利用高密度SNP芯片分析杭猪的群体遗传结构  

Analysis of Population Genetic Structure of Hang Pigs by High Density SNP Chip

作　　者：刘晨龙 卢丹 周泉勇[1] 万明春[1] 郝晓东 张献贺 郑瑞强[4] 季华员[1] LIU Chenlong;LU Dan;ZHOU Quanyong;WAN Mingchun;HAO Xiaodong;ZHANG Xianhe;ZHENG Ruiqiang;JI Huayuan(Institute of Animal Husbandry and Veterinary,Jiangxi Academy of Agricultural Sciences,Nanchang330200,China;Jiangxi Mucun Agriculture and Animal Husbandry Technology Co.Ltd.,Jiujiang332438,China;Beijing Compass Agricultural Technology Co.Ltd.,Beijing102206,China;Jiangxi Agricultural University,Nanchang330045,China)

机构地区：[1]江西省农业科学院畜牧兽医研究所,南昌330200 [2]江西省幕村农牧科技有限公司,九江332438 [3]北京康普森农业科技有限公司,北京102206 [4]江西农业大学,南昌330045

出　　处：《畜牧兽医学报》2022年第8期2502-2513,共12页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：江西省生猪产业技术体系(JXARS-01);国家自然科学基金(32060732;31201786);江西省农业科学院创新基金博士启动项目(20162CBS005);江西社会科学青年创新团队建设项目(2021)。

摘　　要：旨在更好地了解杭猪保种群体的遗传多样性、亲缘关系和家系结构,有效保护和利用杭猪遗传资源。本研究使用50KSNP芯片对30头杭猪(4头公猪,26头母猪)保种个体进行了单核苷酸多态性(single nucleotide polymorphism,SNP)测定,通过Plink软件对获得的基因型数据进行质控,用于最小等位基因频率、观察杂合度、期望杂合度和多态信息含量的计算,分析杭猪保种群的遗传多样性;使用Plink计算连续性纯合片段(runs of homozygosity,ROH)、构建状态同源(identity by state,IBS)距离矩阵,并计算得到基于连续性纯合片段的近交系数;采用Gmatrix软件构建G矩阵,分析杭猪保种群的亲缘关系;使用Mega X软件构建公猪进化树,分析保种群体的家系结构。结果表明,30头杭猪共得到57466个SNPs标记,平均检出率为0.9883±0.0004,通过质检SNPs数为34156;平均最小等位基因频率为0.228±0.137,平均多态信息含量为0.255±0.098;平均观察杂合度为0.359±0.181,平均期望杂合度为0.314±0.140。杭猪保种群体平均IBS遗传距离为0.2417±0.0336,公猪平均IBS遗传距离为0.1783±0.0255;G矩阵分析结果与IBS距离矩阵一致,两个结果均表明杭猪保种群部分个体之间亲缘关系较近。30头杭猪个体共检测到828个ROHs,83.33%的ROH长度在10Mb以内,平均长度为(6.96±9.62)Mb,个体ROH平均总长度为(191.95±201.56)Mb。基于ROH的平均近交系数为0.078±0.082,其中公猪平均近交系数为0.219±0.082,说明杭猪保种群整体的近交程度不严重,但公猪存在近交。进化树结果表明,杭猪保种群体目前只有2个家系,其中1个家系包含4头公猪,另一个家系不含公猪。综上所述,杭猪保种场的保种群公猪的血缘数量少,母猪近交程度低,公猪存在近交,需要引入新血统或创建新血统来维持家系结构的平衡以利于杭猪遗传资源的长期保存,防止杭猪遗传多样性的丢失。The purpose of this study was to better understand the genetic diversity,relationship and family structure of Hang pigs conserved population,protect and utilize the genetic resources of Hang pigs efficiently.The 50KSNP chip was used to detect the single nucleotide polymorphism(SNP)in 30Hang pigs(4male and 26female).And the quality control of SNP genotyping results was conducted by Plink software to calculated the minor allele frequency,observed heterozygosity,expected heterozygosity and polymorphism information content so as to analyze the genetic diversity of Hang pigs conserved population.The runs of homozygosity(ROH)was calculated and identity by state(IBS)distance matrix was constructed by Plink software,the inbreeding coefficient was then calculated based on ROH.The genetic relationship was analyzed according to the G matrix result constructed by Gmatrix software.The boar phylogenetic tree which constructed by Mega X software was used to analyze the family structure of Hang pigs conserved population.The results showed that,57466SNPs were detected in 30Hang pigs,the average genotyping rate was 0.9883±0.0004,there were 34156SNPs passing quality control.The average minor allele frequency,polymorphism information content,average observed heterozygosity and average expected heterozygosity were 0.228±0.137,0.255±0.098,0.359±0.181and 0.314±0.140,respectively.The average IBS genetic distance of Hang pigs conserved population and boar were 0.2417±0.0336and 0.1783±0.0255,respectively,and the result of G matrix was consistent with IBS genetic distance,the IBS genetic distance and G matrix results showed that some individuals in Hang pigs conserved population were closer to each other.A total of 828ROHs were detected in 30Hang pigs,and the length of 83.33%of these ROHs was less than 10Mb,and the average length was(6.96±9.62)Mb,and the average total length of individual ROH was(191.95±201.56)Mb.The average inbreeding coefficient based on ROH of Hang pigs conserved population and boar were 0.078±0.082and 0.219±

关 键 词：杭猪 SNP芯片 遗传多样性 亲缘关系 家系结构 

分 类 号：S828.2[农业科学—畜牧学]