合川黑猪保种群遗传结构及选择信号分析

doi:10.11843/j.issn.0366-6964.2023.05.009

摘要/Abstract

摘要： 旨在研究合川黑猪保种群体的遗传多样性、亲缘关系、近交系数、家系结构和选择信号,以期更好地保护和利用合川黑猪这一遗传资源。本研究利用猪50K SNP芯片,对合川黑猪保种群内所含的58头健康成年种猪进行SNP检测;计算群体的有效含量、多态信息含量、多态标记比例、期望杂合度、观测杂合度、有效等位基因数以及最小等位基因频率,分析保种群体的遗传多样性;利用Plink软件构建状态同源(identity by state,IBS)矩阵和分析每个样本的连续性纯合片段(runs of homozygosity,ROH),Gamatrix(V2)软件构建基因组关系G矩阵,分析合川黑猪保种群的亲缘关系;利用Mega X(V10.0)软件进行群体聚类分析,研究合川黑猪保种群的家系结构;运用Tajima’s D和iHS方法分析合川黑猪群体基因组上受选择的信号区域,挖掘潜在的候选基因。结果表明,合川黑猪保种群体的群体有效含量、平均多态信息含量、多态标记比例、平均有效等位基因数、最小等位基因频率分别为4.2、0.156、0.534、1.38、0.141,说明合川黑猪保种群体的遗传多样性较丰富;群体的平均期望杂合度为0.255,平均观测杂合度为0.271,观测杂合度稍高于期望杂合度,说明该保种群体出现了分化;平均IBS遗传距离为0.199 2± 0.042 9,其中公猪的为0.176 7±0.048 4,IBS遗传距离和基于G矩阵的亲缘关系分析结果均表明,部分个体之间呈现较近的亲缘关系;合川黑猪保种群体内共发现2 246个ROH片段,长度在1~10 Mb之间的ROH数量占比最多,为79.12%,含40~50个ROH的个体数量占比最多,为48.28%,群体平均近交系数为0.175;现有合川黑猪群体包含7个含公猪的家系和1个不含公猪的家系,各家系个体的数量差异较大;利用Tajima’s D方法检测到显著选择信号区域192个,涉及193个候选基因,iHS方法检测到显著选择信号区域303个,涉及331个候选基因。两种方法同时检测到的候选基因有5个,其中HVCN1与精子的活力和低温耐受相关,TRAF3IP1和PER2与机体免疫功能相关。综上所述,合川黑猪保种群体遗传多样性较丰富,但部分个体间存在较大的近交风险,各家系中个体数量的差异明显,个别家系内公猪个体数量少,存在血统流失风险。此外,在适应性进化过程中,合川黑猪繁殖和免疫性状相关的基因受到了一定程度的选择作用。

关键词: 合川黑猪, 50KSNP芯片, 遗传多样性, 遗传结构, 选择信号

Abstract: In order to better protect and utilize the Hechuan black pigs, the geneitc diversity, kinship, inbreeding coefficient, family structure and selection signatures of Hechuan black pigs conserved population were explored in this study. The 50K SNP chip was used to analyze the SNPs in 58 healthy adult Hechuan black pigs conserved population. The effective population size, polymorphic information content, polymorphic marker ratios, expected heterozygosity, observed heterozygosity, effective allele numbers and minor allele frequency was calculated to analyze the genetic diversity of the conserved population. The identity by state (IBS) diatance matrix and runs of homozygosity (ROH) for each sample was calculated by Plink software and the genomic relationship G matrix was calculated by Gamatrix (V2) software to analyze the kinship of the conserved population. The population cluster analysis was calculated by Mega X (V10.0) software to analyze the family structure of the conserved population. Tajima's D and iHS methods were used to analyze the selected signal regions on the genome of Hechuan black pig population and explore potential candidate genes. The results showed that the effective population size, average polymorphic information content, polymorphic marker ratios, average effective allele numbers, minor allele frequency of the Hechuan black pigs conserved population were 4.2, 0.156, 0.534, 1.38 and 0.141 respectively, which indicated that the genetic diversity of Hechuan black pigs conserved population was relatively abundant. The average expected heterozygosity and observed heterozygosity were 0.255 and 0.271, which indicated that the conserved population has been differentiated. The average IBS genetic distance of 58 Hechuan black pigs was 0.199 2±0.042 9, and the average IBS genetic distance of 26 breeding boars was 0.176 7 ±0.048 4. The results of IBS genetic distance and G matrix both suggested that some individuals had closely relattionship with each other. A total of 2 246 ROH, gatherring in individuals with the most ROH by 1-10 Mb length (79.12%) and 40-50 (48.28%) numbers, were founded in the Hechuan black pigs conserved population.A total of 2 246 ROH fragments were found in the Hechuan black pig population. The number of ROH fragments with a length of 1-10 Mb accounted for the most(79.12%), and the number of individuals with 40-50 ROH accounted for the most(48.28%). The average inbreeding coefficient of conserved population was 0.175. The Hechuan black pigs conserved population includes 7 families with boars and 1 family without boars, and the number of individuals in each family were significantly different. Using Tajima's D and iHS methods, 192 and 303 significant selection signal regions were detected, which contained 193 and 331 candidate genes, respectively. Five candidate genes were detected simultaneously by Tajima's D and iHS. HVCN1 was associated with sperm motility and sperm cryotolerance. TRAF3IP1 and PER2 were associated with immune function. In general, the genetic diversity of Hechuan black pigs conserved population was relatively abundant. However, there was a greater risk of inbreeding among some individuals, and the number of individuals in each family was significantly different. The number of boars in some families is small, thus, there was a risk of ancestry loss in this families. In addition, during the adaptive evolution of Hechuan black pigs, the related genes of reproduction and immune traits were selected to a certain extent.

Key words: Hechuan black pigs, 50K SNP chip, genetic diversity, genetic structure, selection signatures

中图分类号:

S828.2

龙熙, 陈力, 吴平先, 张廷焕, 潘红梅, 张亮, 王金勇, 郭宗义, 柴捷. 合川黑猪保种群遗传结构及选择信号分析[J]. 畜牧兽医学报, 2023, 54(5): 1854-1867.

LONG Xi, CHEN Li, WU Pingxian, ZHANG Tinghuan, PAN Hongmei, ZHANG Liang, WANG Jinyong, GUO Zongyi, CHAI Jie. Evaluation of the Genetic Structure and Selection Signatures in Hechuan Black Pigs Conserved Population[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1854-1867.

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