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.

Keywords: Association mapping; Genetic structure analysis; Linkage disequilibrium; Stress susceptibility index (SSI); Stress tolerance index (STI).

Fig. 1

Violin plots showing frequency distribution of (A) plant height, (B) root length, (C) root dry weight, and (D) shoot dry weight of 125 wheat genotypes given two water treatments: drought stress (DS, red) and well-watered (WW, green). Pearson’s correlation analysis visualising correlations between the seedling traits in the (E) drought-stressed and (F) well-watered treatments; PH, plant height; RL, root length; RDW, root dry weight; SDW, shoot dry weight. Significant levels are * p < 0.05, ** p < 0.01, and *** p < 0.001

Fig. 2

Distribution of filtered SNPs on the 21 chromosomes of wheat. The colours indicate the number of SNPs within a 1 Mb interval

Fig. 3

Genetic diversity of the 125 wheat accessions. (A) Population structure estimated by STRUCTURE with optimum sub-population (K = 6), each colour represents one subpopulation. (B) Phylogenetic tree, each branch indicates an accession, and the length of the branches represent the genetic distance. (C) Heat map of relatedness (kinship), blue colour at the middle represents the degree of relatedness. (D) Three-dimensional principal component analysis (PCA) plot illustrating the distribution of accessions based on the first three principal components (PC)

Fig. 4

Scatter plot showing linkage disequilibrium (LD) decay in the three sub-genomes and the whole genome by plotting (r²) against genetic distance (bp) in 125 wheat accessions. The point at which LD is reduced to 50% of its maximum value is indicated by the green vertical line. LD decay at cut off point is shown by green font on the X-axis and with bigger font in the plots

Fig. 5

(A) Manhattan and (B) Q-Q plots of the genome-wide association (GWAS) results for stress susceptibility index (SSI, charts on left) and stress tolerance index (STI, charts on right) of seedling traits. The markers above the significant threshold value of − log10 (p) > 4 (red dotted line) are shown in red colour. PH, plant height; RL, root length; RDW, root dry weight; SDW, shoot dry weight

Fig. 6

The distribution of the identified candidate genes of stress susceptibility index (SSI) and stress tolerance index (STI) for plant height (PH), root length (RL), root dry weight (RDW), and shoot dry weight (SDW) on 17 wheat chromosomes. Numbers indicate the physical positions (Mb) of the genes on the chromosomes