DNA Methylation Changes and Its Associated Genes in Mulberry (Morus alba L.) Yu-711 Response to Drought Stress Using MethylRAD Sequencing

Abstract

Drought stress remains one of the most detrimental environmental cues affecting plant growth and survival. In this work, the DNA methylome changes in mulberry leaves under drought stress (EG) and control (CK) and their impact on gene regulation were investigated by MethylRAD sequencing. The results show 138,464 (37.37%) and 56,241 (28.81%) methylation at the CG and CWG sites (W = A or T), respectively, in the mulberry genome between drought stress and control. The distribution of the methylome was prevalent in the intergenic, exonic, intronic and downstream regions of the mulberry plant genome. In addition, we discovered 170 DMGs (129 in CG sites and 41 in CWG sites) and 581 DMS (413 in CG sites and 168 in CWG sites). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicates that phenylpropanoid biosynthesis, spliceosome, amino acid biosynthesis, carbon metabolism, RNA transport, plant hormone, signal transduction pathways, and quorum sensing play a crucial role in mulberry response to drought stress. Furthermore, the qRT-PCR analysis indicates that the selected 23 genes enriched in the KEGG pathways are differentially expressed, and 86.96% of the genes share downregulated methylation and 13.04% share upregulation methylation status, indicating the complex link between DNA methylation and gene regulation. This study serves as fundamentals in discovering the epigenomic status and the pathways that will significantly enhance mulberry breeding for adaptation to a wide range of environments.

DNA Methylation in Plant Responses and Adaption to Abiotic Stresses

“…Correlation analysis has shown that DNA methylation has multiple effects on gene expression under drought stress, indicating that it directly or indirectly affects gene ex-pression through multiple regulatory pathways. Drought-tolerant plants were found to have a more stable methylome under drought conditions, with differentially methylated regions (DMRs)-related genes mainly related to the stress response, programmed cell death, and other pathways in rice (Oryza sativa L.) [26], mulberry (Morus alba L.) [27], mungbean (Vigna radiata L.) [28], and maize (Zea mays L.) [29]. For example, an in-silico genome-wide DNA methylation (5mC) analysis was performed in rice (Oryza sativa cv.…”

Multi-omics revolution to promote plant breeding efficiency

“…The MSAP and WGBS techniques are frequently used to investigate the methylation status involved in regulating gene expression in plants under environmental stresses. Epigenetic research has revealed that drought-tolerant plants exhibited a more stable methylome, with differentially methylated regions (DMRs) linking genes primarily involved in the programmed cell death and stress response in mulberry ( Ackah et al., 2022 ), mungbean ( Zhao et al., 2022 ) and rice ( Wang et al., 2016 ). Likewise, the differentially methylated epiloci (DME) identified 12 stress-related genes in rice genotypes under high temperature treatment ( Li et al., 2022b ).…”

Species-specific epigenetic responses to drought stress of two sympatric oak species reflect their ecological preferences

“…Beta-glucosidases have very diverse roles in plants: cell wall lignification and degradation, activation of several phytohormones and generation of signal molecules (Morant et al ., 2008). A role for this enzyme in DS responses has also been suggested in Arabidopsis (Han et al ., 2012) and mulberry (Ackah et al ., 2022).…”