Background:Cotton is mainly grown for its natural fiber and edible oil.The fiber obtained from cotton is the indispensable raw material for the textile industries.The ever changing climatic condition,threatens cotton production due to a lack of sufficient water for its cultivation.Effects of drought stress are estimated to affect more than 50％ of the cotton growing regions.To elucidate the drought tolerance phenomenon in cotton,a backcross population was developed from G.tomentosum,a drought tolerant donor parent and G.hirsutum which is highly susceptible to drought stress.Results:A genetic map of 10 888 SNP markers was developed from 200 BC2F2 populations.The map spanned 4 191.3 centi-Morgan (cM),with an average distance of 0.104 7 cM,covering 51％ and 49％ of At and Dt sub genomes,respectively.Thirty stable Quantitative trait loci (QTLs) were detected,in which more than a half were detected in the At subgenome.Eighty-nine candidate genes were mined within the QTL regions for three traits:cell membrane stability (CMS),saturated leaf weight (SLW) and chlorophyll content.The genes had varied physiochemical properties.A majority of the genes were interrupted by introns,and only 15 genes were intronless,accounting for 17％ of the mined genes.The genes were found to be involved molecular function (MF),cellular component (CC) and biological process (BP),which are the main gene ontological (GO) functions.A number of miRNAs were detected,such as miR164,which is associated with NAC and MYB genes,with a profound role in enhancing drought tolerance in plants.Through RT-qPCR analysis,5 genes were found to be the key genes involved in enhancing drought tolerance in cotton.Wild cotton harbors a number of favorable alleles,which can be exploited to aid in improving the narrow genetic base of the elite cotton cultivars.The detection of 30 stable QTLs and 89 candidate genes found to be contributed by the donor parent,G.tomentosum,showed the significant genes harbored by the wild progenitors which can be exploited in developing more robust cotton genotypes with diverse tolerance levels to various environmental stresses.Conclusion:This was the first study involving genome wide association mapping for drought tolerance traits in semi wild cotton genotypes.It offers an opportunity for future exploration of these genes in developing highly tolerant cotton cultivars to boost cotton production.