Dynamic Analysis Of DNA Methylation During Soybean Nodulation Development

As the world’s major oil crop,soybean is irreplaceable in the agricultural economy.The establishment of a symbiotic relationship between leguminous species and nitrogenfixing microorganisms is economical and environmentally friendly,and scientists have always wanted to interpret the symbiotic mechanism of legume species and rhizobia.The epigenetic regulation,especially the dynamic changes of DNA methylation,has a certain role in the regulation of gene expression and silencing of transposable elements during plant growth and development.No pattern of DNA methylation has been reported during soybean nodulation development.Therefore,10 points in the soybean nodulation development were selected in this study.The experimental group and the control group were inoculated with rhizobia and not inoculated,respectively.A total of 20 samples were used for WGBS,mainly includes two parts analysis of whole genome DNA methylation and differentially methylated regions,a comprehensive analysis of the dynamic changes of DNA methylation during soybean nodulation development by bioinformatics analysis.Twenty samples obtained 13 Gb-27 Gb of PE-150 bp reads after being aligned with the reference genome of soybean Wm82,respectively,covering an average of 91% of cytosine sites in the genome.The average sequencing depth was 9X.We first analyzed the dynamic changes of whole-genome DNA methylation in the dynamic process of soybean nodulation development.We found that at the 1st time point,the experimental group CG,CHG and CHH contexts were hypermethylated,while the 7-10 th experimental group CHG and CHH contexts were hypomethylation.By establishing a whole-genome DNA methylation map,it was observed that the dynamic changes in DNA methylation occur mainly in the pericentromere region where transposable elements are enriched on chromosomes.The dynamic change of DNA methylation level in the transposable elements has nothing to do with the type,position,and length of the transposable elements.It is across all transposable elements on the chromosome.The trend of methylation trend of transposition elements and their upstream and downstream components is increasing or decreasing as a whole.In the gene region,promoter and intron regions have higher methylation levels,followed by CDS regions,and UTR regions were relatively lower.The dynamic changes in gene DNA methylation levels are related to the location of the genes;methylation trends in the upstream and downstream regions of genes are subject to change,and the DNA methylation level near the gene transcription start site and transcription termination site is relatively stable.Then we identified differentially methylated regions and found that there were more DMRs at the 1st and 7th-10 th points,among which CHG-DMRs were mostly hypo-DMRs,and CHH-DMRs were mostly hyper-DMRs.Among the DMRs associated with transposable elements,CHG context low differential methylation and CHH context high differential methylation occur frequently.Among the differentially methylated genes,high differential methylation of the CHH context frequently occurs,and occurs frequently in the upstream region of the gene.Finally,we combined the data sets of differentially expressed genes to find a set of genes that were differentially methylated and differentially expressed,most of which appeared late in soybean nodulation development.Through GO enrichment analysis of early and late developmental DM-DEGs,we found early gene sets associated with redox processes,oxidoreductase activity,and heme-binding activity,and also found late-stage and nodulated nitrogen fixation,symbiotic interactions,transmembrane transport and detection of oxygen and other related gene sets.This study can provide reliable candidate genes for the study of soybean nodulation development,provide new understanding for the apparent regulation of soybean nodulation,and provide the theoretical basis of DNA methylation for future soybean breeding.