浦市黑猪保种群体基于SNP芯片的遗传结构分析

Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip

【目的】通过SNP芯片技术分析浦市黑猪群体遗传多样性和家系结构,为保护和利用浦市黑猪资源提供支撑。【方法】利用“中芯一号”50K SNP芯片,对79头成年浦市黑猪(10头公猪、69头母猪)进行SNP测定,采用多种分析软件(Plink、 Gmatix及Mega X)对群体遗传多样性和亲缘关系开展分析,进而构建群体家系结构。【结果】在79头浦市黑猪中共检出57 466个SNPs位点,平均基因型检出率为99.15%。遗传多样性分析提示SNP位点具有多态性,群体存在近交(有效群体含量Ne仅为1.5,且平均观察杂合度<平均期望杂合度)。群体平均状态同源(Idengtical by state,IBS)遗传距离为(0.294 9±0.072 6),公猪为(0.277 1±0.091 8),共检测到长纯合片段(Runs of hemozygosity,ROH)(29.60±16.12)个,其中长度在0~100 Mb的占40.5%,且群体基于ROH的平均近交系数为0.108。IBS距离矩阵、G矩阵结果以及群体ROH值的分析结果均反映出群体内个体之间存在较近的亲缘关系。根据群体进化树结果,将群体划分成2个含公猪的家系,以及1个不含公猪的家系。【结论】浦市黑猪群体家系少,各家系的个体数量差异大,近交程度高。因此,应注重引入或创建新的血统,扩大有效群体含量,降低近交系数。

【Objective】Genetic diversity and family structure of a preserved population of Pushi black pig were analyzed using the SNP bead chip for resource conservation.【Method】SNPs of 79 adult Pushi black pigs consisting of 10 boars and 69 sows were determined using Porcine 50K SNP Beadchips.Software,including Plink,Gmatix,and Mega X,was used to analyze the genetic diversity and phylogenetic relationships to construct phylogenetic structure of the pig population.【Result】A total of polymorphic 57466 SNP loci were found with an average genotype detection rate of 99.15%.The population showed evidence of inbreeding as the effective Ne was merely 1.5 and the average observed heterozygosity slightly below the expected level.The average distance of IBS was(0.2949±0.0726)and that for the boars(0.2771±0.0918).A total of(29.60±16.12)ROHs were detected with 40.5%of them between 0 and 100 Mb in length.The average inbreeding coefficient based on ROH was 0.108.The analysis on IBS distance matrix,G matrix,and population ROHs indicated a close genetic relationship among the individual animals.Based on the evolutionary tree,the population was divided into two families containing boars and one without.【Conclusion】The population of Pushi black pigs under study had only a few families,which varied greatly in number of members in each family and showed a high degree of inbreeding.Consequently,introducing or creating new lineages to expand the gene pool and reduce inbreeding coefficient for the population seemed imperative.