SNP芯片评估柯尔克孜羊群体遗传多样性和遗传结构

doi:10.11843/j.issn.0366-6964.2023.02.015

摘要/Abstract

摘要： 旨在了解柯尔克孜羊群体的遗传多样性和遗传结构，有效地保护和利用其遗传资源。本研究利用绵羊SNP 50K v3芯片检测61只柯尔克孜种羊（31只公羊、30只母羊）个体的单核苷酸多态性（single nucleotide polymorphism，SNP）；Plink （V1.90）软件对数据进行质控，计算群体有效含量、多态标记的比例、观测杂合度、期望杂合度、多态信息含量、有效等位基因数、最小等位基因频率，分析群体的遗传多样性；Plink计算连续性纯合片段（runs of homozygosity，ROH）和近交系数F_ROH；构建状态同源距离矩阵（identical by state，IBS），并采用Gmatrix软件构建G矩阵，解析柯尔克孜羊群的遗传距离和亲缘关系；使用Mega X软件构建种公羊进化树，分析群体家系结构。结果显示，61只柯尔克孜羊共得到64 734个SNPs标记，通过质检的SNPs为56 763个；平均多态信息含量为0.273±0.112，平均观察杂合度和平均期望杂合度分别为0.368±0.140和0.368±0.130，平均最小等位基因频率为0.263±0.147。柯尔克孜羊群平均IBS遗传距离为0.294，G矩阵和IBS距离矩阵结果均表明柯尔克孜羊群个体间亲缘关系较远。61只柯尔克孜羊共检测到200个ROHs，67.5%的ROHs长度在1~5 Mb之间，56只柯尔克孜羊ROH长度在0~50 Mb之间。基于ROH的平均近交系数为0.008 19±0.018 8，其中公羊平均近交系数为0.004 65±0.008，说明柯尔克孜羊群体的近交程度较低。进化树结果表明，柯尔克孜羊群目前有25个家系，大部分家系公羊数量太少。综上所述，SNP芯片评估柯尔克孜羊群体的遗传多样性和遗传结构，发现柯尔克孜羊群体遗传多样性较丰富，群体内近交程度低，虽然家系较多，但是每个家系种公羊数量太少，需要加强种公羊的后代选育，避免血统流失。

关键词: 柯尔克孜羊, SNPs芯片, 遗传多样性, 遗传结构

Abstract: The aim of this study was to investigate the genetic diversity and genetic structure of Kirgiz sheep, and effectively protect and utilize its genetic resources.Sheep SNP 50K v3 chip was used to detect the single nucleotide polymorphism (SNP) of 61 Kirgiz sheep (31 rams and 30 ewes). Plink software (V1.90) was used to conduct the quality control of SNP genotyping results, and calculate the population effective content, the polymorphic marker proportion, observed heterozygosity, expected heterozygosity, polymorphic information content, effective number of alleles, minor allele frequency to analyze the genetic diversity of the Kirgiz sheep; Using Plink to calculate the runs of homozygosity (ROH) and obtain the inbreeding coefficient F_ROH based on ROH; The state homologous distance matrix (identical by state, IBS) was established, and G matrix were constructed by Gmatrix software, the genetic distance and genetic relationship of Kirgiz sheep were explored. Mega X software was used to construct evolutionary tree and analyze the family structure of Kirgiz rams. The results showed that a total of 64 734 SNPs were obtained from 61 Kirgiz sheep, and the number of SNPs passing quality control was 56 763; The average polymorphism information content was 0.273±0.112, the average observed heterozygosity and the average expected heterozygosity were 0.368±0.140 and 0.368±0.130, respectively, and the average minor allele frequency was 0.263±0.147. The average IBS genetic distance of Kirgiz sheep was 0.294. The results of G matrix and IBS distance matrix showed that the genetic relationship between individuals of Kirgiz sheep was farther. A total of 200 ROHs were detected in 61 Kirgiz sheep, 67.5% of which were within 1-5 Mb in length, and the ROH length of 56 Kirgiz sheep was 0-50 Mb. The average inbreeding coefficient based on ROH was 0.008 19±0.018 8, of which the average inbreeding coefficient of rams was 0.004 65±0.008, indicating that the average inbreeding coefficient degree of Kirgiz sheep population was low. The results of phylogenetic tree showed that there were 25 families in Kirgiz sheep population, and most families have too few rams. To sum up, the Kirgiz sheep population has rich genetic diversity and low inbreeding degree in these population, but the number of male sheep in each family is small, so it is necessary to increase the breeding of offspring and prevent the loss of blood to maintain the genetic diversity of Kirgiz sheep.

Key words: Kirgiz sheep, SNPs chip, genetic diversity, genetic structure

中图分类号:

S826.2

李隐侠, 牙生江·那斯尔, 赛里克·都曼, 钱勇, 曹少先, 王伟列, 孟春花, 张俊, 张建丽. SNP芯片评估柯尔克孜羊群体遗传多样性和遗传结构[J]. 畜牧兽医学报, 2023, 54(2): 572-583.

LI Yinxia, YA Shengjiang·Nasier, SAI Like·Duman, QIAN Yong, CAO Shaoxian, WANG Weilie, MENG Chunhua, ZHANG Jun, ZHANG Jianli. Evaluation of Genetic Diversity and Genetic Structure in Kirgiz Sheep Population Based on SNPs Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 572-583.

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