Extended Data Fig. 8: Analyses of genome-wide alteration of gene expression and DNA methylation in salt-tolerant and -sensitive TRILs in response to the stress. | Nature Plants

Extended Data Fig. 8: Analyses of genome-wide alteration of gene expression and DNA methylation in salt-tolerant and -sensitive TRILs in response to the stress.

From: Rapid formation of stable autotetraploid rice from genome-doubled F1 hybrids of japonica–indica subspecies

Extended Data Fig. 8

a, Volcano plots showing differentially expressed genes (DEGs) in the two salt-tolerant TRILs (ST-TRIL1 and ST-TRIL2) and two salt-sensitive TRILs (SS-TRIL1 and SS-TRIL2) vs. their respective mock controls. The dashed line on the x-axis indicates a significance threshold of P = 0.05, while the dashed lines on the y-axis represent log2 (FoldChange) values of ± 1. The number of DEGs is indicated above each panel, with blue and red representing down- and up-regulated genes, respectively, while black representing genes with no significant difference in expression. The x-axis represents log2 (FoldChange), and the y-axis represents the -log10 (FDR-adjusted P). b, DNA methylation patterns in all three cytosine contexts (CG, CHG, and CHH) within gene bodies, DNA transposable elements (DNA-TE), and retrotransposons (Retro-TE), and their 3-Kb upstream and downstream regions in the two salt-tolerant TRILs (ST-TRIL1 and ST-TRIL2) and two salt-sensitive TRILs (SS-TRIL1 and SS-TRIL2). The green lines represent methylation levels in the mock control, while the red lines represent methylation levels under salt treatment.

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