基于SNP芯片检测皖南花猪保种群遗传结构  

Detection of Genetic Structure of Conservation Population in Wannanhua Pig(Sus scrofa domesticus)Based on SNPs Chip

作　　者：王静琳 吴旭东 何志兵 刘阳光 王小芬 丁月云[1] 郑先瑞 张晓东[1] 殷宗俊[1] WANG Jing-Lin;WU Xu-Dong;HE Zhi-Bing;LIU Yang-Guang;WANG Xiao-Fen;DING Yue-Yun;ZHENG Xian-Rui;ZHANG Xiao-Dong;YIN Zong-Jun(College of Animal Science and Technology,Anhui Agricultural University,Hefei 230036,China;Anhui Academy of Agricultural Sciences,Institute of Animal Husbandry and Veterinary Medicine,Hefei 230031,China)

机构地区：[1]安徽农业大学动物科技学院,合肥230036 [2]安徽省农业科学院畜牧兽医研究所,合肥230031

出　　处：《农业生物技术学报》2024年第8期1869-1877,共9页Journal of Agricultural Biotechnology

基　　金：国家自然科学基金(31972531);安徽省生猪产业技术体系项目(AHCYJSTX-05-01)。

摘　　要：皖南花猪(Sus scrofa domesticus)是安徽省乃至中国不可或缺的宝贵猪种资源,研究皖南花猪保种群体的遗传多样性、亲缘关系和家系结构,对揭示皖南花猪目前的群体状况至关重要。本研究基于“中芯一号”芯片(Chinese Chip-1 BeadChip)检测32头皖南花猪的全基因组SNP位点,利用PLINK软件进行观察杂合度(observed heterozygosity,Ho)、期望杂合度(expected heterozygosity,He)和多态信息含量(polymorphic information content,PIC)的计算及连续性纯合片段(runs of homozygosity,ROH)的检测,分析皖南花猪群体的遗传多样性。通过GCTA软件构建G矩阵,解析皖南花猪群体的亲缘关系;MEGA X软件构建群体进化树,分析皖南花猪群体的家系结构。结果显示,32头皖南花猪共检测到42662个SNPs位点,满足质控条件的SNP位点有21317个;群体多态性标记比例(polymorphism marker ratio,P_(N))为0.500,有效群体含量(effective population size,Ne)为3,群体He为0.348,Ho为0.372,平均亲缘系数为0.11。G矩阵的结果显示,大多数皖南花猪之间存在中等程度的亲缘关系。ROH片段共有884个,ROH平均长度为(12.35±2.17)Mb,个体ROH平均长度为(341.19±139.58)Mb;基于ROH的平均近交系数为0.139±0.056,保种群的近交程度较低;聚类分析结果表明,皖南花猪公猪来源于5个血统。综上所述,皖南花猪保种群群体有效含量偏低,遗传多样性中等,近交程度中等,可能含有少量外来血缘。本研究为皖南花猪遗传资源的保护及利用提供科学依据。The Wannanhua pig(Sus scrofa domesticus)is an indispensable valuable pig breed resource in Anhui province and even in China.Studying the genetic diversity,kinship relationships,and pedigree structure of the Wannanhua pig population is crucial for revealing the current population status.The SNP of 32 Wannanhua pigs was detected using Chinese Chip-1 BeadChip.PLINK software was used to calculate the observed heterozygosity(Ho),expected heterozygosity(He)and polymorphic information content(PIC),and to analyse the runs of homozygosity(ROH)of the Wannanhua pig population;Constructing G-matrix using GCTA software to analyze the genetic relationship of Wannanhua pig population.A colony evolutionary tree was built using MEGA X software to analyze the family structure of the Wannanhua pig population.The findings indicated that 42662 SNP loci were identified,with 21317 of them passing the quality control assessment;The polymorphism marker ratio(P_(N))was 0.500;The effective population size(Ne)was 3,the observed heterozygosity(Ho)was 0.372,the expected heterozygosity(He)was 0.348.The average relationship coefficient was 0.11.The G matrix results all indicated that most of the Wannanhua pigs were moderately related.There were 884 ROH fragments in the results,the average ROH length of(12.35±2.17)Mb and the individual ROH length of(341.19±139.58)Mb;The mean inbreeding coefficient based on ROH was 0.139±0.056,indicating that the inbreeding degree of the conserved population was not severe;The results of the cluster analysis showed that the Wannanhua pigs were derived from 5 bloodlines.In summary,the population of the Wannanhua pig conservancy herd had a low effective content,medium genetic diversity,medium degree of inbreeding,and might contain a small amount of foreign blood.This study provides scientific basis for the conservation and utilization of genetic resources of the southern Wannanhua pig.

关 键 词：皖南花猪 SNP芯片 遗传结构 亲缘关系 家系结构 

分 类 号：S828.8[农业科学—畜牧学]