高粱种子发育的表观遗传学调控机制研究

Seed development is an important stage in the plant life cycle which directly impacts crop yield. There is now ample evidence showing that epigenetic regulation via DNA methylation, histone modification and siRNAs plays an essential role in plant seed development. Genomic imprinting primarily occurs in the endosperm in flowering plants. Our previous studies have shown that extensive DNA methylation changes occurred in developing endosperm and which were correlated, at least in part, with tissue-specific gene expression. However, the epigenetic mechanism underlying this relationship remains largely unexplored. This project will investigate genome-wide DNA methylation, H3K27me3 and siRNA dynamics using next-generation Illumina HiSeq technique in developing seed tissues (endosperm and embryo) of a pair of F1 reciprocal hybrids and their parental pure lines of sorghum, and will further analyze the epigenetic regulation networks underlying both endosperm and embryo development. We will also quantify gene expression levels using RNA seq, identify imprinted genes, and will use computational tools to identify the pathways regulated by genomic imprinting. Comparisons of imprinted genes between maize, rice and Arabidopsis will help clarify how genomic imprinting has evolved in phylogenetically closely-related as well as disparate flowering plants. The research we propose will advance understanding of epigenetic mechanisms that regulate plant seed development, and might provide new clues to crop improvement.

种子发育是植物生命周期中的关键阶段，也直接关系到作物的产量形成。DNA甲基化、组蛋白修饰和siRNAs等表观遗传修饰在种子发育过程中起重要调控作用。胚乳是开花植物发生基因组印迹的主要部位。前期研究表明，高粱胚乳发育过程中经历全基因组范围广泛的去甲基化，并与部分胚乳组织特异性基因表达相关，但其具体表观遗传调控机理还不清楚。基于此，本研究将利用Illumina高通量测序及RNAi，测定高粱F1正反杂交种及其纯系亲本种子发育初期胚乳和胚全基因组DNA甲基化、H3K27me3和siRNAs，分析这些表观遗传修饰在胚乳、胚发育过程中的调控网络。同时，测定基因表达量，识别印迹基因，并通过生物信息学分析识别基因组印迹的调节途径，通过与玉米、水稻和拟南芥印迹基因的比较分析，探讨印迹基因与基因组进化的关系。通过本研究，将初步阐明种子发育的表观遗传调控模式，为作物育种和产量形成研究提供新的理论基础和启示。

本项目按研究计划完成。获资助后按照计划任务书提出的4项研究内容开展了研究工作，取得了多项有新意的研究结果。主要发现点如下：（1）利用Illumina高通量测序技术完成了高粱F1正反杂交种授粉后14d胚、胚乳全基因组DNA胞嘧啶甲基化组，分析了不同基因型之间、不同种子器官（胚和胚乳）之间的DNA甲基化水平和模式差异。（2）完成了胚乳全基因组RNA-seq，发现了101个高粱胚乳印迹基因，包括85个母本印迹基因（MEGs）和16个父本印迹基因（MEGs），并采用焦磷酸测序技术进行了实验验证。（3）测定了高粱胚、胚乳全基因组siRNA，鉴定出组织特异表达或差异表达的siRNA，分析了siRNA对基因表达的调控作用。（4）揭示了胚、胚乳全基因组H2K27me3模式，主要分析了其等位基因的父、母源位点的H2K27me3状态。另外，还探讨了不同基因型和不同组织中基因可变剪接特征及其与印迹表达之间的相关关系。本项目的研究结果加深了人们对种子发育过程中基于DNA甲基化修饰的表观遗传学调控机制的原有认识，并可能为作物的遗传改良提供有价值的参考依据。本项目完成了既定计划和指标，发表标注本项目第一资助的SCI论文2篇、国内核心期刊1篇，培养研究生3人。