基于简化基因组测序的永登七山羊遗传多样性分析

Genetic Diversity Analysis of Yongdeng Qishan Sheep Based on Specific-Locus Amplified Fragment Sequencing

旨在通过简化基因组测序(specific-locus amplified fragment sequencing,SLAF-seq)技术分析永登七山羊群体遗传多样性和群体结构,为永登七山羊作为新发现资源申报提供支撑。本研究以甘肃省4个地方绵羊群体(每个群体随机选取10只成年健康母羊)作为研究对象,利用SLAF技术检测全基因组范围内的单核苷酸多态性位点(SNPs)。通过perl编程计算观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)、香浓维纳指数(SHI)和基因多样性指数(Nei)等5个遗传多样性指标;PopLDdecay软件分析每个品种连锁不平衡情况;elgensoft软件进行主成分分析(PCA);mega x软件构建4个绵羊品种的系统发育树;structure软件进行群体遗传结构分析;gcta软件进行亲缘关系分析。结果表明,40只绵羊个体共检测到1658596个SNPs位点,其中大部分SNPs位点位于基因间区域。永登七山羊群体Ho、He、PIC、SHI、Nei指标值分别为0.082、0.277、0.221、0.411和0.305,且永登七山羊的连锁不平衡系数较高,衰减速度较慢,说明永登七山羊群体遗传多样性低;永登七山羊与滩羊、兰州大尾羊和岷县黑裘皮羊之间的遗传分化系数(F_(st))分别为0.0906、0.0980和0.1045,表明永登七山羊与其他3个品种之间分化程度较高;PCA显示,群体间聚类模式差异明显,可将永登七山羊与兰州大尾羊、滩羊和岷县黑裘皮羊区分开;系统发育树结果表明,兰州大尾羊独自聚为一大支,永登七山羊和滩羊聚为另一大支,亲缘关系较近,随后永登七山羊逐渐分离出来独自聚为一小支;structure分析表明,K=2为最优分群数,即4个群体来自两个原始祖先,随着K值逐渐增加,部分永登七山羊个体发生分离,与其他品种遗传背景差异明显。亲缘关系热图显示,每个亚群个体之间亲缘关系较低。结果提示,永登七山羊与兰州大尾羊群体遗传多样性低,永登七山羊与滩羊、兰州大尾羊和岷县黑裘皮羊之间分化明显,这为进一步挖掘永登七山羊种质资源特性提供了理论数据。

The aim of this study was to analyze the genetic diversity and population structure of Yongdeng Qishan sheep by specific-locus amplified fragment sequencing(SLAF-seq),and to provide support for the declaration of Yongdeng Qishan sheep as a newly discovered resource.Four local sheep populations(10 adult healthy ewes randomly selected from each population)in Gansu Province were taken as the research object.Single nucleotide polymorphisms(SNPs)within the whole genome were detected by SLAF technology.Five genetic diversity indexes,such as observed heterozygosity(Ho),expected heterozygosity(He),polymorphism information content(PIC),Shnnon Wiener index(SHI)and Nei diversity index(Nei),were calculated by Perl software.The linkage disequilibrium of each breed was analyzed by PopLDdecay software.elgensoft software was used for principal component analysis(PCA);mega x software was used to build phylogenetic trees of 4 sheep breeds;The structure software was used to analyze the genetic structure of the population;gcta software was used for kinship analysis.A total of 1658596 SNPs were detected in 40 sheep individuals,most of which were located in the intergenic region.The Ho,He,PIC,SHI,and Nei values of Yongdeng Qishan sheep were 0.082,0.277,0.221,0.411,and 0.305,respectively.The higher linkage disequilibrium coefficient and slower decay rate in Yongdeng Qishan sheep indicate the low genetic diversity in the population of Yongdeng Qishan sheep.The genetic differentiation coefficients(F_(st))between Yongdeng Qishan sheep and Tan sheep,Lanzhou fat tail sheep and Minxian black fur sheep were 0.0906,0.0980 and 0.1045,respectively,which indicated a high differentiation degree between Yongdeng Qi-shan sheep and the other 3 breeds.Principal component analysis showed obvious differences in clustering patterns among groups,which could distinguish Yongdeng Qishan sheep from Lanzhou fat tail sheep,Tan sheep and Minxian black fur sheep;The results of phylogenetic tree showed that Lanzhou fat tail sheep was clustered as one big branch alone,Yongdeng Qishan sheep and Tan sheep were clustered as another big branch,and the kinship was relatively close,subsequently Yongdeng Qishan sheep was gradually separated into one small branch alone.The structure analysis showed that K=2 was the optimal number of subpopulations,with 4 populations from two original ancestors.As the K value gradually increased,some QS individuals segregated and differed significantly from the genetic background of other breeds.The kinship heat map showed low kinship between individuals of each group.These results indicated that there was low genetic diversity in Yongdeng Qishan sheep and Lanzhou fat tail sheep,and that there was obvious differentiation between Yongdeng Qishan sheep and Tan sheep,Lanzhou fat tail sheep and Minxian black fur sheep.This provides theoretical data for further mining the characteristics of Yongdeng Qishan sheep germplasm resources.