Tissue-specificity And Genome Interaction Of Epigenetic Modifications In Soybean(Glycine Max(L.)Merr.)

Epigenetic modifications play an important role in maintaining the stability of eukaryotic genome and regulating gene expression,which is involved in all aspects of biological growth and development.Soybean is an staple food and oil crop originated in China,but little is known about its characteristics of epigenetic modifications.In this study,we systematically analyzed the epigenetic modification of soybean in early development from three aspects:Identification of major epigenetic odifications;Tissue specific epigenetic modification difference;Epigenetic modification changes in hybrid.For this purpose,using Williams82(W82)and Jack as well as the F1 progeny of reciprocal crosses were used as materials.We systematically established transcriptome,DNA methylome,H3K4me3,H3K27me3,H3K36me3,H3K9me2,small RNA and other omics data.Furthermore we explore the internal relationship between epigenetic modification(histone modification and DNA methylation),and deeply analyzed its role in gene expression regulation and development,tried to answer whether epigenetic modification are affected by genetic variation,whether there is any tissue specificity,whether epigenomic motification is heriable.The main results are as follows:1.The hybrid progeny had obvious growth advantage phenotype.Hybrid progenies had higher fresh and dry weight,larger leaf area and longer hycotyl length than their parents.2.H3K4me3,H3K27me3,DNA methylation,and small RNAs are key epigenetic modifications in soybeans.There are significant differences in peak numbers,length,and gene expression for the four histone modifications,including H3K4me3,H3K36me3,H3K27me3,H3K9me2 in soybean leaves;Based on the characteristics of H3K4me3,H3K36me3,H3K27me3,H3K9me2,DNA methylation,and small RNAs in the whole genome,the genome is divided into five chromatin states: Active,Bivalent,Repressive,RNA-directed DNA methylation(Rd DM),and Uncategory.Active is mainly characterized by H3K4me3 and H3K36me3,Bivalent by H3K4me3 and H3K27me3,repressive by H3K27me3,Rd DM by H3K9me2,high levels of DNA methylation,and si RNA enrichment,and uncategory has higher levels of CG methylation and is often located in the gene body region.Comparing the differences between the four chromatin states(Active,Bivalent,Repressed,Rd DM)in W82 and Jack,it was found that the Rd DM has more SNP sites,indicating that heterochromatic regions are more susceptible to genetic differences.Therefore,H3K4me3,H3K27me3,DNA methylation,and small RNAs represent the main chromatin states in soybeans and are key epigenetic modifications.Next,we focus on these four types of epigenetic modifications to further explore the dynamic changes in tissue specificity and genomic interaction after soybean hybridization.3.H3K4me3 determines tissue specificity.The comparative analysis of tissue-specific expression and epigenetic modification showed that H3K4me3 was involved in the specificity of soybean tissues,and was divided into three types of modification sites: meristem,vascular tissue and leaf tissue.Among them,the meristem specificity was mainly reflected in the absence of H3K4me3 modification.It is mainly composed of pathways involved in biotic and abiotic stress responses.Vascular tissue-specific,showing a high level of H3K4me3 modification,mainly involved in vascular tissue and cell wall synthesis.Leaf tissue-specific,with moderate levels of H3K4me3 modification,is primarily involved in photosynthesisrelated pathways.Compared with H3K4me3,H3K27me3 had no obvious tissue specificity.By analyzing the different types of DNA methylation,no obvious tissue specificity was found,but the level of DNA methylation was different among different tissues,and the hypocotyl had a higher level of CHH type DNA methylation.4.Hybridization results in distinct changes in genome-wide epigenetic modifications.After comparation of DNA methylation bwtween the progeny and parent,we found that the methylation level of the progeny of four tissue in the whole genome is obviously higher than that of the parent,in which CG and CHG are weakly increase at the chromosome level,while CHH is obviously enhanced,especially in TE rich region,Since there was a weak increase in the gene region and no significant change in the small RNA,we checked the the expression of CMT2 and obtained the higher expression level of CMT2 in F1 than parents,indicating that the increase of CHH was mainly related to CMT2 pathway.In the meristem,the number of H3K4me3 and H3K27me3 modifications in the progeny increased significantly,and the number of H3K4me3 modifications in the leaves increased slightly,while decreased significantly in the progeny of hypocotyls and epicotyls.In leaves,epicotyl and hypocotyl,the number of H3K27me3 modifications in the progeny of the hybrid parents did not change significantly.We systematically identified the types of histone modification interactions,in meristem,H3K4me3 and H3K27me3 were dominated by hybrid vigor(Hv).In leaf,H3K4me3 was dominated by Hv.In epicotyls and hypocotyls,H3K4me3 was dominated by hybrid vigor(Hn).The H3K27me3 in leaves,epicotyl and hypocotyls were mainly non-interaction(NI),which was related to the stable inheritance.The results showed that H3K27me3 had more stable transgenerational inheritance,which was further verified by F2 generation.To summary,this study systematically analyzed the characteristics of the main epigenetic modifications in the early apical tissues of soybean,answered the scientific questions such as the relationship between epigenetic modification and genetic variation,tissue specificity,and heritability of plant epigenetic modifications,and laid a foundation for further analysis of the regulation mechanism of soybean epigenetics and epigenetic breeding.