基于全基因组SNP解析东北梅花鹿育成品种遗传结构研究

Sika deer is an important economic animal in China. Pilose antler as the traditional medicine application has a long history for thousands of years in China. As the number of sika deer in the wild has dropped sharply and even are endangered, the artificial domestication population has gradually replaced wild population in northeast China. After a long directional cultivation and breeding for wild population, there have been seven northeast sika deer bred varieties that have been examined and approved by the national livestock breeds authorized committee of China. Our research found that the genetic background of these bred varieties derived from two sika deer subspecies, but there is a lack of the understanding of their genetic structure. In this study, the genome-wide SNP markers will be investigated by sequencing breeding varieties genome based on the RAD-Seq technology, further the special SNP allelic loci belonged to these bred varieties will also be excavated and annotated by the biological function, which fill the gap of SNP markers of the sika deer genome. The genetic structure of bred varieties will be analyzed deeper based on the selective genome SNP loci, at the same time, the analysis of genetic relationship, genetic differences and genetic structure of these bred varieties will also be conducted. This study will provide further a scientific basis for the protection and utilization of genetic resources for bred varieties industry by revealing the characteristics of genetic structure of bred varieties.

梅花鹿作为我国重要的经济动物，其传统中药鹿茸已有几千年药用历史。由于梅花鹿野生种群数量已急剧下降，濒临灭绝，在东北地区，人工驯养梅花鹿群体已逐渐替代野生种群。经过长期闭锁繁育和定向培育，已有7个东北梅花鹿育成品种通过了国家品种审定委员会审定。申请人前期研究发现，这些育成品种遗传基础广泛，涵盖了2个梅花鹿亚种遗传背景，但对其遗传结构还缺乏系统的了解。本项目拟以东北梅花鹿育成品种为研究对象，紧密跟踪基因组学研究热点，利用RAD测序技术筛选基因组SNP位点，建立一套强有力的分子标记工具。基于该标记，利用现代群体遗传学方法以全新的视角深入解析东北梅花鹿育成品种基础遗传学数据。进一步搞清育成品种遗传多样性水平，品种特异性程度，品种间遗传分化水平、亲缘关系、遗传变异组分和整个群体遗传结构组成划分，为育成品种遗传管理、开发和持续利用提供科学依据。

梅花鹿是有经济价值的物种，包括鹿茸等身体各部位都是传统中药的组分。由于野生梅花鹿处于濒危状态并不允许捕猎，目前几乎所有的梅花鹿都被圈养在中国东北部。因此，有必要深入研究梅花鹿的遗传多样性和遗传结构，以便进行相应的遗传管理。在这个研究中，首先提取和样品纯化42个梅花鹿育成品种的DNA样品，应用6碱基酶切位点和4酶切位点（PstI 和 MseI）酶进行ddRAD-seq建库，低质量reads过滤后，共产生288 Gbp高质量数据，包括14.5亿个reads，平均每个个体4.1 Gbp。共筛选98,166（29.63%）个SNPs，平均测序深度23x。对于每个个体，SNPs数量变化从56,388 (58.62%) 到89,845 (93.41%)，测序深度从9x到50x，相应的个体SNPs频率变化从0.38/Kbp到0.71/Kbp，平均0.74/Kbp。与其它动物比较，SNPs频率稍高于麋鹿（历史上发生过严重的群体瓶颈），但低于大熊猫种群和牛育种群体，相差大约2倍。我们也发现群体里出现杂合子缺陷（FIS> 0）和低的观察杂合度，表明群体可能正在经受长期的净化选择和群体漂变。通过遗传结构分析，发现42只鹿中有6只个体（SP1，SP3，SP4，SP5，AD5和DF4）存在群体分离及子群体现象，PCA分析与其结果一致。我们也获得了高质量的SNPs探针，包括梅花鹿和马鹿特异的SNPs探针，这些探针将作为一种分子工具，能够监控梅花鹿和马鹿杂交状态，或进行品种鉴定等。