The strength and pattern of selection on heritable gene expression.

a, The O. sativa ssp. indica populations showed higher average fitness in the normal (blue) and saline (pink) field (two-tailed paired t-test P = 1.658 x 10-8) and fitness further showed a significant effects of genotype (G) and environment (E); genotype × environment (G×E) was not significant. Analysis of variance (ANOVA) [G and E (P < 0.001), G×E (P = 0.49)]; n=130 accessions. b, Broad-sense heritability (H2) distribution of Oryza sativa spp. indica transcripts. Two-way ANOVA, genotype FDR-adjusted q < 0.001, n = 130 accessions. c-e, The strength of linear selection |S|, linear selection differentials (S), and quadratic selection differentials (C) for genome-wide gene expression in normal (blue) and saline (pink) conditions. f, Conditionally neutral (light gray), and antagonistically pleiotropic transcripts (blue and magenta represent beneficial expression in normal and saline conditions, respectively). Black represents transcripts experiencing selection in the same direction in both environments (expression is beneficial or detrimental in both environments).

Summary statistics of selection on gene expression.

Biological processes and pathways with differential responses to selection under saline conditions.

a, GO biological processes under stronger selection in normal (blue) and saline conditions (pink). b, Linear selection gradients (β), along with direct (D), indirect (I) and total (T) responses to selection on suites of transcripts in normal (blue) and saline conditions (pink).

Salinity stress induces regulatory decoherence.

a, Pearson correlation coefficients between pairs of transcripts (|S| > 0.1 and expression greater than 0 in at least 50% individuals) in normal (x-axis) and saline conditions (y-axis). Pink and blue represent pairs with correlation stronger in saline and normal conditions, respectively; gray represents correlation that is not significantly different between conditions. b, Enrichment of transcripts with significant pairs greater than the median (median significant pair per transcript = 12, n = 853) involved in regulatory decoherence post salt exposure.

Traits with different selection profiles under salt stress.

Linear (β) and quadratic (γ) selection gradients on the traits LOP (leaf osmotic potential), Chl_a (chlorophyll a content), and FT (flowering time). Error bars represent mean ± SE; dots and asterisks indicate significance of selection-gradient at two-sided unadjusted P < 0.1 and P < 0.05.

Genetic architecture of gene expression variation during salt stress.

a, Effect sizes of genes with both cis and trans factors under saline conditions showing excess of reinforcing cis-trans (teal) in comparison to compensating cis-trans (salmon). b, Inter-varietal variation in gene expression for genes under compensating control is significantly lower than for those under reinforcing control; one-sided Mann-Whitney P = 0.0028. c, Frequency distribution of MAF (minor allele frequency) for cis-eQTLs (blue) and trans-eQTLs (yellow) in saline conditions against the genome-wide background (gray).