基于SNP芯片的川中黑山羊保种效果评估  

Evaluation of the Conservation Effect in Chuanzhong Black Goat Based on SNP Chip

作　　者：王莉娟 曹伟 王小强 杨舒慧 李强 WANG Lijuan;CAO Wei;WANG Xiaoqiang;YANG Shuhui;LI Qiang(Sichuan Animal Husbandry Station,Chengdu 610041,China)

机构地区：[1]四川省畜牧总站,成都610041

出　　处：《中国草食动物科学》2025年第2期34-42,共9页China Herbivore Science

基　　金：四川省“天府青城计划”天府农业大师项目(川青城第944号);现代农业产业技术体系四川肉羊创新团队(SCCXTD-2024-14)。

摘　　要：为准确评估川中黑山羊的保种效果,使用山羊65K SNP芯片对307只川中黑山羊(25只公羊,282只母羊)进行了单核苷酸多态性(SNP)测定,采用Plink(V1.90)软件计算群体的多态性标记比例、期望杂合度、观测杂合度,SNe P(V1.1)软件计算有效群体含量;采用Plink软件构建状态同源(IBS)距离矩阵,GCTA(V1.94)软件构建基因组亲缘关系矩阵(G矩阵);采用Mega X(V10.0)分析了川中黑山羊保种群的家系结构;采用Plink软件计算每个样本的连续性纯合片段(ROH)的个数和长度,并计算基于ROH的近交系数。结果表明,川中黑山羊保种群体的有效群体含量(Ne)为43.700,多态标记比例(P_(N))为0.884;多态信息含量(PIC)、最小等位基因频率(MAF)分别为0.268、0.275;观察杂合度(Ho)、期望杂合度(He)分别为0.369、0.372;群体平均遗传距离为0.295 4±0.012 5,基于ROH的平均近交系数F_(ROH)为0.049±0.041,保种群体公羊可划分为12个家系,以满足保种场至少6个血缘的数量要求。综上所述,川中黑山羊保种群体遗传多样性丰富,近交程度低,保种效果良好。In order to evaluate the conservation effect of Chuanzhong Black goats,the 65K SNP chip was used to analyze single nucleotide polymorphism in 307 healthy adult Chuanzhong Black goats,which concluded 25 rams and 282 ewes.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 analyzed by Plink software and the genomic relationship G matrix was analyzed by GCTA(V1.94)software.The Mega X(V10.0)software was used to analyze 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 effective population size of this population was 43.700,proportion of polymorphic markers was 0.884,minimum allele frequency and polymorphic information content were 0.268 and 0.275,respectively,observed heterozygosity and expected heterozygosity were 0.369 and 0.372,respectively.The average IBS genetic distance of whole group was 0.2954±0.0125,and the average inbreeding coefficient based on ROH was 0.049±0.041.The whole conserved population could be divided into 12 families,which satisfied the needs of at least 6 families in conservation farm.In conclusion,the Chuanzhong Black goats had average genetic diversity,low level of inbreeding coefficient,and with remarkable conservation effect.

关 键 词：川中黑山羊 SNP芯片 保种效果 遗传多样性 遗传结构 

分 类 号：S827.2[农业科学—畜牧学]