Identification of candidate gene associated with cotton defoliation using integrated BSA-seq and RNA-seq analyses

Cotton is an important economic crop in China, and the current cotton industry is transitioning toward mechanization, with chemical defoliation being a key factor in this development. Breeding defoliant-sensitive cultivars can promote rapid and concentrated leaf abscission, effectively reduce trash content in seed cotton, improve mechanical harvesting efficiency, and advance the mechanization process of cotton production. In this study, we employed bulked segregant analysis (BSA) and transcriptome profiling to elucidate the molecular mechanisms underlying cotton defoliation. BSA-seq analysis identified nine major loci associated with defoliation. Integrating RNA-seq and tissue-specific expression profiles, we screened 22 differentially expressed genes (DEGs) that are highly expressed in stem and leaf organs. Based on expression pattern analysis, haplotype analysis, studies on the regulatory relationship between the gene and ethylene, and functional annotation of Arabidopsis homologs, we selected the cotton homolog GhAMT1;2, located at ChrD11: 56738327-56740667 bp, as the core candidate gene. This gene encodes a root high-affinity ammonium transporter involved in nitrogen metabolism. Subsequent virus-induced gene silencing (VIGS) experiments demonstrated that GhAMT1;2 exhibits downregulated expression following defoliant treatment and positively regulates cotton defoliation. This study successfully mapped defoliation-associated loci and validated gene function, providing a theoretical foundation for breeding and improving machine-harvestable cotton varieties.