Evaluating the potential penalty of sclerotinia stem rot resistance on agronomic and seed quality traits in a Canadian soybean germplasm panel

Genome-wide association studies (GWAS) have become a pivotal tool in identifying marker-trait associations (MTAs), thus ultimately facilitating the improvement of desirable traits like disease resistance in plants. However, the introduction of new alleles poses challenges due to the potential co-integration of undesirable traits. This study builds upon the findings of MTAs for sclerotinia stem rot (SSR) resistance in soybeans (Glycine Willd.) that we reported previously. By employing the same soybean genetic diversity GWAS panel used in the previous study, we performed a set of genomic analyses to examine any potential linkage drag. This was performed through GWAS that aimed to explore the co-localization of MTAs associated with SSR resistance so as to assess the effects of resistance alleles on both agronomic and seed quality traits. Of the 29 MTAs identified in this study, only seven protein-related MTAs shared a chromosome with the previously identified SSR resistance MTA. In addition, there seems to be no yield penalty for the partially resistant soybean genotypes. To the contrary, in certain instances, an advantage was associated with carrying SSR resistance alleles concerning the agronomic and seed quality traits. While these findings are promising, they should be considered preliminary and warrant further investigation. We anticipate that these results will provide a solid foundation for studying the potential effects of SSR resistance alleles on other desirable traits in soybean.