基于全基因组重测序探索树鼩近交衰退现象的遗传机制

Recently, we and collaborators had successfully deciphered the genome information of the Chinese tree shrew (Tupaia belangeri chinensis) and proved that tree shrew is the closest relative of primates. Meanwhile, we also elucidated the genetic basis of using tree shrew to create a viable animal model alternative to primates in biomedical research (Fan et al. 2013 Nature Communications). Although the release of Chinese tree shrew genome enables more researchers to use this species as the model animal in their studies, there are some obstacles for researchers to get a stable result when use the wild Chinese tree shrews, which have a high heterogeneous genetic background. To solve this problem, we attempted to establish the inbred strains of Chinese tree shrew with a highly identical genetic background recently. However, we encountered a serious problem of inbreeding depression during our work. Nonetheless, this offers a great opportunity and a good experimental model for us to investigate the genetic mechanism of inbreeding depression. In this study, we will perform a high throughput whole-genome sequencing for four tree shrew inbred families (including individuals belonging to F0, F2 and F3 generations), to obtain an overview of the genetic diversity of wild Chinese tree shrews as represented by F0 individuals. These data will be very useful for us to dissect the potential genetic variations that confer inbreeding depression and to guide the efforts in establishing Chinese tree shrew inbred lines. We will focus on the key regulatory genes / variants that are associated with the inbreeding depression in each family. Our results will reveal the genetic mechanism of inbreeding depression by using tree shrew as a good example, and provide important information to direct the future efforts in establishing Chinese tree shrew inbred strains.

我们前期基于树鼩基因组分析显示，树鼩与灵长类动物亲缘关系近，在较多方面具备替代灵长类动物用于生物医药研究的遗传基础（Fan et al. 2013 Nature Communications）。尽管树鼩全基因组信息的破译会大大促进其在生物医药研究中的应用，但一个瓶颈是目前用于实验的树鼩多来自野生群体，遗传异质性高，对研究结果的稳定性会造成影响。为解决树鼩个体高遗传一致性这一需求，我们近期开展了近交系培育工作，但出现严重的近交衰退，这严重阻碍了树鼩品系建立的进程。本研究拟从我们近交群体中选取4个代表性家系（含F0、F2和F3代），利用全基因组重测序技术，从全基因组水平获取F0个体代表的野生树鼩遗传多样性信息，筛查近交后代中与近交衰退关联的遗传位点，并鉴别近交衰退中的关键调控基因。研究结果可以深入地揭示近交衰退的遗传基础，也为实验树鼩的近交系亲本筛选和品系建立提供重要的指导信息。

树鼩（Tupaia belangeri chinensis）是一种与灵长类亲缘关系较近的小型哺乳动物，作为实验动物研究引起了广泛的关注。但是树鼩动物模型的创制还存在着但还存在一些瓶颈，包括1）基因组组装以及注释还需要进一步完善，以提供更加准确的遗传学信息；2）目前用于实验的树鼩多来自野生群体，群体遗传变异以及相关参数不明确，并且会对研究结果的稳定性会造成负面影响。为了满足对实验树鼩遗传背景高一致性这一需求，我们从2012年开始便开展了树鼩近交系培育工作，并发现了严重的近郊衰退现象。本研究从参考基因组，群体遗传学以及近交衰退3个方面，对树鼩的遗传学基础数据进行了改进以及详尽的解析，获得了以下成果：1）利用单分子实时（Single Molecular Real-Time, SMRT）测序技术，结合高通量染色质构象捕获技术（Hi-C技术: high throughput chromosome conformation capture）测序数据，完成了新版的树鼩基因组（KIZ version 2: TS_2.0）高精度的测序、组装和注释工作，填补了老版本基因组编码区所有缺口(gap); 2）利用野生树鼩全基因组重测序数据，详细解析了树鼩群体遗传变异以及参数，并将相关数据增加/更新到了树鼩基因组数据库 (www.treeshrewdb.org）中; 3）利用树鼩近交家系全基因组重测序数据，解析了树鼩家系近交过程中的基因组的变化，鉴定出了10个自发、早发白内障候选基因。本项目的实施产生了SCI论文4篇，培养了博士研究生1人，职称晋升2人。最为重要的是，为树鼩动物模型的创制提供了可靠的基础数据，并初步阐释了树鼩近交衰退的分子机制。