| Rice is one of the most important food crop in the world to provide food for more than half of the world’s population. Meanwhile, rice is as a ideal model crop for studying various biological phenomena. The yield of rice has been greatly improved by cultivation of hybrid rice, which exhibit heterosis. Currently, the hybrid rice used in the cultivation is generally generated by crossing within indica subspecies. Although with limited genetic difference between parents, the indica-indica rice hybrids can exhibit a high level of heterosis, suggesting that epigenetic modifications play an important role in heterosis. Therefore, study on the indica subspecies hybrid rice is meaningful uncover epigenetic mechanism of heterosis. Besides, the shoot apical meristem of rice is responsible for vegetative and reproductive growth in different developmental stages. Study the dynamic patterns of histone modifications variation in this process will be helpful for us to understand epigenetic regulation of plant cell division and differentiation.In this research, we used ChIP-seq to investigate epigenome of histone modifications H3K27me3 and H3K36me3 in three indica rice varieties Guanluai 4# (GL), Yangdao 6# (93-11), Teqing (TQ) and their two hybrids GL x 93-11 and GL x TQ, combining with DNA sequence data and RNA sequencing data. And, we studied the dynamic patterns of H3ac, H4ac, H3K4me3, H3K27me3 and H3K9mel during panicle development in Nongken 58, via immunofluorescence staining. The main results were as follows:1) For each sample, we got more than 2.4G data for each ChIP-seq of H3K27me3and H3K36me3using leaves of Guanluai4#,93-11, Teqing and their hybrids GL×TQ and GL×93-11 as materials.2) We found that there were large number of differentially modified histone modifications peaks and differentially modified genes between. Moreover, the numbers of differentially modified histone modifications peaks and differentially modified genes between parents were related with the heterosis levels of their hybrids. The hybrids of parents with greater level of epigenetic difference could exhibited higher level of heterosis.3) By comparing the DNA sequence difference between the differentially modified genes, we found that degree of histone modification difference is proportional to the density of SNPs. However, there were still half of the differentially modified genes with no SNPs detected. Thus, we speculated that the formation of the histone modifications differences are caused by both genetic difference and environmental factors.4) Allele-specific H3K27me3 and H3K36me3 in two rice indica subspecies hybrids were investigated using ChIP-seq technology, combining with DNA sequencing and RNA sequencing data. A large number of allele-specific H3K27me3 and H3K36me3 genes were detected in our study, which accounted for more than 22% and 11% of the analyzed genes, respectively.5) There was a correlation between parental histone modifications difference and hybrid allelic modification difference, which increased along with modification difference level between parents.52.48 to 70.40% of the differentially modified genes between parents can be inherited by the hybrids and formed allele-specific histone modification, while 53.45 to 66.82% of the allele-specific histone modification genes did not exist modification difference between two parents, indicating that histone modification reprogramming happened between alleles of differentially modified genes.6) The histone modification reprogramming in hybrids resulted in an increase of non-additive modified genes, which lead to an overall decline in the levels of non-additive inherited H3K27me3 and H3K36me3 modified genes in Guangluai 4#× Teqing, and an overall decline in levels of non-additive inherited H3K36me3 modified genes while an overall increase in levels of H3K27me3 modified genes in Guanluai4#× 93-11.7) We also found that the ASHM genes constituted the main part of differentially modified genes between parents and hybrids, which further lead to differentially expressed genes between parents and hybrids and resulted in heterosis.8) We also detected a correlation between allelic histone modification and allelic gene expression, and found a significant correlation between allele-specific H3K36me3 modification and allele-specific gene expression.9) The dynamic patterns of H3ac, H4ac, H3K4me3, H3K27me3 and H3K9mel were studied in rice shoot apical meristem and inflorescence using immunofluorescence technique. We found that besides the spikelet differentiation stage, tissue-specific histone modifications were widely investigated in rice vegetative and reproductive growth stages, and revealed the relationship between rice tissues and histone modifications. |
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