High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean

Abstract

Background Continuous cropping stress involves such factors as biological barriers, allelopathic autotoxicity, deterioration of soil physicochemical properties, and soil fertility imbalance and is regarded as a kind of comprehensive stress limiting soybean yield and quality. Genomic DNA methylation is an important regulatory mechanism for plants to resist various environmental stresses. Therefore, it is especially worthwhile to reveal genomic methylation characteristics under stress and clarify the relationship between DNA methylation status and continuous cropping stress adaptability in soybean. Results We generated a genome-wide map of cytosine methylation induced by this kind of comprehensive stress in a tolerant soybean variety (Kang Xian 2, KX2) and a sensitive variety (He Feng, HF55) using whole-genome bisulfite sequencing (WGBS) technology. The expression of DNA demethylase genes was detected using real-time quantitative PCR (qRT-PCR). The functions of differentially methylated genes (DMGs) involved in stress response in biochemical metabolism and genetic information transmission were further assessed based on Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results showed that genomic DNA demethylation was closely related to continuous cropping comprehensive stress adaptability in soybean, which was further verified by the increasing expression of DNA demethylases ROS1 and DML. The demethylation of mCpG and mCpHpG (mCpApG preferred) contexts was more critical, which mainly occurred in gene-regulatory regions at the whole-chromosome scale. Moreover, this kind of stress adaptability may be related to various stress responders generated through strengthened glucose catabolism and amino acid and fatty acid anabolism, as well as fidelity transmission of genetic information. Conclusions Genomic DNA demethylation was closely associated with continuous cropping comprehensive stress adaptability, highlighting the promising potential of screening continuous cropping-tolerant cultivars by DNA methylation index and further exploring the application of DNA demethylases in soybean breeding. Electronic supplementary material The online version of this article (10.1186/s12870-019-1670-9) contains supplementary material, which is available to authorized users.

A Comparative Analysis of Transcription Networks Active in Juvenile and Mature Wood in Populus

“…DNA methylation acts as an epigenetic mechanism to regulate gene expression in plants (Fraga et al, 2002a;Vining et al, 2012;Matzke and Mosher, 2014;Liang et al, 2019). In this study, we found that the methylation level of the auxin transport genes PILS2, AUX1, and PIN7 was different between JW and MW.…”

“…In plant, most of DNA methylation occurs at the fifth carbon of cytosine (including three cytosine contexts, CG, CHG, and CHH, where H represents A, C, or T) to form 5-methylcytosine by DNA methyltransferase (Goll and Bestor, 2005;Law and Jacobsen, 2010;He et al, 2011). Evidence indicates that DNA methylation can regulate gene expression in numerous biological processes including response to abiotic stresses (Wang et al, 2011;Dowen et al, 2012;Ci et al, 2015;Su et al, 2018;Liang et al, 2019), plant development and morphogenesis (Lafon-Placette et al, 2013), and wood formation (Wang et al, 2016). The degree of DNA methylation is also related to plant development phases.…”

A Comparative Analysis of Transcription Networks Active in Juvenile and Mature Wood in Populus

“…DNA methylation act as an epigenetic mechanism to regulate gene expression in plants [21,[66][67][68]. In this study, we found that the methylation level of the auxin transport genes PILS2, AUX1, PIN7 was different between JW and MW.…”

“…In plant, most of DNA methylation occurs at the fth carbon of cytosine (including three cytosine contexts, CG, CHG and CHH, where H represents A, C or T) to form 5-methylcytosine by DNA methyltransferase [14][15][16]. Evidence indicates that DNA methylation can regulate gene expression in numerous biological processes including response to abiotic stresses [17][18][19][20][21], plant development and morphogenesis [22] and wood formation [23]. The degree of DNA methylation is also related to plant development phases.…”

Active DNA Demethylation in Plants

“…Several studies have reported changes in DNA methylation levels and/or expression of DML homologs in different species subject to additional types of abiotic stresses such as drought [118,119,120], high or low temperatures [121,122], continuous cropping [123], and exposure to heavy metals [124] or ionizing radiation [125]. Active DNA demethylation has also been involved in the plant response to abscisic acid (ABA), a phytohormone that plays a crucial role in coordinating various signal transduction pathways during abiotic stresses.…”