| 运用SNP芯片评估马身猪保种群体的遗传结构 |
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| 引用本文： | 蔡春波,张雪莲,张万峰,杨阳,高鹏飞,郭晓红,李步高,曹果清.运用SNP芯片评估马身猪保种群体的遗传结构[J].畜牧兽医学报,2021,52(4):920-931. |
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| 作者姓名： | 蔡春波 张雪莲 张万峰 杨阳 高鹏飞 郭晓红 李步高 曹果清 |
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| 作者单位： | 山西农业大学动物科学学院, 太谷 030801 |
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| 基金项目： | 三晋学者支持计划专项经费（2016；2017）；国家自然科学基金（31872336）；山西省“1331”工程（J201811301）；山西省青年基金（201901D211376）；山西省优秀博士奖励（SXYBKY2018012）；山西农业大学科技创新（2018YJ35） |
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| 摘 要： | 旨在研究马身猪保种群体的遗传多样性、亲缘关系和家系结构。本研究利用Illumina CAUPorince 50 K SNP芯片检测39头保种马身猪的单核苷酸多态性（single nucleotide polymorphism，SNP）；采用Plink软件计算最小等位基因频率、多态信息含量、观察杂合度和期望杂合度，分析保种群体的遗传多样性；采用Plink软件构建状态同源（identity by state，IBS）距离矩阵和分析连续性纯合片段（runs of homozygosity，ROH），采用Gmatix软件构建G矩阵，分析保种群体的亲缘关系；采用Mega X软件构建群体进化树，分析保种群体的家系结构。结果显示，39头保种马身猪中共检测到43 832个SNPs位点，平均基因型检出率为0.980 1；通过质控的SNPs位点有28 859个，其中72.4%具有多态性，该款SNP芯片适用于分析马身猪的遗传多样性。有效等位基因数为1.563 4，多态信息含量为0.412，最小等位基因频率为0.258，表明马身猪保种群体的遗传多样性比较丰富；平均观察杂合度为0.354 1，平均期望杂合度为0.349 9，说明马身猪保种群体出现了分化；平均IBS遗传距离为0.284 2，其中公猪为0.285 2，IBS距离矩阵和G矩阵结果均表明部分种猪之间存在亲缘关系；ROH共有8 131个，其中46.15%的长度在400～600 Mb之间，平均近交系数为0.237，说明保种群体的近交程度高；群体进化树结果表明，马身猪保种群体来源于3个家系，各家系的个体数量差异明显。马身猪保种群体的遗传多样性较丰富，但近交程度高，家系少，各家系的个体数量差异大，容易引起遗传多样性的丢失，因此，需从原种场引入新的血统，扩大保种群体数量，降低近交系数。
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| 关 键 词： | 马身猪 保种群体 SNP芯片 遗传多样性 亲缘关系 家系结构 |
| 收稿时间： | 2020-08-28 |
Evaluation of Genetic Structure in Mashen Pigs Conserved Population Based on SNP Chip |
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| CAI Chunbo,ZHANG Xuelian,ZHANG Wanfeng,YANG Yang,GAO Pengfei,GUO Xiaohong,LI Bugao,CAO Guoqing.Evaluation of Genetic Structure in Mashen Pigs Conserved Population Based on SNP Chip[J].Acta Veterinaria et Zootechnica Sinica,2021,52(4):920-931. |
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| Authors: | CAI Chunbo ZHANG Xuelian ZHANG Wanfeng YANG Yang GAO Pengfei GUO Xiaohong LI Bugao CAO Guoqing |
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| Institution: | College of Animal Science, Shanxi Agricultural University, Taigu 030801, China |
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| Abstract: | The study aimed to explore the genetic diversity, relationship and family structure of Mashen pigs conserved population. Illumina CAUPorince 50 K SNP chip was used to detect the single nucleotide polymorphism (SNP) in 39 Mashen pigs. The minor allele frequency, polymorphism information content, observed heterozygosity and expected heterozygosity were calculated by Plink software to analyze the genetic diversity of conserved population. The identity by state (IBS) distance matrix was constructed and runs of homozygosity (ROH) was analyzed by Plink software. The G matrix was constructed by Gmatix software. IBS, ROH and G matrix were used to analyze the genetic relationship of conserved population. The phylogenetic tree constructed by Mega X software was used to analyze the family structure of conserved population. The result showed that 43 832 SNPs were detected in 39 Mashen pigs, and the average genotype detection rate was 0.980 1. Twenty-eight thousand eight hundred and fifty-nine SNPs met the demand of quality control, and 72.4% of which were polymorphic sites, which indicated that the SNP chip was suitable for analyzing the genetic diversity of Mashen pigs. The effective allele number, polymorphism information content and minor allele frequency were 1.563 4, 0.412, and 0.258, respectively, which indicated that the genetic diversity of Mashen pigs conserved population was abundant. The average observed heterozygosity and expected heterozygosity were 0.354 1 and 0.349 9, which suggested the conserved population of Mashen pigs had differentiated. The IBS genetic distance of 39 Mashen pigs was 0.284 2, and the IBS genetic distance of 20 breeding boars was 0.285 2. The results of IBS distance matrix and G matrix both showed that some breeding pigs had relationship with each other. Eight thousand one hundred and thirty one ROHs were detected in conserved population of Mashen pigs, 46.15% of which were between 400 and 600 Mb in length. The average inbreeding coefficient of conserved population based on ROH was 0.237, which indicated the high degree of inbreeding in conserved population. The result of phylogenetic tree showed that all individuals belonged to 3 families and the number of each family was significantly different. The genetic diversity of conserved population in Mashen pigs is abundant, but the inbreeding coefficient is high, the family of conserved population is few, and the number of individuals in each family varies greatly, which can lead to the loss of genetic diversity. Therefore, importing the new blood from the original conservation farm of Mashen pigs, expanding population size and decreasing inbreeding coefficient are essential ways in the future. |
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| Keywords: | Mashen pig conserved population SNP chip genetic diversity relationship family structure |
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