水稻是世界上最为重要的粮食作物，也是重要的单子叶模式植物。水稻基因组中超过35%的区域由转座元件和重复序列区构成，与拟南芥不同，水稻中异染色体是不连续分布的，散在分布于基因间区。DNA甲基化、组蛋白共价修饰和小分子RNA是高等植物中三种重要的表观遗传调控的机制，它们通过直接调控水稻基因或者调控转座元件影响基因表达和植物发育。穗发育是影响水稻产量三要素的关键因素之一。当控制DNA甲基化(OsDRM2)、组蛋白甲基化(JMJ703)和小分子RNA代谢(OsDCL3a)的关键因子突变后，出现二次枝梗和穗变短等多效的发育异常的表型，直接影响水稻的产量。因此，揭示调控水稻穗发育的表观遗传机制对于产量的提高至关重要。本研究拟利用前期获得的水稻相关突变体，通过表观遗传组学研究手段，系统鉴定受DNA甲基化等表观调控的直接参与水稻穗发育位点，揭示水稻穗型发育调控的表观遗传机制，最终为水稻育种奠定理论基础。

Rice is not only the most important stable food source in the world, but also one of the best experimental systems for monocots. Approximately 35% of the rice genome is heterochromatic, composed of transposable elements (TEs) and other repeats. Unlike in Arabidopsis where repetitive sequences are clustered in the pericentromeric regions, heterochromatin is discontinuous in rice with TEs scattered throughout the intergenic regions. Epigenetic regulation pathways such as DNA methylation, histone modifications and RNA interference are critically important for rice development and yield through two major modes of action: whereas some pathways (such as H3K4 methylation) directly target rice genes, other pathways (e.g. DNA methylation and RNAi) affect gene expression by targeting nearby TEs. Panicle development is one of three critical factors to determine rice yield. Mutations in de novo DNA methyltransferase 2 (OsDRM2), H3K4 demethylase (JMJ703) and 24nt-siRNA processing enzyme (DCL3a) lead to pleiotropic developmental defects including reduced secondary branches and shorten panicles, which drastically decreases yield. It is therefore critically important to understand the functions of epigenetic pathways in regulating rice development. Here, we propose to identify genome-wide alterations in epigenetic modifications and gene expression patterns at a genome-wide level, using the mutants that we previous isolated. We are particularly interested in identifying genes for which transcriptional misregulation is directly correlated with phenotypic changes that affect yield. It is expected that the results will significantly broaden our understanding of the regulatory roles of epigenetic pathways in rice development, and provide valuable insights for the improvement of rice breeding.

水稻是世界上最重要的粮食作物，也是重要的单子叶模式植物。水稻基因组中超过35%的区域是由转座元件和重复序列构成的异染色质区。然而，与拟南芥不同，水稻异染色质区是不连续分布的，散在分布于基因间区。RNAi沉默机制、DNA甲基化和组蛋白共价修饰是高等植物中三种重要的表观遗传调控机制，它们通过直接调控基因或者调控转座元件影响邻旁基因表达来调控植物发育。植物中，来自于转座元件或重复序列的24-nt siRNA，通过指导同源位点的DNA甲基化与组蛋白H3K9甲基化修饰，不仅在转录水平上对其进行沉默，也可影响基因组中其邻近基因的表达。OsDCL3a是水稻中主要负责加工24-nt siRNA RNA的关键蛋白。实验室前期研究发现，水稻OsDCL3a RNAi株系表现出株高降低、叶夹角变大、二次枝梗数减少和穗变短等多效发育异常表型。水稻H3K4去甲基化酶JMJ703抑制逆转座元件Karma和LINE1的转座，jmj703-1突变体引起多个与水稻产量性状相关的发育缺陷，导致穗粒数变少以及种子变小等。然而，OsDCL3a和JMJ703如何通过表观遗传调控进而影响水稻重要农艺性状的分子机理尚不明确。本项目利用jmj703-1突变体和OsDCL3a RNAi植株为材料，通过收集不同穗发育时期的突变体和对照材料，进行全基因组DNA甲基化、H3K4me3和H3K9me2 ChIP-seq、小分子RNA (OsDCL3a RNAi/WT) 分析，与相同材料的RNA-seq数据进行比较，找出参与穗发育调控的靶位点并进行相关实验验证。结合第二代测序、生物信息分析技术及分子实验等方法进行研究，我们得到以下结果：水稻OsDCL3a在幼穗发育时期主要负责来源于转座子或重复序列的24-nt siRNA加工过程。受OsDCL3a调控的许多基因都参与水稻穗发育过程，并受到复杂的网络调控。依赖OsDCL3a的24-nt siRNA主要通过RdDM途径指导靶位点 (<1kb的重复序列上) 发生DNA甲基化来调控水稻发育。水稻JMJ703主要通过调节特定位点的H3K4me3修饰状态，从而调控包括与水稻穗发育相关基因的表达，最终调控水稻的穗发育过程。以上研究结果揭示了表观遗传机制在水稻穗发育中的作用方式，增进了我们在全基因组水平上对表观遗传调控水稻重要农艺性状分子机制的认知，为水稻产量改良育种提供了新的线索。