Salt stress is a major abiotic factor that considerably negatively affects crop growth, development, and ultimately, yield at the global scale. Upland cotton (Gossypium hirsutum L.), being moderately salt tolerant, provides a suitable model for dissecting salt-responsive traits. This study evaluated the cotton recombinant inbred line (RIL) population under salt stress conditions at the early growth stage. The conduct of association mapping used the general linear (GLM) and mixed linear (MLM) models, as implemented in TASSEL software. The identification of significant marker–trait associations succeeded, with the marker BNL3977 found to be significantly associated with fresh plant weight and fresh shoot weight. Meanwhile, the marker BNL2655 showed an association with total plant length, total root length, and leaf number under salt stress conditions. Genomic positions of these markers in the TM-1 reference genome had flanking sequences extracted and analyzed using the AUGUSTUS gene prediction tool, which identified putative coding regions. These predicted gene sequences underwent comparison against the NCBI database using BLAST, revealing candidate genes potentially involved in salt responses. Notably, several genes were distinct, including GDSL, GhGLIP, receptor-like protein kinase 5, GhUGT80B1, SRK2, GRP, ACD11, GhCSL, CBSX5, STY46, and CRF1, which play vital roles within salt stress conditions.
Upland cotton (G. hirsutum L.), recombinant inbred lines, salt stress conditions, mapping, marker-trait associations, growth traits, candidate genes
The results provide valuable insights into the genetic mechanism underlying salt tolerance in upland cotton (G. hirsutum L.). Similarly, they offer promising targets for marker-assisted selection (MAS) in breeding programs aimed at developing salt-tolerant cultivars. These results can be beneficial in developing salt-tolerant cotton cultivars in Uzbekistan.