Genome-wide association study of drought tolerance in wheat (Triticum aestivum L.) identifies SNP markers and candidate genes

Abstract Drought stress poses a severe threat to global wheat production, necessitating an in-depth exploration of the genetic basis for drought tolerance associated traits. This study employed a 90 K SNP array to conduct a genome-wide association analysis, unravelling genetic determinants of key traits related to drought tolerance in wheat, namely plant height, root length, and root and shoot dry weight. Using the mixed linear model (MLM) method on 125 wheat accessions subjected to both well-watered and drought stress treatments, we identified 53 SNPs significantly associated with stress susceptibility (SSI) and tolerance indices (STI) for the targeted traits. Notably, chromosomes 2A and 3B stood out with ten and nine associated markers, respectively. Across 17 chromosomes, 44 unique candidate genes were pinpointed, predominantly located on the distal ends of 1A, 1B, 1D, 2A, 3A, 3B, 4A, 6A, 6B, 7A, 7B, and 7D chromosomes. These genes, implicated in diverse functions related to plant growth, development, and stress responses, offer a rich resource for future investigation. A clustering pattern emerged, notably with seven genes associated with SSI for plant height and four genes linked to both STI of plant height and shoot dry weight, converging on specific regions of chromosome arms of 2AS and 3BL. Additionally, shared genes encoding polygalacturonase, auxilin-related protein 1, peptide deformylase, and receptor-like kinase underscored the interconnectedness between plant height and shoot dry weight. In conclusion, our findings provide insights into the molecular mechanisms governing wheat drought tolerance, identifying promising genomic loci for further exploration and crop improvement strategies. Graphical Abstract (1) A diverse panel of wheat genotypes was cultivated under both well-watered and drought stress conditions; (2) Phenotyping involved washing, scanning, drying and weighing plants to evaluate the stress susceptibility (SSI) and stress tolerance (STI) indices for four drought tolerance-related traits; (3) Genotyping was performed by extracting DNA and using the wheat 90 K Illumina iSelect array; (4) Phenotypic and genotypic data were utilized in a genome-wide association analysis (GWAS) using a mixed linear model (MLM); (5) Population structure assessment, principal component analysis (PCA), and kinship analysis were conducted; (6) Candidate genes were identified, and (7) their molecular functions were analysed and discussed.