基于简化基因组测序评估小骨山羊群体遗传多样性和群体结构  

Population Genetic Diversity and Population Structure Analysis of Small-boned Goat Based on Specific-Locus Amplified Fragment Sequencing

作　　者：王浩宇 马克岩 李讨讨 栗登攀 赵箐 马友记[1] WANG Haoyu;MA Keyan;LI Taotao;LI Dengpan;ZHAO Qing;MA Youji(College of Animal Science and Technology,Gansu Agricultural University,Lanzhou 730070,China)

机构地区：[1]甘肃农业大学动物科学技术学院,兰州730070

出　　处：《畜牧兽医学报》2025年第3期1170-1179,共10页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：甘肃省2022年农业种质资源普查项目(GSCQ-2022-03);农业农村部政府购买服务合同项目(19221204);中央财政农业产业发展资金项目“甘肃省羊遗传资源普查”(CFCAD2023-019)。

摘　　要：旨在分析小骨山羊群体的遗传多样性,为明确其是否为新种质资源提供理论依据。本研究以小骨山羊、河西绒山羊和内蒙古绒山羊(阿尔巴斯型)为研究对象,每个群体选取20只成年健康母羊,使用SLAF-seq技术检测全基因组范围内核苷酸多态性(SNPs)。遗传多样性通过使用perl编程计算次要等位基因频率(MAF)、观测杂合度(Ho)、期望杂合度(He)、基因多样性指数(Nei)、多态信息含量(PIC)和香浓维纳指数(SHI);使用PopLDdecay进行连锁不平衡分析(LD);使用VCFtools计算群体分化指数(Fst)。通过使用EIGENSOFT进行主成分分析(PCA)、MEGA X构建NJ树和ADMIXTURE进行群体结构分析。通过使用PLINK计算IBS距离、使用GCTA计算亲缘关系并构建矩阵。结果,共检测到5253776个SNPs,大部分位于基因间区。小骨山羊除Ho(0.197)外,其余遗传多样性指标最高。小骨山羊平均MAF、He、Nei、PIC、SHI分别为0.216、0.302、0.312、0.247、0.466。LD分析表明,小骨山羊r 2最高,衰减速度最慢。Fst分析显示,小骨山羊与河西绒山羊分化水平低(0.043),与内蒙古绒山羊(阿尔巴斯型)分化水平中等(0.052)。PCA分析显示,小骨山羊与河西绒山羊、内蒙古绒山羊(阿尔巴斯型)较为聚集,从PC1>0可以将部分小骨山羊与其它群体区分。NJ树结果表明,大部分小骨山羊汇聚为独立的一支,其余存在混群现象。群体结构分析显示,K=1为最佳分群数,小骨山羊有独特的遗传结构。IBS距离矩阵和亲缘关系G矩阵显示出相同的结果,3个群体之间亲缘关系较远,小骨山羊群体内亲缘关系较近。本研究基于SLAF-seq获得SNPs数据分析小骨山羊遗传多样性和群体遗传结构。结果表明上述结果提示,小骨山羊与河西绒山羊分化程度低,与内蒙古绒山羊(阿尔巴斯型)呈中等分化。小骨山羊的遗传多样性相对其它两个群体较高,但是存在选择压力和群体规模小的问题。小骨山羊群体部The aim of this study was to analyze the genetic diversity and population genetic structure of the Small-boned goat population,and to provide a theoretical basis for clarifying whether it is a new germplasm resource.In this study,the Small-boned goats,Hexi cashmere goats and Inner Mongolia cashmere goats(Albas)were used as subjects,20 adult healthy ewes were selected from each group.DNA was extracted from 5 mL of blood collected from the jugular vein,and Genome-wide nucleotide polymorphisms(SNPs)were detected using the SLAF-seq technique.Genetic diversity was calculated by using perl programming for minor allele frequency(MAF),observed heterozygosity(Ho),expected heterozygosity(He),Nei diversity index(Nei),polymorphic information content(PIC),and Shannon Wiener index(SHI);PopLDdecay was used for linkage disequilibrium analysis(LD);and VCFtools was used for population differentiation index(Fst).Population genetic structure was illustrated by principal component analysis(PCA)using EIGENSOFT,construction of NJ trees by MEGA X and population structure analysis by ADMIXTURE.Kinship was illustrated by calculating IBS distances using PLINK,calculating kinship using GCTA and constructing matrices.A total of 5253776 SNPs were detected,most of which were located in the intergenic region.Small-boned goats had the highest genetic diversity indexes except Ho(0.197).The mean MAF,He,Nei,PIC,and SHI of Small-boned goats were 0.216,0.302,0.312,0.247,and 0.466,respectively.LD analysis showed that Small-boned goats had the highest r 2 and the slowest rate of decay.Fst showed that the Small-boned goat had a low level of differentiation from the Hexi cashmere goat(0.043)and a medium level of differentiation from the Inner Mongolian cashmere goat(Albas,0.052).PCA analysis showed that Small-boned goats were more aggregated with Hexi cashmere goats and Inner Mongolian cashmere goats(Albas),and some of the Small-boned goats could be distinguished from the other groups from PC1>0.The results of the NJ-tree showed that the majority of the

关 键 词：小骨山羊 种质资源 遗传多样性 群体遗传结构 简化基因组测序 

分 类 号：S827.2[农业科学—畜牧学]