基于SNP芯片的丫杈猪保种群体遗传结构研究

doi:10.11843/j.issn.0366-6964.2023.06.011

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (6): 2308-2319.doi: 10.11843/j.issn.0366-6964.2023.06.011

基于SNP芯片的丫杈猪保种群体遗传结构研究

陶璇¹, 杨雪梅¹, 梁艳¹, 刘一辉², 汪勇³, 孔繁晶⁴, 雷云峰¹, 杨跃奎¹, 王言¹, 安瑞¹, 杨坤¹, 吕学斌¹, 何志平^1*, 顾以韧^1*

1. 四川省畜牧科学研究院, 动物遗传育种四川省重点实验室, 成都 610066;
2. 四川省畜牧总站, 成都 610041;
3. 泸州市农业农村局, 泸州 646000;
4. 泸州市现代农业发展促进中心, 泸州 646000

收稿日期:2022-09-20 出版日期:2023-06-23 发布日期:2023-06-16
通讯作者: 顾以韧,主要从事猪遗传育种与繁殖研究,E-mail:463849195@qq.com;何志平,主要从事猪遗传育种与繁殖研究,E-mail:813674728@qq.com
作者简介:陶璇(1982-),男,四川金堂人,副研究员,硕士,主要从事猪遗传育种与繁殖研究,E-mail:631950921@qq.com
基金资助:
国家重点研发项目(2021YFD1301101;2021YFD1301104);四川省科研院所基本科研项目(SASA202102);四川省科技创新人才项目(2022JDRC0037);四川省重大科技专项(2021ZDZX0011;2021ZDZX0008);国家自然科学基金区域创新发展项目(U19A2036);四川省重点研发项目(2021YFYZ0030;2021YFYZ0009;2019YFN0004;2020YFN0147;2022YFN0047;2023YFN0088);财政部和农业农村部:国家现代农业产业技术体系(CARS-35);现代农业产业技术体系四川创新团队(SCCXTD-2023-08-01;SCCXTD-2023-08-05;SCCXTD-2023-08-08);四川省财政专项(SASA2022CZYX001)

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

TAO Xuan¹, YANG Xuemei¹, LIANG Yan¹, LIU Yihui², WANG Yong³, KONG Fanjing⁴, LEI Yunfeng¹, YANG Yuekui¹, WANG Yan¹, AN Rui¹, YANG Kun¹, Lü Xuebin¹, HE Zhiping^1*, GU Yiren^1*

1. Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China;
2. Sichuan Animal Husbandry Station, Chengdu 610041, China;
3. Luzhou Municipal Bureau of Agriculture and Rural Affairs, Luzhou 646000, China;
4. Luzhou Modern Agriculture Development Promotion Center, Luzhou 646000, China

Received:2022-09-20 Online:2023-06-23 Published:2023-06-16

摘要/Abstract

摘要： 旨在研究丫杈猪保种群体的遗传多样性、亲缘关系和家系结构。本研究采用"中芯一号"芯片检测了166头丫杈种猪的单核苷酸多态性(single nucleotide polymorphism,SNP);利用Plink软件计算观察杂合度、期望杂合度、多态信息含量、最小等位基因频率,分析丫杈猪群体的遗传多样性;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GCTA软件构建G矩阵,分析丫杈猪群体的亲缘关系;采用Mega X软件构建群体进化树,分析丫杈猪群体的家系结构。结果显示,166头丫杈猪共检测到45 211个SNPs位点,通过质量控制的SNP位点有36 243个;有效等位基因数为1.529,多态性信息含量为0.254,多态性标记比例为0.875,最小等位基因频率为0.233;期望杂合度为0.329,观察杂合度为0.344;状态同源平均遗传距离为0.259 5,状态同源距离矩阵和G矩阵结果均表明大部分丫杈猪呈中等程度的亲缘关系;ROH片段共有3 226个,其中40.96%的长度在0~100 Mb之间,基于ROH的平均近交系数为0.069;群体进化树结果表明,丫杈猪公猪被分为8个血缘,数量与传统系谱记录的相同,但血缘间有个体差异。综上所述,丫杈猪保种群的有效群体含量偏低,遗传多样性中等偏低,近交程度不严重,可引入或创建新血缘,扩大有效群体含量,提高群体遗传多样性。

关键词: 丫杈猪, SNP芯片, 遗传多样性, 遗传结构

Abstract: This experiment was conducted to study the genetic diversity, relationship and family structure of Yacha pigs conserved population. The single nucleotide polymorphism (SNP) in 166 Yacha pigs was detected by 50K SNP bead chip. The observed heterozygosity, expected heterozygosity, polymorphism information content and minor allele frequency were calculated by Plink software to analyze the genetic diversity of Yacha conserved population. The runs of homozygosity (ROH) were calculated and identity by state (IBS) distance matrix was constructed by Plink software. The genetic relationship was analyzed according to the G matrix result constructed by GCTA software. The phylogenetic tree constructed by Mega X software was used to analyze the family structure of Yacha conserved population. The results showed that, 45 211 SNPs were detected in 166 Yacha pigs, in which 36 243 SNPs passed quality control. The effective allele number, polymorphism information content, proportion of polymorphic markers, minor allele frequency were 1.529, 0.254, 0.875 and 0.233, respectively. The expected heterozygosity and observed heterozygosity were 0.329 and 0.344, respectively. The average IBS genetic distance of Yacha conserved population was 0.259 5, the result of IBS genetic distance and G matrix showed that most Yacha pigs had moderately genetic relationship. A total of 3 226 ROHs were detected, and the length of 40.96% of these ROHs was less than 100 Mb. The average inbreeding coefficient based on ROH was 0.069. The phylogenetic tree result showed that, there were 8 families in Yacha boars, which is the same as that by manual pedigrees, but with individual differences among families. In summary, the effective population size and the genetic diversity of Yacha conserved population is low, while the inbreeding degree is not serious. Therefore, it’s necessary to importing or creating new blood to expand the effective population content and improve the genetic diversity of the population.

Key words: Yacha pig, SNP chip, genetic diversity, genetic structure

中图分类号:

S828.2

陶璇, 杨雪梅, 梁艳, 刘一辉, 汪勇, 孔繁晶, 雷云峰, 杨跃奎, 王言, 安瑞, 杨坤, 吕学斌, 何志平, 顾以韧. 基于SNP芯片的丫杈猪保种群体遗传结构研究[J]. 畜牧兽医学报, 2023, 54(6): 2308-2319.

TAO Xuan, YANG Xuemei, LIANG Yan, LIU Yihui, WANG Yong, KONG Fanjing, LEI Yunfeng, YANG Yuekui, WANG Yan, AN Rui, YANG Kun, Lü Xuebin, HE Zhiping, GU Yiren. Analysis of Genetic Structure of Conservation Population in Yacha Pig Based on SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2308-2319.

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基于SNP芯片的丫杈猪保种群体遗传结构研究

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

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