基于SNP芯片分析青峪猪保种群体的遗传结构

doi:10.11843/j.issn.0366-6964.2020.02.007

畜牧兽医学报 ›› 2020, Vol. 51 ›› Issue (2): 260-269.doi: 10.11843/j.issn.0366-6964.2020.02.007

基于SNP芯片分析青峪猪保种群体的遗传结构

刘彬^1,2, 沈林園^1,2, 陈映^1,3, 李强³, 廖坤⁴, 郭芝忺^1,2, 张顺华^1,2, 朱砺^1,2*

1. 四川农业大学动物科技学院, 成都 611130;
2. 四川农业大学畜禽遗传资源发掘与创新利用四川省重点实验室, 成都 611130;
3. 四川省畜牧总站, 成都 610041;
4. 通江县畜牧站, 通江 636700

收稿日期:2019-07-18 出版日期:2020-02-23 发布日期:2020-02-22
通讯作者: 朱砺,主要从事猪的遗传育种研究,E-mail:zhuli7508@163.com
作者简介:刘彬(1994-),男,四川德阳人,硕士,主要从事猪的遗传育种研究,E-mail:13018240830@163.com;沈林園(1987-),男,四川广安人,讲师,主要从事猪的遗传育种研究,E-mail:shenlinyuan0815@163.com
基金资助:
国家重点研发计划项目（2018YFD0501004）；四川省科技支撑项目（2016NYZ0050）；国家现代农业产业技术体系四川生猪创新团队项目（SCSZTD-3-008）；四川省畜牧总站畜禽遗传资源保护项目

Analysis of Genetic Structure of Conservation Population in Qingyu Pig Based on SNP Chip

LIU Bin^1,2, SHEN Linyuan^1,2, CHEN Ying^1,3, LI Qiang³, LIAO Kun⁴, GUO Zhixian^1,2, ZHANG Shunhua^1,2, ZHU Li^1,2*

1. College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
2. Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China;
3. Sichuan Animal Husbandry Station, Chengdu 610041, China;
4. Tongjiang County Animal Husbandry Station, Tongjiang 636700, China

Received:2019-07-18 Online:2020-02-23 Published:2020-02-22

摘要/Abstract

摘要： 为了更好地了解青峪猪在世代更替过程中遗传结构的变化，更好的保护和利用青峪猪遗传资源，本研究利用50K SNP芯片，对青峪猪保种群内141头（26头公猪，115头母猪）健康成年个体进行SNP测定，通过多种分析软件对青峪猪保种群体和各个世代进行系谱校正，进而实施群体遗传多样性、遗传距离以及遗传结构变化等分析。结果显示，该封闭保种群由3个重叠世代构成，群体有效含量为12头，且整个群体可以分为6个含有公猪的家系和1个不含公猪的家系。其中，第3世代的有效群体含量最少，仅为3头，多态性标记比例随着世代的增加不断下降；141头青峪猪的平均遗传距离为（0.260 4±0.025 2），26头种公猪的遗传距离为（0.263 3±0.023 7）。随着繁殖世代的增加，各世代群体的遗传距离有轻微的上升趋势，部分种猪之间的亲缘关系和遗传距离较近；在141头青峪猪群体中共检测到1 481个基因组上长纯合片段（runs of hemozygosity，ROH），78.01%的长度在200 Mb以内，基于ROH值计算的近交系数表明整个群体的平均近交系数为0.055，且各世代的近交系数在不断上升，到第3世代时已经达到了0.075。综上所述，通过对青峪猪分子水平的群体遗传结构研究表明，该保种群体在闭锁的继代繁育过程中存在群体遗传多样性损失，需要加强选配或导入外血以确保青峪猪遗传资源的长期保存。

关键词: SNP芯片, 青峪猪, 群体遗传结构

Abstract: In order to better understand the genetic structure changes of Qingyu pig in the process of generation replacement, and better protect and utilize the genetic resources of Qingyu pig, the 50K SNP chip was used to measure SNP of 141 healthy adult individuals (26 boars, 115 sows) in Qingyu pig population. The pedigree of Qingyu pig population and each generation was corrected by various analysis softwares, and then the genetic diversity, genetic distance and genetic structure changes were analyzed. The results showed that the closed population was composed of 3 overlapping generations, the effective size of the population was 12, and the whole population could be divided into 6 families with boar and 1 family without boar. Among them, the effective size of the 3rd generation was the least, only three. The proportion of polymorphism markers decreased with the increase of generation. The average genetic distance of 141 Qingyu pigs was (0.260 4±0.025 2), and that of 26 boars was (0.263 3±0.023 7). With the increase of reproductive generations, the genetic distance of each generation population had a slight upward trend, and the genetic relationship and genetic distance between some breeding pigs were relatively closer; in 141 Qingyu pig population, 1 481 long homozygous segments (ROH) were detected, 78.01% of which were within 200 Mb. The inbreeding coefficient based on the ROH value showed that the average inbreeding coefficient of the whole population was 0.055, and the inbreeding coefficient of each generation continuously rose, reaching 0.075 by the 3rd generation. In conclusion, the study on the genetic structure of Qingyu pig population at the molecular level shows that there is a loss of population genetic diversity in the process of closed subsequent breeding, and it is necessary to strengthen the selection mating system or introduce external blood to ensure the long-term preservation of the genetic resources of Qingyu pig.

Key words: SNP chip, Qingyu pig, population genetic structure

中图分类号:

S828.2

刘彬, 沈林園, 陈映, 李强, 廖坤, 郭芝忺, 张顺华, 朱砺. 基于SNP芯片分析青峪猪保种群体的遗传结构[J]. 畜牧兽医学报, 2020, 51(2): 260-269.

LIU Bin, SHEN Linyuan, CHEN Ying, LI Qiang, LIAO Kun, GUO Zhixian, ZHANG Shunhua, ZHU Li. Analysis of Genetic Structure of Conservation Population in Qingyu Pig Based on SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(2): 260-269.

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基于SNP芯片分析青峪猪保种群体的遗传结构

Analysis of Genetic Structure of Conservation Population in Qingyu Pig Based on SNP Chip

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