Integrated transcriptome and methylome analyses reveal the molecular regulation of drought stress in wild strawberry (Fragaria nilgerrensis).
Subject Categories::D710 Agricultural Biology
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AbstractBackground: Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress. Results: The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway. Conclusion: F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtleand multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor
CitationCao Q, Huang L, Li J, Qu P, Tao P, Crabbe MJC, Zhang T, Qiao Q (2022) 'Integrated transcriptome and methylome analyses reveal the molecular regulation of drought stress in wild strawberry (Fragaria nilgerrensis).', BMC Plant Biology, 22 (613)
JournalBMC Plant Biology
SponsorsThis work is supported by grants from National Natural Science Foundation of China (32060085 to Q.Q. and 32260094, 32060237 to T.Z.) and Applied Basic Research Project of Yunnan (202101AZ070001-166 to T.Z.). We would like to thank the Postgraduate Research and Innovation Foundation of Yunnan University (2021Z119 to Q.C., 2021Y428 to J.L.).
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