Genetic Architecture of Cyst Nematode Resistance Revealed By Genome-Wide Association Study in Soybean

Bi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Although this approach successfully mapped a large number of SCN resistance QTL, it captures only limited allelic diversity existing in parental lines and also has limitations for genomic resolution.  In this study, a genome-wide association study (GWAS) was performed in a diverse set of over 550 soybean plant introductions (PIs) in maturity groups III to V to detect QTL/genes associated with SCN resistance to HG type 0. Over 45,000 single nucleotide polymorphism (SNP) markers generated by the SoySNP50K iSelect BeadChip (http//www.soybase.org) were utilized for analysis. The GWAS identified 14 loci distributed over different chromosomes comprising 60 SNPs significantly associated with SCN resistance. Results also confirmed six QTL that were previously mapped using bi-parental populations, including the rhg1 and Rhg4 loci. GWAS identified eight novel QTL, including QTL on chromosome (Chr.) 10, which were previously mapped by using a bi-parental population. In addition, previously known loci for six simple traits like flower color, pubescence color, seed coat color, plant growth habit, lodging, and pod shattering were precisely identified with GWAS approach performed in this study. Candidate genes at promising GWAS loci will be helpful to reveal the molecular mechanism involved in SCN resistance. The present study showed GWAS can be employed as an effective strategy for identifying complex traits in soybean and for narrowing GWAS-defined genomic regions, which facilitates positional cloning of the causal gene(s).