Integrative Genome-Wide Association and Transcriptome Analyses Identify Candidate Genes for Salt Tolerance During Cotton Germination

Genome-wide association analysis and transcriptomics were used to investigate salt tolerance traits during germination in 300 Gossypium hirsutum L. germplasm accessions, with the objective of identifying genes and molecular markers associated with salt tolerance. Under 200 mmol L−1 NaCl stress, six traits were evaluated, germination rate, root length, shoot length, root fresh weight, shoot fresh weight, and total fresh weight, as well as their respective salt tolerance indices. A total of 1277 significantly associated single-nucleotide polymorphism (SNP) markers were identified and mapped to 94 quantitative trait loci (QTLs). Of these, 49 QTLs were detected by three or more analytical models, and three QTLs were prioritized for further investigation. Subsequent analysis of these QTLs identified 73 candidate genes potentially involved in cotton salt tolerance. Integration of transcriptomic data revealed that three candidate genes were among the differentially expressed genes (DEGs). Examination of their RNA-seq expression profiles demonstrated significant differences in fragments per kilobase of transcript per million mapped reads (FPKM) values across sampling time points. These three candidate genes are therefore predicted to be associated with salt tolerance during cotton germination. The results provide new insights into the molecular regulatory mechanisms of salt stress tolerance in cotton and offer valuable genetic resources and molecular markers for the genetic improvement of salt tolerance.