基于70 K SNP芯片分析济宁青山羊保种群体的遗传结构

doi:10.11843/j.issn.0366-6964.2023.07.016

摘要/Abstract

摘要： 旨在探究山东济宁青山羊保种群体的遗传多样性、亲缘关系及家系结构。本研究利用Illumina 70 K Goat SNP芯片对40只成年济宁青山羊全基因组范围内的SNP进行检测，利用Plink软件、GCTA工具和R语言，对济宁青山羊的遗传结构、亲缘关系和近交系数进行分析，以期揭示个体之间的亲缘关系。结果共得到67 088个SNPs，个体的基因型检出率达到了98%以上；通过Plink （V1.90）软件质控，过滤掉一个样本，剩余的SNPs有57 991个，其中85.5%的SNPs具有多态性；各位点平均有效等位基因数为1.697，平均多态信息含量（PIC）为0.283，最小等位基因频率（MAF）为0.293，群体平均观察杂合度（Ho）为0.409，平均期望杂合度（He）为0.418；济宁青山羊保种群体的平均状态同源（IBS）遗传距离为0.333 4。23只种公羊的平均IBS遗传距离为0.330 3，IBS遗传距离和G矩阵结果均表明部分种羊之间有亲缘关系。在40只个体中共检测到347个长纯合片段（ROH），基于ROH值计算的群体平均近交系数为0.047 9，近交程度低，群体遗传多样性丰富。基于IBS距离矩阵、G矩阵，结合邻接系统发育树，以公羊间分子亲缘系数0.1为标准进行聚类，将23只公羊划分为14个家系。综上，济宁青山羊保种群体遗传多样性较丰富，近交程度低，保种效果良好，建议后续工作持续关注各家系数量，确保家系结构维持平衡。

关键词: 济宁青山羊, SNP 芯片, 遗传多样性, 亲缘关系, 群体遗传结构

Abstract: This study aimed to analyze the genetic diversity, kindship, and population structure of Jining gray goat conservation population. The Illumina 70 K goat SNP chip was used to screen the whole genome SNPs in 40 Jining gray goats, the genetic structure, kinship, and inbreeding coefficient of the breeding Jining gray goats were analyzed by Plink software, GCTA tool and R language to reveal the genetic relationship between the individuals. The results showed that a total of 67 088 SNPs were detected, and the call rate was higher than 98%. There were 57 991 SNPs met the demand of quality control, and 85.5% of which were polymorphic sites. The average effective allele number was 1.697, the average polymorphism information content was 0.283, and the minor allele frequency was 0.293, which implied that the genetic diversity was abundant in Jining gray goats conservation population. The average observed heterozygosity was 0.409, greater than that of expected heterozygosity (0.418). The average IBS genetic distance was 0.333 4, and the IBS genetic distance of 23 breeding bucks was 0.330 3. A total of 347 runs of homozygous (ROH) were detected in 40 individuals. The inbreeding coefficient of whole population was 0.047 9 based on the ROH value, which indicated a low level of inbreeding and rich in population genetic diversity. Combined the results of IBS matrix, G matrix, and phylogenetic tree, 23 bucks were clustered into 14 families according to the coefficient of relationship was 0.1. In conclusion, the Jining gray goats have rich genetic diversity, low level of inbreeding, and with remarkable conservation effect. It is suggested that, the number and structure of families in Jining gray goat conservation population should be focused in the future work.

Key words: Jining gray goat, SNP chip, genetic diversity, relationship, population genetic structure

中图分类号:

S827.2

张任豹, 周东辉, 周李生, 高霄霄, 柳楠, 贺建宁. 基于70 K SNP芯片分析济宁青山羊保种群体的遗传结构[J]. 畜牧兽医学报, 2023, 54(7): 2836-2847.

ZHANG Renbao, ZHOU Donghui, ZHOU Lisheng, GAO Xiaoxiao, LIU Nan, HE Jianning. Analysis of Genetic Structure of Conservation Population in Jining Gray Goats Based on 70 K SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2836-2847.

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