Multi‐Omics Analysis Reveals the Mechanism Underlying the Edaphic Adaptation in Wild Barley at Evolution Slope (Tabigha)

Abstract

At the microsite "Evolution Slope", Tabigha, Israel, wild barley (Hordeum spontaneum) populations adapted to dry Terra Rossa soil, and its derivative abutting wild barley population adapted to moist and fungi-rich Basalt soil. However, the mechanisms underlying the edaphic adaptation remain elusive. Accordingly, whole genome bisulfite sequencing, RNA-sequencing, and metabolome analysis are performed on ten wild barley accessions inhabiting Terra Rossa and Basalt soil. A total of 121 433 differentially methylated regions (DMRs) and 10 478 DMR-genes are identified between the two wild barley populations. DMR-genes in CG context (CG-DMR-genes) are enriched in the pathways related with the fundamental processes, and DMR-genes in CHH context (CHH-DMR-genes) are mainly associated with defense response. Transcriptome and metabolome analysis reveal that the primary and secondary metabolisms are more active in Terra Rossa and Basalt wild barley populations, respectively. Multi-omics analysis indicate that sugar metabolism facilitates the adaptation of wild barley to dry Terra Rossa soil, whereas the enhancement of phenylpropanoid/phenolamide biosynthesis is beneficial for wild barley to inhabit moist and fungi pathogen-rich Basalt soil. The current results make a deep insight into edaphic adaptation of wild barley and provide elite genetic and epigenetic resources for developing barley with high abiotic stress tolerance.

Dynamic DNA methylation changes reveal tissue-specific gene expression in sugarcane

“…Compared with unexpressed genes, CG gene body methylation levels of expressed genes were higher than those of unexpressed genes, whereas non-CG methylation was lower in expressed gene body regions than that in unexpressed genes. Consistent with previous studies (Cai et al, 2021;Xu et al, 2018), DNA methylation levels at the transcription start site (TSS) and transcription end site (TES) were significantly reduced in expressed genes compared with those in unexpressed genes. Additionally, a significant increase in CHH promoter methylation was observed in the expressed genes.…”

“…Wang et al, 2015;Xu et al, 2018;. CG methylation of gene body regions is always positively correlated with gene expression (Cai et al, 2021;H. Wang et al, 2015;Xu et al, 2018), but we observed that the highest-expressed genes did not have the highest CG methylation levels in the gene body (Figures 4 and S11).…”

“…Cumulative evidence has shown that methylation of the gene body and flanking regions is involved in regulating gene expression (Cai et al, 2021;H. Wang et al, 2015;Xu et al, 2018;.…”

“…Wang et al, 2015;Xu et al, 2018;. CG methylation of gene body regions is always positively correlated with gene expression, whereas non-CG methylation of gene body regions negatively correlates with gene expression (Cai et al, 2021;H. Wang et al, 2015;Xu et al, 2018).…”

“…Wang et al, 2015;Xu et al, 2018). In addition, recent studies have shown that CHH methylation of promoter regions could promote adjacent gene expression (Cai et al, 2021;Gent et al, 2013;Xu et al, 2018). To explore the relationship between DNA methylation and gene expression in sugarcane, we first performed RNA-seq of the same tissues for DNA methylation analysis.…”