Mapping quantitative trait loci associated with soybean resistance to common cutworm and soybean compensatory growth after defoliation using SNP marker-based genome-wide association analysis

Abstract

Resistance and tolerance are different plant defense mechanisms against herbivores. In this study, four compensatory growth (tolerance) indexes—the ratios of treatment to control for plant height (RPH), branching number of the stem (RBN), seed number per plant (RSN), and seed weight per plant (RSW)—and three resistance indexes—larval weight (LW), pupal weight (PW), and larva-consumed leaf weight (LCL)—were used to evaluate soybean (Glycine max (L.) Merr) defense against common cutworm (CCW; Spodoptera litura Fabricius). The phenotypic variations of seven traits among 170 accessions were significant (ANOVA, P 20 %) in this population. The decay distance of linkage disequilibrium was approximately 639 kb on average in intrachromosomal regions. Approximately 80 % of the intervals between two neighboring single-nucleotide polymorphisms were less than 600 kb. The natural population was divided into two subpopulations with little population structure. The genetic relationship among the accessions was distant. Fifty-one quantitative trait loci (QTLs) were significantly associated with the seven traits: six for RPH, nine for RBN, seven for RSN/RSW, one for RBN/RSN/RSW, six for LW, nineteen for LCL, and three for PW (−Log P ≥ 2.00, P ≤ 0.01). Single QTLs contributed 2.8–11 % of the phenotypic variance. Three QTLs were co-associated with soybean resistance and compensatory growth at the 0.05 significant level. Of these three QTLs, the qSCCW18-3 located in the promoter sequence of the soybean Rubisco activase β subunit gene (GmRCAβ) and its resistance allele reduced LW and increased plant height.