SVs have a widespread impact on gene expression. (A) SVs have an impact on gene expression in sorghum leaf across all developmental stages. The differentially expressed gene (DEG) analysis was performed by comparison of expression profiles in RTx430, Tracy, and Ramada with the expression profile in Tx623 (as control) in leaf tissue at three development stages. The blue and pink bars represent the percentages of SV-associated and non-SV-associated DEGs, respectively. The P-values on the top of SV-associated DEG bars, which were adjusted using Bonferroni correction, indicate the hypergeometric testing results for enrichment of DEGs in SV-associated genes. DEGs were significantly enriched in SV-associated genes, with SV-associated DEGs increased 1.1%∼4.3% compared with non-SV-associated DEGs in different sorghum lines. Only the results in leaf tissue were showed here. Similar results were also observed in stem tissue (see Supplemental Fig. S11A,B). (B) SV-associated DEG count changed according to different impact predictions. Different classes of variant effects were predicted by SnpEff (v5.0) (Cingolani et al. 2012). The vertical axis showed the SV-associated DEG count. The blue, pink, and green bars represent the DEG counts associated by high impact SVs (impact_HIGH), moderate impact SVs (impact_MODERATE), and low impact SVs (impact_LOW), respectively, in leaf tissue of different sorghum lines in three developmental stages (preflower, flower, and milk). The P-values show the significance levels between groups (see Methods). Differential DEG counts between “impact_HIGH” and “impact_MODERATE” were all statistically significant. The significant level of DEG counts between “impact_MODERATE” and “impact_LOW” varied depending on lines and stages. In general, higher impact SVs associated more DEGs.
