Integrated methylome and transcriptome analysis unravel the cold tolerance mechanism in winter rapeseed(Brassica napus L.)

Abstract

Background Cytosine methylation, the main type of DNA methylation, regulates gene expression in plant response to environmental stress. The winter rapeseed has high economic and ecological value in China's Northwest, but the DNA methylation pattern of winter rapeseed during freezing stress remains unclear. Result This study integrated the methylome and transcriptome to explore the genome-scale DNA methylation pattern and its regulated pathway of winter rapeseed, using freezing-sensitive (NF) and freezing-resistant (NS) cultivars.The average methylation level decreased under freezing stress, and the decline in NF was stronger than NS after freezing stress. The CG methylation level was the highest among the three contexts of CG, CHG, and CHH. At the same time, the CHH proportion was high, and the methylation levels were highest 2 kb up/downstream, followed by the intron region. The C sub-genomes methylation level was higher than the A sub-genomes. The methylation levels of chloroplast and mitochondrial DNA were much lower than the B. napus nuclear DNA, the SINE methylation level was highest among four types of transposable elements (TEs), and the preferred sequence of DNA methylation did not change after freezing stress. A total of 1732 differentially expressed genes associated with differentially methylated genes (DMEGs) were identified in two cultivars under 12 h and 24 h in three contexts by combining whole-genome bisulfite sequencing( and RNA-Seq data. Function enrichment analysis showed that most DMEGs participated in linoleic acid metabolism, alpha-linolenic acid metabolism, carbon fixation in photosynthetic organisms, flavonoid biosynthesis, and plant hormone signal transduction pathways. Meanwhile, some DMEGs encode core transcription factors in plant response to stress. Conclusion Based on the findings of DNA methylation, the freezing tolerance of winter rapeseed is achieved by enhanced signal transduction, lower lipid peroxidation, stronger cell stability, increased osmolytes, and greater reactive oxygen species (ROS) scavenging. These results provide novel insights into better knowledge of the methylation regulation of tolerance mechanism in winter rapeseed under freezing stress.

DNA methylation-mediated ROS production contributes to seed abortion in litchi

“…Therefore, we propose that DNA methylation-mediated excessive ROS accumulation in 'NMC' disrupts intracellular ROS homeostasis during early embryo development, ultimately leading to seed abortion. Recent reports have highlighted the critical roles of DNA methylation-mediated ROS homeostasis in various aspects of plant development and stress response, including salt stress (Chen et al 2015 ; Hu et al 2021 ), heat stress (Ma et al 2018 ; Sakai et al 2022 ; Zhu et al 2021 ), chilling/freezing stress (Guo et al 2019 ; Zheng et al 2022 ), and fruit ripening (He et al 2020 ). Based on our findings, we suggest that DNA methylation-mediated ROS homeostasis also plays a role in seed development in litchi.…”

“…Mutations in MSD , such as the oiwa mutant, disrupt ROS homeostasis, resulting in high ROS levels in the embryo sac and leading to sterility or arrested embryogenesis (Victoria Martin et al 2013 ). Recently, there have been reports highlighting the crucial roles of DNA methylation-mediated ROS homeostasis in various aspects of plant development and stress response, including salt stress (Chen et al 2015 ; Hu et al 2021 ), heat stress(Ma et al 2018 ; Sakai et al 2022 ; Zhu et al 2021 ), chilling/freezing stress(Guo et al 2019 ; Zheng et al 2022 ), and fruit ripening (He et al 2020 ). For instance, the application of 5-azaC, an inhibitor of DNA methyltransferase, has been found to enhance the rates of superoxide anion (O 2 − ) production, thereby contributing to the ripening of berry fruits (Guo et al 2019 ).…”

Integration of Metabolome and Transcriptome Reveals the Major Metabolic Pathways and Potential Biomarkers in Response to Freeze-Stress Regulation in Apple (Malus domestica)

“…Freezing stress responses are regulated by a complex interplay of genes and environmental factors, and involve a variety of physiological pathways [ 61 , 62 , 63 , 64 ]. In this study, we identified 12 pathways that included 16 DAMs and 65 DEGs through combined transcriptome and metabolome analysis.…”

An emerging role beyond genetics: DNA methylation in horticultural quality shaping

“…Besides, peach mealiness is another major issue of CI, which highly reduces consumer acceptance and market value. The related epigenetic mechanisms have been recently discovered: 144 mCHH-DMRs amounted most both in normal and mealy fruit after 30-day storage at 0 °C and most DMRs were not de novo developed during the cold storage, they just underwent changes of methylation degree. Further, the potential mealiness-regulating candidates, Cytochrome P450 82A (CYP82A) and UDP-arabinose 4 Epimerase 1 (UA4E1), were expression-downregulated and promoter-hypermethylated in mealy fruit.…”