistance, and would be of interest to crop improvement specialists.

Technical Abstract: Arbuscular mycorrhizal fungi (AMF) form associations with over 80% of all terrestrial plant species and assist them 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 was to identify genomic regions associated with mycorrhizal colonization in soybean using genome-wide association analysis. A diverse panel of 350 exotic soybean accessions inoculated by AMF (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 11-70%. 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 included homologs to known nodulin protein families and other symbiosis-specific genes. The results showed there was a substantial genetic component in soybean to the level of colonization by R. intraradices. This information could be applied to develop AMF-sensitive soybean cultivars that may enhance nutrient uptake, drought tolerance, and disease resistance.