水稻泛基因组图谱的基因注释、表达分析与数据库构建

Rice is an important grain crop in China. There are many groups of Oryza sativa and its ancestral Oryza rufipogon, which are widely distributed and can adapt to a variety of ecological and agronomic conditions. The rich genetic diversity in Oryza sativa and Oryza rufipogon serves as the main sources in rice breeding，and will be a key resource for breed improvement in response to the increased food demand and environmental change. In previous work, we constructed a pan-genome dataset of O. sativa-O. rufipogon species complex through deep sequencing and de novo assembling of 66 divergent accessions. Inter-genomic comparisons identified 23 million sequence variants in the rice genome. This catalog of sequence variations includes many known quantitative trait nucleotides, and will be helpful in pinpointing new causal variants underlying complex traits. We also systemically investigate the whole set of coding genes using this pan-genome data, which reveals extensive presence and absence variation among rice accessions. .In this study, based on our previous work, we will perform intensive study in the pan genome of the cultivated rice and wild rice. By sequencing the multiple tissues of the rice varieties in the pan-genome study, we will get comprehensive gene expression data. With the whole set of the transcription data, we will provide high-confidence gene annotations of the sequenced rice varieties, which will greatly increasing the reliability of core and variable gene identification in the pan-genome. At the same time, we will also study the effects of various transposable elements in rice on the expression of core genes and variable genes, as well as the copy number variation in the rice genomic sequences of each variety. We will also construct a convenient search and display system for rice pan-genome databases on our website. This pan-genome resource will further promote evolutionary and functional studies in rice.

亚洲栽培稻及其祖先种普通野生稻丰富的遗传多样性在驯化和现代育种中发挥了重要的作用，并将成为应对粮食需求增长和环境变化，进行品种改良的关键资源。在之前的工作中，我们对一部分栽培稻和野生稻品种进行了泛基因组的初步研究。我们鉴定了水稻基因组中的2300万个序列变异，以及水稻种质间广泛的存在-缺失（PAV）变异。. 在本研究中，我们在此前的工作基础上，将对栽培稻和野生稻的泛基因组进行深入挖掘和研究。通过对之前泛基因组研究工作中的所有品种进行多个组织的转录组测序，以获取全面的基因表达数据。有了这些转录组数据，我们将对各品种水稻序列进行高可信度的基因注释，从而大幅提升对泛基因组中的核心基因和可变基因鉴定的可靠性。同时，我们也将研究水稻中各类转座元件对核心基因和可变基因的表达影响，以及各品种水稻基因组序列中的拷贝数变异。最后，我们还将构建一个方便检索的水稻泛基因组数据库检索系统。

泛基因组相对于单一参考基因组，提供了更多的在基因水平和核苷酸水平上的变异的信息，特别是对于植物基因组学来说，它能够为表型数据和基因型数据之间架起更多宝贵的联系。研究各种代表性栽培稻和野生稻的等位基因、特异基因、以及其相关联的序列变异，能够使研究人员对栽培水稻的重要农艺性状基因进行深入地解析，并对后续水稻分子育种进行优化，以应对逐渐增长的全球人口和快速变化的气候所带来的挑战。本研究依赖多组织的转录组测序以及一套整合多种方法的基因注释流程，完成了56个水稻品种的精确基因注释；以IRGSP-1.0版本的参考基因组序列，重新鉴定了所有66个品种的序列变异，使通用性得到了提高；对30个水稻品种进行了三代基因组测序和基因注释，获得了高精度的基因组序列和等位基因信息；整合了二代66个品种与三代30个品种的高质量基因组，开展了序列变异鉴定、核心-可变基因鉴定、重要农艺性状等位基因鉴定和基因组进化等方面的研究；并初步构建了水稻泛基因组数据库。上述工作产生的水稻泛基因组序列变异信息、高质量水稻核心-可变基因、重要农艺性状等位基因鉴定、水稻泛基因组数据库等研究结果，可以为水稻分子遗传学、水稻功能基因研究、以及水稻分子育种提供重要的信息和平台。