基于SNP芯片监测通城猪的保种效果

doi:10.11843/j.issn.0366-6964.2022.08.010

畜牧兽医学报 ›› 2022, Vol. 53 ›› Issue (8): 2514-2523.doi: 10.11843/j.issn.0366-6964.2022.08.010

基于SNP芯片监测通城猪的保种效果

袁娇^1,2, 徐国强^1,2, 周翔^1,2,3,4, 徐三平⁵, 李胜⁵, 黎望明⁵, 刘榜^1,2,3,4*

1. 华中农业大学动物科学技术学院, 武汉 430070;
2. 华中农业大学农业动物遗传育种与繁殖教育部重点实验室, 武汉 430070;
3. 生猪健康养殖省部共建协同创新中心, 武汉 430070;
4. 湖北省地方猪品种改良工程技术研究中心, 武汉 430070;
5. 通城县国营种畜场, 通城 437400

收稿日期:2022-01-06 出版日期:2022-08-23 发布日期:2022-08-23
通讯作者: 刘榜,主要从事地方猪的遗传资源保护和种质创新研究,E-mail:liubang@mail.hzau.edu.cn
作者简介:袁娇(1995-),女,新疆伊宁人,硕士,主要从事动物遗传育种研究,E-mail:649663181@qq.com
基金资助:
国家自然科学基金重点项目（31930104）

SNP Chip-Based Monitoring of Population Conservation Effect of Tongcheng Pigs

YUAN Jiao^1,2, XU Guoqiang^1,2, ZHOU Xiang^1,2,3,4, XU Sanping⁵, LI Sheng⁵, LI Wangming⁵, LIU Bang^1,2,3,4*

1. College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, China;
2. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China;
3. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China;
4. The Engineering Technology Research Center of Hubei Province Local Pig Breed Improvement, Wuhan 430070, China;
5. Agricultural and Rural Bureau of Tongcheng County, Tongcheng 437400, China

Received:2022-01-06 Online:2022-08-23 Published:2022-08-23

摘要/Abstract

摘要： 旨在基于SNP芯片信息分析通城猪保种群的群体结构和遗传多样性，对保种效果进行监测。本研究利用“中芯一号”50K SNP芯片对68头通城猪的全基因组SNP进行扫描，通过以下两方面评估保种效果：1）群体结构。通过群体分层、遗传距离、亲缘关系以及公猪基因组家系等分析，研究通城猪个体间的群体结构；2）遗传多样性。估算等位基因频率、有效等位基因数、多态信息含量、多态性标记比例、杂合度、核苷酸多样性等多态性和杂合性相关参数估计遗传多样性，分析有效群体含量和连续性纯合片段（runs of homozygosity，ROH），综合评估保种效果。结果显示：1）保种群无明显分层，遗传距离为0.27，亲缘系数为0.17；2）基因组等位基因频率为0.77，有效等位基因数为1.52，多态信息含量均值为0.31，多态性标记比例为88.28%，观测杂合度为0.32，期望杂合度为0.31；20世代前通城猪有效群体含量为105头，当前世代有效群体含量为94头；ROH共计有184个，平均ROH长度为23.71 Mb，其中28.80%的长度在15~20 Mb之间；基因组近交系数为0.04%，具较低水平的近交程度。通城猪保种群是一个没有分层的纯种群体，具有丰富的遗传多样性，得到了有效保护。

关键词: 通城猪, 保种, 群体结构, 遗传多样性

Abstract: This study aimed to analyze the population structure and genetic diversity of Tongcheng pig conservation population based on SNP chip information and to monitor the conservation effect. In this study, "Zhongxin No.1" 50K SNP chip was used to scan the whole genome SNPs of 68 Tongcheng pigs, and the population conservation effect was evaluated from two aspects:1) Population structure. Based on the analysis of population stratification, genetic distance, kinship, and boar genome family, the population structure among Tongcheng pigs were studied; 2) Genetic diversity. Allele frequency, effective number of alleles, polymorphism information content, proportion of polymorphic loci, heterozygosity, nucleotide diversity, and other polymorphism and heterozygosity-related parameters were employed to estimate genetic diversity and to analyze effective population size and runs of homozygosity (ROH). Based on these parameters, comprehensive evaluation of population conservation effects was conducted. The results showed that:1) The conservation population exhibited no obvious stratification with the genetic distance of 0.27, and they had a medium kinship 0.17; 2) The genome allele frequency was 0.77; the effective number of alleles was 1.52; the mean polymorphism information content was 0.31; the proportion of polymorphic markers was 88.28%; the observed heterozygosity was 0.32; and the expected heterozygosity was 0.31. The effective population size of Tongcheng pigs before the 20th generation was 105, and the effective population size of the current generation was 94. There were 184 ROHs in total. The average ROH length was 23.71 Mb, of which 28.80% was between 15 and 20 Mb in length. The genomic inbreeding coefficient was 0.04%, indicating a low level of inbreeding. Taken together, the results show that the conservation population of Tongcheng pigs is a pure breed without stratification, and Tongcheng pigs had rich genetic diversity with remarkable population conservation effect.

Key words: Tongcheng pig, conservation, population structure, genetic diversity

中图分类号:

S828.2

袁娇, 徐国强, 周翔, 徐三平, 李胜, 黎望明, 刘榜. 基于SNP芯片监测通城猪的保种效果[J]. 畜牧兽医学报, 2022, 53(8): 2514-2523.

YUAN Jiao, XU Guoqiang, ZHOU Xiang, XU Sanping, LI Sheng, LI Wangming, LIU Bang. SNP Chip-Based Monitoring of Population Conservation Effect of Tongcheng Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2514-2523.

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基于SNP芯片监测通城猪的保种效果

SNP Chip-Based Monitoring of Population Conservation Effect of Tongcheng Pigs

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