Genome-wide association study and transcriptome analysis reveal candidate genes associated with mesosulfuron-methyl tolerance in wheat.

This study identified and validated stable genetic loci associated with MSM tolerance, predicted the underlying candidate genes, and provided marker-assisted selection tools for improving wheat herbicide tolerance. Mesosulfuron-methyl (MSM) is one of the few herbicides conferring high efficacy in eliminating poaceae weeds. Improper application, however, can result in phytotoxicity and yield reduction in wheat. Cultivating herbicide-tolerant wheat varieties is therefore of significant agricultural importance, though the genetic basis of this tolerance remains poorly understood. This study performed a genome-wide association study (GWAS) on 539 wheat accessions to explore the genetic foundation of MSM tolerance. Four stable genetic loci associated with MSM tolerance, designated as QMSL-3D.1, QMSL-4A.1, QMSL-5A.1/QMSH-5A.1, and QMSL-5B.1, were identified on chromosomes 3D, 4A, 5A, and 5B, respectively. Pyramiding superior alleles of these loci reduced the mean herbicide damage rating (HDR) by 32.1% and 26.6% under the two tested MSM dosages, respectively, though these alleles collectively explained a minor proportion of the phenotypic variation. Transcriptomic comparison between the MSM-tolerant cultivar Chang 4640 and susceptible cultivar Xinong 928 under MSM treatment identified two differentially expressed candidate genes, TraesCS5A02G398300 and TraesCS5B02G403400. These two homoeologous genes encoded aspartate-semialdehyde dehydrogenase, a key enzyme involved in the biosynthesis of essential amino acids. Furthermore, six Kompetitive Allele-Specific PCR (KASP) markers closely linked to the identified tolerance loci and candidate genes were developed. Field evaluation across multiple years and MSM concentrations screened out five wheat varieties with stable MSM tolerance. Collectively, this study identifies valuable genetic loci and molecular markers for wheat MSM tolerance, provides preliminary transcriptomic insights into herbicide response, and offers a useful resource for subsequent tolerance gene validation and wheat molecular breeding.