Genome-Wide Association Analysis Reveals Genetic Variations and Candidate Genes Associated with Salt Tolerance Related Traits in Gossypium Hirsutum

Abstract Background: As a pioneer industrial crop in saline-alkali lands, cotton is more resistant to salt and drought stresses. However, abiotic stresses still have significant negative effects on its growth and development. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results: In this study, a genome-wide association study of salt tolerance related traits at seedling stage was performed based on two years of phenotype identification for 217 representative upland cotton cultivars by Genotyping By-Sequencing platform. A total of 51,060 polymorphic SNPs unevenly distributed in 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (-log10p>4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for RPH, A07 for RSFW, A08 and A13 for RSDW were expressed in both two environments, indicating that they were likely to be stable QTLs. A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected to conduct preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions: These results provided important genetic variations and candidate genes for accelerate the improvement of salt tolerance in cotton.