Fig. 2: Population-level transcriptome dynamics of wheat in response to water scarcity.

a Principal component analysis (PCA) of the population-level transcriptome of root tissue under WW, DS1, and DS2 conditions. Each dot represents a sample from one accession, with conditions distinguished by different colors and symbols. b Comparison of the expression coefficient of variation (CV) (left), fold-change (FC) (middle), and CV of expression FC (right) among expressed genes in root tissue of 110 representative accessions among different water conditions. Boxes indicate the interquartile range (IQR) with the median line, and whiskers extend to 1.5 × IQR. ns no significance; ***P ≤ 2.20e-14 (Wilcoxon rank-sum test). c Distribution of expressed genes in population accessions. Genes expression in > 95% of accessions was classified as core (orange), <5% as unique (blue), and 10-90% as other (gray). d Enriched Gene Ontology (GO) terms for core, unique, and other genes. Bar length represents fold enrichment, and color indicates −Log₁₀(P.adj) from Fisher’s exact test. e Heatmap of k-means clustered root DEGs (left), with known drought-responsive genes (center), and enriched GO terms for each cluster (right). Bar length represents fold enrichment, and color indicates −Log₁₀(P.adj) from Fisher’s exact test. f Hierarchical clustering dendrogram of population DEGs in root tissue using weighted correlation network analysis (WGCNA) (top) and heatmap of top module–trait correlations (bottom). Color represents Pearson correlation coefficients (values in squares) and asterisk indicates significance (P < 0.05, two-sided Student’s t-test). g Comparison of the gene expression CV of 110 representative accessions between two grouped modules, which were significantly associated with traits or not. Boxes indicate the interquartile range (IQR) with the median line, and whiskers extend to 1.5 × IQR. ns no significance; ***P ≤ 1.70e-15 (Wilcoxon rank-sum test). h GO enrichment analysis of the root top trait-associated modules in (f). Dot size represents fold enrichment, and color indicates −Log₁₀(P value) from Fisher’s exact test. i Comparison of the expression level of the Red module in root tissue among water conditions. Each gene in the module was plotted as a dot, and its expression levels under different water conditions were linked with gray lines. ns no significance; *P < 0.05; **P < 0.01 (Wilcoxon rank-sum test). j Co-expression network for the hub genes of the Red module in root tissue. Node (circle) size reflects the connectivity, and osmoregulatory-related genes were highlighted in blue color and red symbol.