The molecular basis for cotton seedling response to salt stress based on genome-wide association study and...

This study identified 39 SNPs significantly associated with RSR and ST traits, associating to 36 functional genes responding to salt stress, through the joint analysis of GWAS and transcriptome under salt stress in cotton seedlings. These findings offered a molecular foundation for improving salt tolerance of cotton. Improving the survival rate of cotton seedlings under salt stress is a crucial breeding objective for the future. In this study, the GWAS of relative seedling emergence rate (RSR) and salt tolerance grade (ST) traits were operated on salt-stressed cotton seedlings of 373 upland cotton core collections, and identified 39 significantly associated SNPs comprised of 283 genes. Transcriptome sequencing of 18 samples from salt-tolerant and -sensitive variety groups screened out 11,624 long non-coding RNAs (lncRNAs) and 70,478 mRNAs from cotton seedlings under salt stress, including 453 differentially expressed lncRNAs and 6009 mRNAs. Joint analysis of GWAS and differentially expressed mRNAs revealed 36 salt responsive genes significantly associated with RSR and ST traits. VIGS assay further verified that Gh_D07G0886 negatively regulated and Gh_A13G0145 positively regulated the salt tolerance of cotton seedlings, which was consistent with their expression patterns in response to salt stress. These findings offered molecular foundation for improving salt tolerance of cotton.