Analysis Of Maize Epigenome

Epigenetic modifications play important roles in plant development. Firstly, gene imprinting is a phenomenon that controlled by epigenetic modification. Imprinted genes are important for seed development. Secondly, epigenetic variations could be the substrates of artificial selection in the breeding process. Maize, as one of most important crops aroud the world, provides us a model system to investigate epigenetic regulation of imprinted genes and the epigenetic variations and their association with gene expression, which is helpful to improve the ability of improving crops. Although there are some models that explain epigenetic regulation of imprinted genes, many questions are still not answered. Moreover, extensive genetic variations occurred during the modern maize breeding process, but epigenetic variations are not explored.In this study, we first profile maize epigenome in B73inbred. Then, imprinted genes were divided into subgroups by using RNA-seq data from various tissues. Each subgroup of imprinted genes was compared with parental-of-origin differentially methylated regions (pDMR) and parental-of-origin allele-specific H3K27me3(pH3K27me3). Results showed that maternally expressed imprinted genes (MEGs) and paternally expressed imprinted genes (PEGs) had different patterns of pDMR and pH3K27me3. Allele-specific expression of MEGs was not directly related to pH3K27me3, and only a subset of MEGs was associated with maternal-specific DNA demethylation, which was primarily located in the upstream and5’portion of gene body regions. In contrast, allele-specific expression of a majority of PEGs was related to maternal-specific H3K27me3, with a subgroup of PEGs also associated with maternal-specific DNA demethylation.We further dissected epigenetic variation of DNA methylation by analyzing MethylC-seq data of four Chinese elite inbred lines with know pedigree information. First, differentially methylated sites (DMSs) were identified to estimate the rate of epimutation. Results showed that the order of magnitude of DNA methylation variation was10-5, which was3-4orders of magnitude high than that of DNA sequence mutation. By analyzing the characteristics of epimutation sites, DMSs were found to be enriched in genic regions rather than transposable element regions. Additionally, DMSs were not randomly distributed across the genome, and they tend to clusters. Detailed analysis of DMSs showed that characteristics of sites of DNA methylation variations resembled that of DRM1/2targets, which was involved in RdDM (RNA-directed DNA methylation) pathway in Arabidopsis. Previous study showed that targets of RdDM pathway were subjected to chromatin states. These results together suggested that chromatin state is an important factor that affects stability of DNA methylation. There are three possibilities that could lead epigenetic variations during breeding process:1) spontaneous-arising;2) combinations of different alleles through recombination;3) paramutation in the heterozygotes. Results showed that there were50%DMSs that were spontaneous-arising, and50%DMS that were caused by paramutation or distant trans-genetic variations. Moreover,161differentially expressed genes (DEGs) were identified, and were found to significantly be associated with promoter and genic DNA methylation variations. Functional annotation of the DEGs showed some of them may invovled in important developmental process, probably affecting phenotypes.Results showed:1) only one subgroup of MEGs (or PEGs) were related to pDMR, whereas nearly all PEGs were related to pH3K27me3, these relationships were determined by the expression patterns of imprinted genes;2) epigenetic variations did occur in some special regions during the breeding process and were potential substrates of artificial selection. Correlation between pDMR and pH3K27me3and imprinted genes were helpful to understand the epigenetic regulation of imprinted genes, which have great significance to control seed development. Additionally, analysis of epigenetic variations during breeding process provides us new avenues for crop improvement.