Integrating meta-QTL analysis and VIGS to decipher GhPCMP-E17-mediated abiotic stress tolerance in upland cotton

• MQTLs for abiotic stress-related were identified in upland cotton. • Nine major MQTLs were detected in upland cotton. • A key gene ( GhPCMP-E17 ) with drought and salt stress tolerance was identified. Cotton ( Gossypium spp.), a globally important cash crop, is increasingly threatened by abiotic stresses that significantly affect yield and fiber quality. In this study, data on 3,016 abiotic stress-related quantitative trait loci (QTLs) described in 31 published papers were integrated through meta-QTL analysis, a total of 34 MQTLs were identified. Nine major MQTLs with numerous initial QTLs, high R 2 values, narrow confidence intervals (CIs), and close colocalizations were successfully detected. Combined with the transcriptome data, the candidate gene GhPCMP-E17 was identified. Through virus-induced gene silencing (VIGS) technology, the role of GhPCMP-E17 in the response to abiotic stress was clarified. Compared with the TRV:00 plants, the GhPCMP-E17 -silenced plants presented more severe wilting and yellowing under drought and salt stress conditions. Silencing GhPCMP-E17 weakens the function of antioxidant enzymes, thereby increasing the accumulation of reactive oxygen species. These results indicate that downregulation of GhPCMP-E17 gene expression enhances the sensitivity of cotton plants to drought and salt stress. This research provides excellent genetic resources for adaptive abiotic crop breeding in upland cotton.