基于SNP芯片的盆周山地猪保种群体保种效果评估  

Evaluation of the Conservation Effect in Penzhoushandi Conserved Population Based on SNP Chip

作　　者：龙熙[1] 柴捷[1] 陈力 潘红梅[1] 张亮[1] 陈四清[1] 郭宗义[1] 张廷焕 LONG Xi;CHAI Jie;CHEN Li;PAN Hongmei;ZHANG Liang;CHEN Siqing;GUO Zongyi;ZHANG Tinghuan(Chongqing Academy of Animal Sciences,Chongqing 402460,China)

机构地区：[1]重庆市畜牧科学院,重庆402460

出　　处：《华北农学报》2022年第S01期358-365,共8页Acta Agriculturae Boreali-Sinica

基　　金：重庆市自然科学基金面上项目(cstc2021jcyj-msxmX0800);重庆市技术创新与应用发展专项产业类重点项目(cstc2019jscx-gksbX0099);重庆市绩效激励引导专项项目(19540);“十二五”农村领域国家科技计划课题子课题(2015BAD03B02-6)。

摘　　要：为了更好地保护和利用盆周山地猪这一遗传资源,利用猪50K SNP芯片,对盆周山地猪保种群内所含的152头健康种猪进行了SNP检测,利用Plink软件计算群体的多态性标记比例、期望杂合度、观测杂合度,SNeP(V1.1)软件计算有效群体含量;利用Plink软件构建状态同源(IBS)矩阵,Gamatrix(V2)软件构建基因组关系G矩阵;利用Mega X(V10.0)分析盆周山地猪保种群家系结构;利用Plink软件计算每个样本的连续性纯合片段(ROH)个数和长度,并计算基于ROH的近交系数。结果表明,整个盆周山地猪保种群体的多态性标记比例为0.6601,有效群体含量为7.4头;群体期望杂合度为0.2892、观测杂合度为0.2947;群体平均IBS遗传距离为(0.2341±0.0273),公猪的平均IBS距离为(0.2280±0.0335);现有群体大致可分为5个包含公猪的家系和1个不含公猪的家系,家系A和D的公猪数量相对较少;在盆周山地猪保种群中共发现ROH片段3737个,含21~25个ROH的个体数量占比最多(32.24%),ROH长度在100~200 Mb的个体数量占比最多(42.11%),群体平均近交系数为0.085。综上所述,盆周山地猪保种群体遗传多样性较丰富,但部分个体间存在较大的近交风险,群体家系较少,个别家系内公猪个体数量少,存在血统流失风险。The aim of this study was to better understand the Penzhoushandi pigs.The 50K SNP chip was used to analyze the SNPs in 152 healthy adult Penzhoushandi pigs conserved population.The proportion of polymorphism markers,expected heterozygosity and observed heterozygosity were calculated by Plink software and the effective size of conserved population was calculated by SNeP(V1.1)software.The IBS distance matrix was analysed by Plink software and the genomic relationship G matrix was analyzed by Gamatrix(V2)software.The Mega X(V10.0)software was used to analysis the family structure of conserved population.The numbers and length of ROHs and inbreeding coefficient based on ROHs of each sample were calculated by Plink software.The results showed that the proportion of polymorphism markers was 0.6601 and the effective size of conserved population was 7.4.The expected heterozygosity and observed heterozygosity were 0.2892 and 0.2947.The average IBS genetic distance of whole group was(0.2341±0.0273),and the average IBS genetic distance of boars was(0.2280±0.0335).The whole conserved group could be divided into 5 families with boars and 1 family without boars.The size of boars in family A and D was relatively small.A total of 3737 ROHs,gatherring in individuals with the most ROHs by 21-25(32.24%)numbers and 100-200 Mb length(42.11%),were founded in the Penzhoushandi pigs conserved population.The average inbreeding coefficient of conserved population was 0.085.In general,the genetic diversity of the Penzhoushandi pigs conserved population was relatively rich,but there was also existing a risk of inbreeding among some individuals.The families in the conserved population were relatively less,and the number of boars in some families was small.Thus,there was a risk of ancestry loss in this families.Therefore,selection and breeding measures should be strengthened or extra ancestry should be introduced to ensure the long-term preservation of the genetic diversity of Penzhoushandi pigs.

关 键 词：盆周山地猪 50K SNP芯片 保种群体 遗传结构 保种效果 

分 类 号：S858.28[农业科学—临床兽医学]