QTL mapping and functional analysis reveal the critical role of GbABC1K in regulating cotton salt tolerance

Salt stress is among the major abiotic stresses in cotton cultivation. Identifying salt-tolerant genes and understanding their functions are crucial for improving the salt tolerance of cotton. In this study, a recombinant inbred line (RIL) population, derived from a cross between G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124, was used to detect quantitative trait loci (QTLs) related to salt tolerance. A total of 16 QTLs were identified on 10 chromosomes, explaining 1.73–15.36 % of the phenotypic variation. Concurrently, QTL-seq analysis in a BC 1 F 2 population revealed six genomic regions associated with salt tolerance. Among these, qSA05.1 overlapped with two QTLs and exhibited relatively narrow genomic interval with a major effect, making it a priority locus for further analysis. Sequence comparison and qRT-PCR revealed that a protein kinase encoding gene, GbABC1K , was the most likely candidate gene. Virus-induced gene silencing (VIGS) of GbABC1K significantly decreased the salt tolerance of cotton. Further transcriptome analysis showed that silencing GbABC1K altered the expression of genes involved in photosynthesis, metabolism, and stress responses. Notably, we found that most of these differentially expressed genes (DEGs) were associated with plant antioxidant processes, and mainly involved in ascorbate metabolism, glutathione metabolism and POD-encoding genes. Biochemical experiments indicated that silencing GbABC1K led to a decrease in the antioxidant capacity of cotton, thereby disrupting reactive oxygen species (ROS) homeostasis. Furthermore, the exogenous methyl viologen (MV, a ROS inducer) experiments further verified the crucial role of GbABC1K in mediating ROS homeostasis. These findings highlight GbABC1K as a critical regulator of salt tolerance in cotton via antioxidant system modulation, providing new genetic resources and insights for understanding the mechanisms of salt tolerance in cotton. • QTL mapping and QTL-seq analysis identified a stable and major-effect salt-tolerant QTL qSA05.1. • qRT-PCR and VIGS experiments analysis confirmed GbABC1K as the most likely candidate gene. • RNA-seq and biochemical analyses revealed that GbABC1K is involved in maintaining ROS homeostasis.