Identification of single nucleotide polymorphisms in soybean associated with resistance to common cutworm (Spodoptera litura Fabricius)

Common cutworm (CCW; Spodoptera litura Fabricius) is a major leaf-eating insect that affects soybean crops in central and southern China. Understanding CCW-associated traits in soybean will provide insights for improved breeding strategies for resistance. The purpose of this study was to explore the genetic mechanisms underlying resistance to CCW. In this study, one natural population consisting of 219 soybean landraces from a wide geographic range was employed. Three traits, namely larval weight (LW), duration of larval stage (DLS) and pupal weight (PW) were evaluated as indicators for CCW resistance. Using 1536 single nucleotide polymorphisms (SNPs), a genome-wide association analysis was conducted to identify genomic regions associated with LW, DLS and PW in this natural population. Seven SNP-trait associations were identified using a mixed linear model (MLM). Four SNPs were co-associated with two traits. Three loci were significantly associated with CCW-resistance. Most of the detected loci were located within genomic regions previously identified as quantitative trait loci (QTLs) for these traits. The region on chromosome 6, which co-associated with LW and DLS, included several QTLs for reaction to disease or insect, such as Fusarium virguliforme, corn earworm and bean pyralid. On chromosome 7, two SNPs have been reported to associate with CCW, corn earworms, soybean aphid and bean pyralid moth infestations. Two putative genes (MYC2-like and JAM2-like) on chromosome 7 that may be associated with resistance to CCW were identified. These markers, located in previously reported QTLs, are consistent with previous findings and may represent important targets for the identification of CCW resistance-related genes. These results may provide a profound understanding of the genetic basis for resistance to CCW in soybean and the foundation for resistance to biotic stress through marker-assisted selection breeding strategies for CCW.