Pinpointing genomic regions conferring herbicide tolerance in cassava via genome-wide association mapping

Abstract

Cassava (Manihot esculenta Crantz) is a tropical crop of major socioeconomic importance, whose productivity can be limited by sensitivity to herbicides used for weed management. This study aimed to perform a genome-wide association study (GWAS) in 194 cassava genotypes to identify genomic regions associated with tolerance to the herbicides mesotrione, S-metolachlor, and chloransulam-methyl. The evaluations performed at 3, 6, 9, 15, and 30 days after application (DAA) were used to characterize the temporal progression of phytotoxicity. Based on this analysis, the phenotype obtained at 9 days after application (PhytoX9DAA) was selected for genome-wide association analyses because it represented the period of greatest symptom expression and the highest discrimination among genotypes. GWAS analyses were performed using de-regressed BLUPs and the MLM, MLMM, and BLINK models, incorporating kinship (K) and population structure (Q) matrices. Significant markers were detected across multiple chromosomes, and the corresponding genomic windows contained candidate genes with functional annotations related to herbicide response. The predominant functional categories included membrane transport, channel activity, signal peptide processing, protein phosphorylation, cellular signaling, and metabolic regulation. Key candidate genes included Manes.02G151900 and Manes.02G152700 (chromosome 2), associated with transmembrane transport and signal peptide processing; Manes.09G060900 (chromosome 9), associated with protein kinase activity, ATP binding, and protein phosphorylation; and Manes.15G083800 and Manes.15G084000 (chromosome 15), associated with S-adenosylmethionine-dependent methyltransferase activity, membrane-related functions, and protein phosphorylation. These genes participate in biochemical pathways involved in cellular signaling, membrane transport, and metabolic regulation that may contribute to herbicide tolerance. Overall, the results demonstrate that herbicide tolerance in cassava is a quantitative and polygenic trait governed by numerous small-effect loci. The integration of cellular signaling, metabolic regulation, and membrane transport supports the physiological resilience of the species under chemical exposure, providing valuable insights for breeding strategies and marker-assisted selection. The first genomic dissection of herbicide tolerance in cassava revealed herbicide-specific genetic architectures and candidate loci for mesotrione and S-metolachlor tolerance.