Genome-Wide Association Studies Reveal Novel Loci for Herbivore Resistance in Wild Soybean (Glycine soja)

The production of soybean [Glycine max (L.) Merr.] is seriously threatened by various leaf-feeding insects, and wild soybean [Glycine soja Sieb. & Zucc.] has a greater resistance capacity and genetic diversity. In this study, a natural population consisting of 121 wild soybean accessions was used for detecting insect resistance genes. The larval weight (LW) of the common cutworm (CCW), the resistance level (RL) and the index of damaged leaf (IDL) were evaluated as resistance indicators to herbivores. An association synonymous SNP AX-94083016 located in the coding region of the respiratory burst oxidase gene GsRbohA1 was identified by genome-wide association study (GWAS) analyses. The overexpression of GsRbohA1 in soybean hairy roots enhanced resistance to CCW. One SNP in the promoter region cosegregated with AX-94083016 contributing to soybean resistance to CCW by altering GsRbohA1 gene expression and reactive oxygen species (ROS) accumulation. Two major haplotypes, GsRbohA1(A) and GsRbohA1(G), were identified based on the SNP. The resistant haplotype GsRbohA1(A) predominates in wild soybeans, although it has been gradually lost in landraces and cultivars. The nucleotide diversity around GsRbohA1 is much lower in landraces and cultivars than in its ancestors. In conclusion, a new resistant haplotype, GsRbohA1(A), was identified in wild soybean, which will be a valuable gene resource for soybean insect resistance breeding through introducing into improvement lines, and it offers a strategy for exploring resistance gene resources from its wild relatives.