A Genome Wide Association Study For Drought Stress Tolerance In Upland Cotton(Gossypium Hirsutum L.)

Cotton is an industrial crop grown in different developed and developing countries of the world.Changing climatic conditions have posed major biotic and abiotic threats to the sustainable production of cotton crop.Drought stress is one of the major abiotic threats to the cotton production.Drought stress tolerance is a polygenic complex trait.Despite considerable efforts to investigate the genetic mechanism of drought stress tolerance conundrum,identification of key genes with major and minor contribution is yet to be explored.The use of diverse germplasm is of utmost importance in such studies.Prior studies have adopted several methods to find candidate genes but there was a lacuna to study role of single nucleotide polymorphism?SNP?markers with GWAS in diverse cotton germplasm.In this study we used 419 cotton accessions from diverse genetic backgrounds,collected from several cotton producing countries.A number of drought stress tolerance phenotyping and SNPs genotyping of419 accessions were associated using efficient mixed model association expedited?EMMAX?.A total of858 SNPs above�log₁₀?p-value?>6 were found.Among them,227 SNPs were distributed on the gene regions.SNPs distribution on sub genomes showed that 55.73%significant SNPs were distributed on At sub genome whereas,44.26%SNPs were distributed on Dt sub genome.On the bases of linkage disequilibrium?LD?21 highly significant SNP signals in association with different drought tolerance related traits were found.SNPs were distributed on different chromosomes which reveals the complex nature of drought tolerance mechanism.We found 308 genes associated with 21 SNP signals.Different screening methods were used for final selection of candidate genes.In this study we not only identified some genes which were reported in previous studies but also found some novel genes associated with drought stress tolerance.Interestingly we found some common SNPs peak signals for different drought tolerance traits.For instance,we identified A08?5409457 SNP signal at 8^th chromosome of At sub genome,common for seedling length?SL?PEG?and relative seedling length in drought stress?SL?PEG?0?.Similarly we found SNP signal D07?32849393 associated with root length in drought stress?RL?PEG?and number of roots?No.of roots?PEG?,these two different traits having common SNP signal association corroborates the narrative that drought stress tolerance is a complex mechanism controlled in an interestingly connected morphological and physiological way.In the same way we found another SNP signal D07?10461652 in association with leaf area under drought stress?LA?PEG?and leaf width under drought stress?LW?PEG?.This association of same SNPs signals across different traits/phenotypes put forth a clue of probable pleiotropic effect involved in controlling different traits under drought stress.Genome wide association study,RNA�seq data and results of qRT-PCR assisted us to find genes coding for dehydration responsive element binding protein DREB,Rapid alkalization factor-like protein RAFL,VCPE,cytochrome CYP450,heat shock protein Hsp2 and bZIP transcription factor that takes part in ABA regulation in cotton cropsLarge scale germplasm evaluation for drought stress will provide an opportunity to select some promising drought tolerant accession to be used in breeding program and identification of natural variation and candidate genes will support for better understanding of the complex mechanism of drought tolerance in upland cotton.