Bulk Segregant Analysis Integrated with Transcriptomic and Proteomic Approaches Reveals Candidate Genes Associated...

Drought is one of the most severe and frequently occurring abiotic stresses that significantly threaten cotton production. In this study, to identify key genes associated with drought resistance in upland cotton, BSA-seq was integrated with RNA-seq (R) and proteomic (P) approaches conducted on an F₂ population and two parental accessions exhibiting extreme drought resistance: the drought-sensitive accession "2406211" (A) and the drought-resistant accession "2403739" (B). After crossing the two parent plants, the F₂ generation from these accessions was used to construct pools representing the two extreme drought resistance traits. BSA-seq analysis identified five QTL regions on chromosomes A02 (9.10 Mb-11.10 Mb), A07 (18.20 Mb-20.70 Mb), A09 (39.80 Mb-42.40 Mb), D03 (8.90 Mb-13.80 Mb), and D04 (10.80 Mb-13.40 Mb). RNA-Seq analysis revealed a total of 5844 differentially expressed genes (DEGs) in RAW1 (W1, control condition) versus RAW2 (W2, drought stress), comprising 2499 up-regulated and 3345 down-regulated genes. In RBW1 versus RBW2, 6586 DEGs were detected, with 3286 up-regulated and 3300 down-regulated genes. Proteomic analysis identified 1352 differentially expressed proteins (DEPs) in PAW1 versus PAW2, including 453 up-regulated and 899 down-regulated proteins, and 3440 DEPs in PBW1 versus PBW2, with 1773 up-regulated and 1667 down-regulated proteins. By integrating transcriptomic and proteomic data to analyze genes located within the BSA target regions, we identified 5 DEGs/DEPs, including GH_D04G0687, GH_A02G0703, GH_A07G1211, GH_A07G1202, and GH_D04G0702, as potential candidate genes within the drought-resistance target intervals. This study expands transcriptomic and proteomic resources and identifies novel gene targets for the genetic improvement and breeding of cotton cultivars.