浦市黑猪保种群体基于SNP芯片的遗传结构分析

邓缘; 崔清明; 陈四海; 左剑波; 刘莹莹; 朱吉; 任慧波; 胡雄贵; 李华丽; 喻国均; 陈晨; 彭英林

doi:10.19303/j.issn.1008-0384.2023.11.007

浦市黑猪保种群体基于SNP芯片的遗传结构分析

doi: 10.19303/j.issn.1008-0384.2023.11.007

1.
湖南省畜牧兽医研究所，湖南　长沙　410131
2.
湖南省泸溪县畜牧水产事务中心，湖南　泸溪　416100

基金项目: 湖南省自然科学基金项目（2021JJ30386）；湖南省创新平台与人才计划项目（2021NK1009）；湖南省重点研发计划项目（2020NK2024、2019NK2193）；湖南省重点实验室开放研究基金项目（2017TP1030）

详细信息

作者简介:
邓缘（1981 —），男，硕士，高级畜牧师，主要从事猪遗传育种方向研究，E-mail：369409457@qq.com

通讯作者:
陈晨（1986 —），男，博士，副研究员，主要从事猪遗传育种方向研究，E-mail：2004chch@163.com

彭英林（1965 —），男，博士，研究员，博士生导师，主要从事猪遗传育种方向研究，E-mail：13907487646@126.com

中图分类号: S828
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出版历程
- 收稿日期: 2023-02-03
- 修回日期: 2023-05-14
- 网络出版日期: 2023-12-21
- 刊出日期: 2023-11-28

Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip

1.
Hunan Institute of Animal and Veterinary Science, Changsha, Hunan　410131, China
2.
Animal Husbandry and Aquatic Products Affairs Center of Luxi County, Luxi, Hunan　416100, China

摘要

摘要: 目的通过SNP芯片技术分析浦市黑猪群体遗传多样性和家系结构，为保护和利用浦市黑猪资源提供支撑。方法利用“中芯一号”50K SNP芯片，对79头成年浦市黑猪（10头公猪、69头母猪）进行SNP测定，采用多种分析软件（Plink、Gmatix及Mega X）对群体遗传多样性和亲缘关系开展分析，进而构建群体家系结构。结果在79头浦市黑猪中共检出57466个SNPs位点，平均基因型检出率为99.15%。遗传多样性分析提示SNP位点具有多态性，群体存在近交（有效群体含量Ne仅为1.5，且平均观察杂合度＜平均期望杂合度）。群体平均状态同源（Idengtical by state，IBS）遗传距离为（0.294 9±0.072 6），公猪为（0.277 1±0.091 8），共检测到长纯合片段（Runs of hemozygosity，ROH）（29.60±16.12）个，其中长度在0～100 Mb的占40.5%，且群体基于ROH的平均近交系数为0.108。IBS距离矩阵、G矩阵结果以及群体ROH值的分析结果均反映出群体内个体之间存在较近的亲缘关系。根据群体进化树结果，将群体划分成2个含公猪的家系，以及1个不含公猪的家系。结论浦市黑猪群体家系少，各家系的个体数量差异大，近交程度高。因此，应注重引入或创建新的血统，扩大有效群体含量，降低近交系数。
- 浦市黑猪 /
- 保种群体 /
- SNP芯片 /
- 遗传多样性 /
- 亲缘关系
Abstract: Objective Genetic diversity and family structure of a preserved population of Pushi black pig were analyzed using the SNP bead chip for resource conservation. Method SNPs of 79 adult Pushi black pigs consisting of 10 boars and 69 sows were determined using Porcine 50K SNP Beadchips. Software, including Plink, Gmatix, and Mega X, was used to analyze the genetic diversity and phylogenetic relationships to construct phylogenetic structure of the pig population. Result A total of polymorphic 57466 SNP loci were found with an average genotype detection rate of 99.15%. The population showed evidence of inbreeding as the effective Ne was merely 1.5 and the average observed heterozygosity slightly below the expected level. The average distance of IBS was (0.2949±0.0726) and that for the boars (0.277 1±0.091 8). A total of (29.60±16.12) ROHs were detected with 40.5% of them between 0 and 100 Mb in length. The average inbreeding coefficient based on ROH was 0.108. The analysis on IBS distance matrix, G matrix, and population ROHs indicated a close genetic relationship among the individual animals. Based on the evolutionary tree, the population was divided into two families containing boars and one without. Conclusion The population of Pushi black pigs under study had only a few families, which varied greatly in number of members in each family and showed a high degree of inbreeding. Consequently, introducing or creating new lineages to expand the gene pool and reduce inbreeding coefficient for the population seemed imperative.
- Pushi black pig /
- preserved population /
- SNP chip /
- genetic diversity /
- phylogenetic relationship

HTML全文

图 1 基因组DNA电泳图

M：DNA相对分子质量标准；1−10：基因组DNA。

Figure 1. Electrophoresis of genomic DNA

M: DNA Marker；1−10: Genomic DNA.

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图 2 各染色体质控后SNP数量

Figure 2. SNP typing on chromosome after quality control

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图 3 浦市黑猪保种群遗传多样性结果

Figure 3. Genetic diversity of preserved population of Pushi black pigs

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图 4 浦市黑猪保种群G矩阵可视化结果

矩阵中每一个小方格代表两两样本之间的亲缘关系值，两个体亲缘关系越近，对应方格越接近红色。

Figure 4. Visualized G matrix on Pushi black pig population

Small square in matrix shows relationship between pair of samples; redder color indicates closer relationship.

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图 5 浦市黑猪公猪样本聚类分析结果

图中数字为公猪耳号，被评估为同一家系的样本标注同一种颜色。

Figure 5. Clusters of Pushi black boars

Codes are IDs of individual boars; pigs of same family shown in same color.

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图 6 浦市黑猪群体所有样本聚类分析结果

图中数字为个体号，标颜色的为公猪样本，一种颜色代表一个家系。

Figure 6. Clusters of all Pushi black pigs

Codes are IDs of individual pigs; boars are colored; same family shown in same color.

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图 7 浦市黑猪ROH长度的样本数分布

Figure 7. Distribution of total ROH length of Pushi black pigs

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图 8 基于ROH片段数量的浦市黑猪样本数

Figure 8. Sample number of Pushi black pigs based on number of ROH fragments

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图 9 基于ROH的近交系数可视化结果

P1代表浦市黑猪群体F_ROH的中位数，P2和P3分别代表浦市黑猪群体F_ROH的上四分位数和下四分位数。图中越宽的部分表示处于该水平值的群体F_ROH的样本数越多，反之则越少。

Figure 9. Visualized inbreeding coefficient based on ROH

P1: Median F_ROH of Pushi black pigs; P2 and P3: upper and lower quartile F_ROH of Pushi black pigs, respectively; wider portion indicates more samples at median F_ROH.

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