Quantitative trait loci analysis identifying novel genomic regions for off-target dicamba tolerance in soybean [Glycine max (L.) Merr.]

Off-target dicamba exposure continues to cause substantial injury and yield loss in non-dicamba-tolerant (non-DT) soybean production areas, creating an urgent need for new cultivars with inherent tolerance to unintended dicamba exposure. To support the development of the soybean breeding pipeline, this study aimed to identify genomic regions associated with natural variation for off-target dicamba tolerance. A bi-parental recombinant inbred line population of 188 F₄-derived lines was evaluated across four environments, and quantitative trait loci (QTL) analysis identified six loci on chromosomes 6, 9, 10, 13, 19, and 20, collectively explaining 44.7% of the phenotypic variation. Two loci, qDIC_09.1 and qDIC_13.1, were classified as major QTLs based on their higher phenotypic variation explained (9.9% and 13.5%, respectively). Within the physical intervals of these major QTLs, 43 putative candidate genes were selected based on the functional annotations of differentially expressed genes previously characterized under dicamba exposure in Arabidopsis. These included genes encoding glutathione S-transferase, cytochrome P450, and uridine 5’-diphosphate-glycosyltransferase proteins, which participate in key phases of herbicide detoxification. Of 43 putative candidate genes, gene expression analysis revealed 10 putative candidate genes that are highly expressed in the aboveground tissues in soybean. Nucleotide divergence analyses further revealed a large selective sweep spanning qDIC_13.1, suggesting domestication-driven erosion of potentially beneficial alleles associated with detoxification capacity. The genomic regions and putative candidate genes identified here provide valuable resources for marker development, allele mining, and breeding strategies to improve tolerance to off-target dicamba exposure in non-DT soybean cultivars.