【作者】 王睿；

【导师】 姜雨；

【作者基本信息】 西北农林科技大学 ， 农业硕士（专业学位）， 2022， 硕士

【摘要】 遗传变异图谱是群体遗传分析和功能研究的重要基础,因此构建高质量绵羊的遗传变异图谱将促进对其遗传多样性和育种历史更全面的了解,推动绵羊育种产业的发展。目前,绵羊上利用最新三代技术组装高质量参考基因组,家养绵羊及其野生近缘种的基因组重测序数据也得到大量释放,这为绵羊变异图谱构建提供了重要的数据支持。本研究收集分析了已经发表的家养绵羊和野生绵羊的重测序数据共计1116个,包括绵羊属的7个野生近缘种和135个家养绵羊品种,完成了群体遗传结构的分析,构建了绵羊基因组变异数据库,计算了39个绵羊品种的近交系数,并筛选了与肉用性状相关基因。具体结果如下:1.本研究通过1116只绵羊的重测序数据比对,鉴定到了~83百万个SNPs和~7百万个In Dels。系统发育树和PCA结果显示,野生近缘种和家养绵羊分离,家养绵羊又可分为欧洲、美洲、非洲和亚洲四个类群。此外,本研究发现绵羊不同品种可形成较好的聚类,个别品种聚类和采样地的不一致反映了绵羊近期的迁移、引种和选育历史。2.本研究构建了世界绵羊变异数据库Sheep Var(http://animal.nwsuaf.edu.cn/code/index.php/sheepvar),根据前期遗传结构的分析结果,计算每个变异位点在不同群体和品种中的频率分布,使用动态交互表格展示遗传变异信息,引入Ec harts地图工具映射变异频率,便于用户筛选候选变异位点,可以有效帮助用户扩大验证群体,获取更加精确的候选位点。Sheep Var还加入了532 GWAS和2274 QTLs数据,方便通过基因检索实现性状查询。此外,本研究还提供了Bla st和Blat等工具用于在线进行序列分析,并开发了Lift Over在线坐标转换工具实现绵羊不同参考基因组之间的坐标转换。3.对六个类群绵羊品种的长纯合片段(ROH)和近交系数(FROH)的检测和计算发现,欧洲群体的ROH数目及FROH值大都高于其他地区的绵羊群体,表明对欧洲地区绵羊品种的人工选择强度高于其他地区,这可能与欧洲规范的绵羊育种计划和方案有关。其他大量高度选育的品种平均近交系数均高于0.04,高于其他品种绵羊。本研究的39个绵羊品种的近交系数为预防绵羊育种近交衰退提供了数据参考。其中,近交系数的结果显示Ouessant sheep平均近交系数为0.232,地理隔离可能是导致该品种近交水平高主要原因。本研究选取高度选育的五个肉用绵羊品种,通过Fst和πratio进行选择信号计算,结果显示五个品种共享的受选择区域有123个,覆盖156个基因,其中31个基因与之前报道的生长性状相关的QTLs或GWAS区间重合。此外,本研究鉴定到不同肉用品种特异的受选择区域,并分别鉴定到杜泊绵羊38个、无角陶赛特绵羊48个、萨福克绵羊54个、白萨福克绵羊36个和特克塞尔绵羊42个与QTLs和GWAS区间重合的基因。其中,在无角陶赛特绵羊中鉴定到可能影响总脂肪面积的GHR基因。综上,本研究通过收集分析1116只绵羊的重测序数据,构建了世界绵羊综合变异数据库,为绵羊育种工作者筛选育种候选靶点,有效进行扩群研究提供了便利。此外,本研究的近交系数可作为绵羊育种工作的重要参考,受选择分析鉴定到体重、体型和脂肪沉积等性状相关的候选基因,可用于肉用绵羊品种的选种育种工作。更多还原

【Abstract】 A genetic variation map is an important prerequisite for population genetic analysis and functional research.Therefore,building a high-quality genetic variation map of sheep will promote a more comprehensive understanding of their genetic diversity,research on sheep breeding history,and the development of the sheep breeding industry.At present,high-quality reference genomes are assembled on sheep using the latest three-generation technologies,and the genome resequencing data of domestic sheep and their wild relatives have also been released in large quantities,which provides important data support for the construction of variation map.In this study,a total of 1116 published resequencing data of domestic and wild sheep were collected and analyzed,including 7 wild relatives and 135 domestic sheep breeds of ovis,completing analysis of the population genetic structure,constructing the sheep variation database,calculating the inbreeding number of 39 sheep breeds and screening some meat trait-related genes.The results are as follows:1.In this study,～83 M SNPs and ～7 M In Dels were identified by aligning the resequencing data of 1116 sheep.The results of the phylogenetic tree and PCA showed that wild relatives and domestic sheep were significantly separated,and domestic sheep could be divided into four groups: Europe,America,Africa,and Asia.In addition,this study found that the same species clustered together,and the inconsistency between cluster and sample of individual breeds reflect the recent breeding history of sheep.2.This study constructed the world sheep variation database,Sheep Var(http://animal.nwsuaf.edu.cn/code/index.php/sheep Var).The frequency distribution of each variation in different groups and breeds was calculated according to the analysis results of the previous genetic structure.This database employs dynamic interactive tables to display genetic variation information and introduces the Echarts map tool to map variation frequency,which is convenient for users to screen candidate variant sites,which can effectively help users expand verification groups and obtain more accurate candidate site.Sheep Var also adds 532 GWAS and 2274 QTLs to facilitate trait queries through gene retrieval.In addition,this study also provided online sequence analysis tools such as Blast and Blat and developed the Lift Over online coordinate conversion tool to realize coordinate conversion of different reference genomes of sheep.3.The detection of the long homozygous fragment(ROH)and calculation of inbreeding coefficient(FROH)of six populations found that the number of ROH and FROH values of European populations were higher than those of sheep populations in other regions,which indicated that the intensity of artificial selection in Europe was higher than that in other regions.This is probably relevant to European normative sheep breeding programs.The average inbreeding coefficients of other highly selective breeds were all higher than 0.04,which was higher than that of other breeds of sheep.The inbreeding coefficients of 39 sheep breeds in this study provide data reference for preventing inbreeding depression in sheep breeding.The results of the inbreeding coefficient showed that the average inbreeding coefficient of Ouessant sheep was 0.232,and geographical isolation may be the main reason for the high inbreeding level of this breed.In this study,five highly selective bred meat sheep breeds were selected,and the selection signal was calculated by Fst and π ratio.The results showed that the five breeds shared 123 selected regions,covering 156 genes,of which 31 were overlapped with QTLs or GWAS associated with previously reported growth traits.For example,ECH1 gene plays a role in fatty acid oxidation pathway.In addition,this study identified selected regions specific to different meat breeds and identified 38 genes in Dorper sheep,48 genes in Poll Dorset sheep,54 genes in Suffolk sheep,36 genes in White Suffolk sheep and 42 genes in Texel sheep that overlap with QTLs and GWAS intervals.Among them,GHR genes that may affect the total fat area were identified in Poll Dorset sheep.In conclusion,by collecting and analyzing the resequencing data of 1116 sheep,this study constructed a comprehensive global sheep variation database,which provided convenience for sheep breeders to screen candidate breeding targets and conduct effective herd expansion research.In addition,the inbreeding coefficient of different breeds in this study can be used as an important reference for sheep breeding work.Candidate genes related to body weight,body shape,and fat deposition were identified by selection analysis,which can be used for the selection and breeding of meat sheep breeds.更多还原