Integrated Genomic and Transcriptomic Analysis Reveals Candidate Genes Underlying Herbicide Resistance in Sorghum

Background: Herbicide-resistant germplasms provide critical genetic resources for improving weed control and understanding resistance mechanisms in crops. Results: In this study, 356 sorghum accessions were screened for herbicide tolerance at the seedling stage using gradient herbicide treatments. Under application of the ACCase inhibitor 10% feproxydim, five accessions showed reduced phytotoxicity: IS1219 displayed the highest resistance, while IS10867, SJ72, SJ85, and PI61 exhibited moderate tolerance. For the ALS inhibitor mesosulfuron-methyl, only two accessions, SJ304 and PI47, showed visible tolerance. To elucidate the molecular basis of resistance, a bulked segregant analysis sequencing (BSA-Seq) approach was applied to resistant and susceptible gene pools constructed from the IS1219 × RTx430 F₂ population. The analysis identified a major quantitative trait locus (QTL) for herbicide resistance located on chromosome 1.Transcriptome (RNA-Seq) data of leaf tissues collected after feproxydim treatment revealed five co-expressed candidate genes within the mapped interval. Among them, Sobic.001G431500 , encoding a carboxylesterase 17 (α/β-hydrolase), plays a pivotal role in feproxydim resistance. This gene was markedly upregulated in the resistant line (IS1219) but not in the susceptible line (RTx430), indicating that enhanced hydrolytic or metabolic activity may be a major resistance mechanism. Protein sequence comparison also showed that the IS1219 allele carries a missense and deletion mutation at and after position 300 (V300A and P301_P303del). Conclusions: These findings clarify the physiological and molecular mechanisms underlying herbicide resistance in sorghum and provide valuable genetic resources for breeding herbicide-tolerant varieties.