栽培稻和野生稻基因表达调控位点的全基因组鉴定与比较分析

The variances of regulatory sites in gene transcription play important role on phenotype diversity among closely related species. Genome-wide identification and comparative analysis of gene transcription regulatory sites between cultivated and wild rice is helpful to understand the evolution of rice gene function and explore the excellent wild rice gene pool which could be used in rice breeding. This proposal is planning to identify the regulatory sites on whole-genome scale from cultivated rice, African rice and wild rice with well-used epigenomics methods such as ChIP-seq and DNase-seq. Then we will select regulatory sites with variance of DNA sequence or epigenetic modifications among the species and perform an associated analysis with gene expression from RNA-seq to check the effect of variant regulatory sites. We will employ SNP data to research the evolution and putative consequence of regulatory sites among rice species. This proposal will take full advantage of multidisciplinary science between wet-lab and bioinformatics analysis, of which success will help us to understand the evolution.of non-coding functional regions, genetic and epigenetic variation putatively causing phenotype diversity among rice species and prove useful data to explore excellent wild rice genes and functional elements in genetic improvement.

基因表达调控位点的变异对近缘物种间表型的差异有着重要影响。通过对栽培稻和野生稻基因表达调控位点的全基因组鉴定与比较分析，对于探讨水稻基因的功能进化，深入挖掘野生稻优质基因资源有着重要意义。本项目利用成熟的ChIP-seq、DNase-seq等表观基因组学方法，对栽培稻日本晴和93-11、非洲稻和野生稻的基因表达调控位点进行全基因组范围的鉴定。在此基础上比较水稻品种间调控位点的DNA序列与表观遗传学修饰的差异，并利用RNA-seq技术来探讨这些差异对基因表达的影响。其次，利用水稻丰富的重测序数据，研究这些调控位点的进化规律，探讨基因表达调控位点在水稻品种间的分化及其影响。本项目将充分利用实验与生物信息分析两学科交叉的优势，其预期研究结果将增加我们对非编码功能区域进化规律的认识，有助于了解水稻品种间性状差异的来源，进一步分析和挖掘水稻基因组中的功能性元件，加速野生稻资源利用。

基因表达调控位点的变异对近缘物种间表型的差异有着重要影响,这些性状差异并不仅仅取决于基因序列的变化，非基因区调控序列也发挥着重要作用。不同遗传材料的优良性状中常常由于调控位点的变异而形成，但水稻不同近缘种间调控位点的变异及其影响尚不清楚。本研究通过对栽培稻和野生稻基因表达调控位点的全基因组鉴定与比较分析，探讨水稻调控位点的功能进化及其影响。通过利用ATAC-seq、ChIP-seq等表观基因组学方法，整合或构建了日本晴、93-11、非洲稻等基因表达调控位点的全基因组图谱，发现这些水稻近缘物种间调控位点的基因组序列整体趋向于保守，证明这些位点具有生物学功能而受到进化上的选择。但非洲稻与栽培稻之间调控位点的分布有明显的差别，非洲稻80%的调控位点分布于基因间区，而日本晴与93-11的调控位点有42%-47%位于基因间区，展示了这些材料间调控位点的变异性。物种特异性的调控位点与转录调控、底物特异的转运蛋白等功能密切相关。本研究初步探讨了基因表达调控位点在水稻品种间的分化及其影响，有助于了解水稻品种间性状差异的来源，为进一步分析和挖掘水稻基因组中的功能性元件打下了良好基础。