An environmental differential association analysis of antibiosis to common cutworm in a Chinese soybean germplasm population and optimization of the cross design

Common cutworm (CCW) is one of the more serious leaf-feeding pests of soybean, causing significant yield losses in China. We have studied a sample (526 accessions) of the Chinese soybean germplasm population by association analysis using 233 polymorphic markers. Our aim was to detect quantitative trait loci (QTL) and corresponding alleles relating heritable antibiosis resistance to CCW using larva weight (LW) as an indicator. A two-stage procedure with a multi-loci genetic model at the second stage was used in the association mapping study, which was conducted on an individual year basis due to very significant accession 9 year interaction in the ANOVA. The results showed an environmental differential association, with 26 and 43 QTL (217 and 421 alleles, respectively) detected in 2009 and 2011, respectively. Among those, ten loci on chromosomes 2, 8, 12, 14, 16, and 17, with a total of 124 alleles, were common between years. Accordingly, detected QTL-allele matrices of the population in each individual year were established, which showed a greater variation in allele effect variation in 2011 than in 2009. The breeding potential of possible combinations among the 526 accessions was estimated and the top ten crosses common between the years identified based on their predicted values. The best crosses were mainly those between resistant 9 resistant accessions. Transgressive progenies with a much lower LW than the best accession (approx. 0-30 vs. 149 mg, respectively) were obtained. Our results imply that association analysis can, with suitable markers and improved procedures, detect many of the QTL/multialleles in a germplasm population and provide full genetic information in matrix form for use in optimized cross-design and marker-assisted progeny selection.