基于简化基因组测序(Super-GBS)的子午岭黑山羊保种群遗传结构评估  

Evaluation of the Population Structure of the Ziwuling Black Goat Based on Super-GBS

作　　者：苟想珍[1] 杨军祥[1] 赵子惠[1] 冯玲霞[1] 陈万辉[1] 李玉洁 张忠钰 马克岩 蒋东平 常嵘 文亚洲 王珂[1] 马友记[3] GOU Xiangzhen;YANG Junxiang;ZHAO Zihui;FENG Lingxia;CHEN Wanhui;LI Yujie;ZHANG Zhongyu;MA Keyan;JIANG Dongping;CHANG Rong;WEN Yazhou;WANG Ke;MA Youji(Key Laboratory of Livestock and Poultry Resources(Goat)Evaluation and Utilization of Ministry of Agriculture and Rural Affairs,Animal Husbandry and Veterinary Research Institute of Gansu,Pingliang 744000,China;Station of Huachi County Animal Science and Veterinary,Qingyang 745000,China;College of Animal Science and Technology,Gansu Agricultural University,Lanzhou 730070,China;Pingchuan District Animal Husbandry and Veterinary Technical Service Center,Baiyin 730900,China;Animal Health Supervision Institute of Ganzhou District,Zhangye 734000,China;Gansu Sheep Breeding Technology Extension Station,Zhangye 734000,China)

机构地区：[1]甘肃省畜牧兽医研究所/农业农村部畜禽资源(羊)评价利用重点实验室,平凉744000 [2]华池县畜牧兽医站,庆阳745000 [3]甘肃农业大学动物科学技术学院,兰州730070 [4]白银市平川区畜牧兽医技术服务中心,白银730900 [5]张掖市甘州区动物卫生监督所,张掖734000 [6]甘肃省绵羊繁育技术推广站,张掖734000

出　　处：《畜牧兽医学报》2024年第10期4334-4345,共12页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：甘肃省自然基金重点项目(22JR5RA759);甘肃省重点人才项目(2023RCXM67)。

摘　　要：旨在分析子午岭黑山羊的群体遗传多样性和亲缘关系以及家系结构,为子午岭黑山羊的保护和利用提供依据。本研究通过简化基因组测序(super-genotyping by sequencing,Super-GBS)技术对99只(10公/89母)成年子午岭黑山羊进行全基因组SNP检测。利用Plink软件计算观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)、核苷酸多样性(Pi)、有效等位基因数(Ne)及次要等位基因频率(MAF)等6项遗传多样性指标;GCTA软件进行主成分分析及基因组亲缘关系G矩阵构建;Plink软件构建IBS遗传距离矩阵,R语言绘制热图;PHYLP构建系统发育树;detect RUNS工具检测ROH。结果表明,99只子午岭黑山羊个体共检测到996042个SNPs。子午岭黑山羊群体的PIC、Pi、Ne及MAF值分别是0.161、0.193、1.295、0.130,且Ho(0.167)低于He(0.192),说明子午岭黑山羊群体遗传多样性较低。G矩阵和IBS遗传距离结果均表明子午岭黑山羊群体间大部分个体间亲缘关系较远。主成分分析结果揭示子午岭黑山羊群体内部不存在明显分化,系统发育树结果说明子午岭黑山羊群体公羊可大致分为6个家系,所有家系公羊数量较少。子午岭黑山羊群体的近交系数FROH为0.0496,说明子午岭黑山羊群体内部近交程度相对较低。综上所述,子午岭黑山羊群体遗传多样性较低,大部分个体间亲缘关系较远,群体内近交程度较低,后期应注意后代的选育,避免血统流失。This study aimed to assess the genetic diversity and population structure of the Ziwuling black goat,laying the groundwork for the preservation and utilization of this breed.The whole-genome SNP analysis of a total of 99 adult Ziwuling black goats(10 males and 89 females)was performed by super-genotyping by sequencing(super-GBS).Genetic diversity parameters including observed heterozygosity(Ho),expected heterozygosity(He),polymorphic information content(PIC),nucleotide diversity(Pi),effective allele number(Ne),and minor allele frequency(MAF)were calculated using Plink software.Principal component analysis and construction of genetic relationship G matrix were conducted using GCTA software.IBS genetic distance matrix was built using Plink software,and a heatmap was plotted using R language.A phylogenetic tree was constructed using PHYLP,while runs of homozygosity(ROH)were detected using the detect RUNS tool.A total of 996042 SNPs were detected in the 99 individuals of Ziwuling black goats.The PIC,Pi,Ne,and MAF values of Ziwuling black goats were 0.161,0.193,1.295,0.130,respectively,indicating a relatively low genetic diversity with Ho(0.167)lower than He(0.192).Both the G matrix and IBS genetic distance results showed that most individuals in the Ziwuling black goat population had distant genetic relationships.The principal component analysis revealed no obvious differentiation within the Ziwuling black goat population,while the phylogenetic tree indicated that the rams could be roughly divided into 6 lineages,with few rams in each lineage.The inbreeding coefficient FROH of the Ziwuling black goat population was 0.0496,suggesting a relatively low level of inbreeding within the population.In conclusion,the genetic diversity of the Ziwuling black goat population is relatively low,with most individuals having distant kinship relations and a low level of inbreeding within the group.It is recommended to pay attention to the breeding of offspring in order to avoid loss of genetic diversity in the future.

关 键 词：子午岭黑山羊 简化基因组测序 群体结构 遗传多样性 家系结构 亲缘关系 

分 类 号：S827.2[农业科学—畜牧学]