Genome-Wide Association Analysis Revealed Genetic Architecture of Cyst Nematode Resistance in a Diverse Panel of Soybean Germplasm Accessions.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating plant-parasitic pests causing severe annual soybean yield losses worldwide. Conventional genetic analysis commonly utilizing bi-parental mapping populations to identify and characterize quantitative trait loci (QTL) controlling resistance to SCN. 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, we performed a genome-wide association study (GWAS) in a diverse panel of over 550 soybean germplasm accessions 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 employed for analysis. The GWAS identified 14 loci distributed over different chromosomes (Chr.) 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 Chr. 10, which were previously reported by using a bi-parental population. In addition, previously known loci for qualitative traits, such as flower color, pubescence color, seed coat color, plant growth habit, etc. were also precisely mapped with GWAS approach performed in this study. Candidate genes 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 and for narrowing GWAS-defined genomic regions, which facilitates positional cloning of the causal gene(s) in soybean.