Fig. 7: Integrated transcriptome and methylome analyses of salt-tolerant and salt-sensitive TRILs.
a, Principal component analysis (PCA) showing cluster stratification based on genomewide gene expression profiles of two salt-tolerant TRILs (ST-TRIL1 and ST-TRIL-2) and two salt-sensitive TRILs (SS-TRIL1 and SS-TRIL2) under both mock control and salt-stress conditions. PC1 and PC2 represent the first and second principal components which respectively account for 32.8% and 13.3% of the variability. The results indicate that global gene expression profiles of the two salt-tolerant TRILs are more similar to their own mock counterparts than to the other samples, while profiles of the two salt-sensitive TRILs are similarly departed from all remaining samples including their own mock counterparts. This suggests that the salt-tolerant and salt-sensitive TRILs are poles apart in their robustness to the stress. b, Venn diagrams showing the relationships of salt stress vs mock DEGs among the 4 TRILs. Numbers indicate the counts of DEGs for various comparisons. Groups I and II (top) highlight the salt stress-induced DEGs that are uniquely upregulated in each of the two salt-tolerant TRILs, while Groups III and IV (bottom) show the salt stress-induced DEGs that are uniquely downregulated in each of the two salt-sensitive TRILs. c, Expression patterns of genes of the 4 groups (I–IV) across the 4 TRILs (depicted by a heat map) and their significantly enriched gene ontology (GO) terms. d, Heat map depicting expression patterns of the 9 identified genes associated with stress-induced biotic respiratory burst in the 4 TRILs, highlighting their significant overexpression in the two salt-tolerant TRILs in response to the stress compared with the two salt-sensitive TRILs. e, Venn diagram showing an intersection analysis reflecting correlation of the Group I genes in c with CHH hypermethylation in the two salt-tolerant TRILs. f, GO enrichment analysis was conducted on 27 genes—those at the centre of the overlap across the 3 gene sets in e—that exhibited both CHH hypermethylation and upregulated expression only in the two salt-tolerant TRILs. g, Heat map depicting the comparison of CHH methylation (blue) and expression levels (red) under the salt stress vs mock conditions for genes that exhibited concomitant CHH hypermethylation and upregulated expression only in the two salt-tolerant TRILs. For c, d and g, the colour scale indicates the gene expression/methylation level normalized by Z-score.
