全基因组选择信号解析剑白香猪和从江香猪的遗传差异

doi:10.11843/j.issn.0366-6964.2023.09.005

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (9): 3631-3641.doi: 10.11843/j.issn.0366-6964.2023.09.005

全基因组选择信号解析剑白香猪和从江香猪的遗传差异

袁巍^1,2,3, 毕欢^1,2,3, 张雨丹^1,2,3, 张依裕^1,2,3, 顾晓龙⁴, 杨红文⁵, 陈伟^1,2,3*

1. 贵州大学动物科学学院高原山地动物遗传育种与繁殖教育部重点实验室, 贵阳 550025;
2. 贵州省动物遗传育种与繁殖重点实验室, 贵阳 550025;
3. 贵州大学香猪研究所, 贵阳 550025;
4. 贵州省贵阳德康农牧有限公司, 贵阳 550025;
5. 贵州省畜禽遗传资源管理站, 贵阳 550025

收稿日期:2023-03-17 发布日期:2023-09-22
通讯作者: 陈伟,主要从事动物遗传育种的研究,E-mail:chenweigzu@163.com
作者简介:袁巍(1997-),男,湖南隆回人,硕士生,主要从事动物遗传育种的研究,E-mail:y-weii@qq.com
基金资助:
贵州省科技计划项目(黔科合支撑[2022]一般087);贵州大学引进人才科研项目(贵大人基合字[2019]34号);贵州省优秀青年科技人才培养计划黔科合平台人才([2021]5630号);贵州省生猪产业发展项目(2021);贵州省科技支撑计划(黔科合支撑[2021]一般147)

Deciphering Genome-wide Selection Signals Reveals Genetic Differences between Jianbai and Congjiang Xiang Pigs

YUAN Wei^1,2,3, BI Huan^1,2,3, ZHANG Yudan^1,2,3, ZHANG Yiyu^1,2,3, GU Xiaolong⁴, YANG Hongwen⁵, CHEN Wei^1,2,3*

1. Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountain Region of Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China;
2. Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China;
3. Institute of Xiang Pig Research, Guizhou University, Guiyang 550025, China;
4. Guizhou Dekang Agriculture and Animal Husbandry Co. Ltd., Guiyang 550025, China;
5. Guizhou Provincial Station for Animal Genetic Resources Management, Guiyang 550025, China

Received:2023-03-17 Published:2023-09-22

摘要/Abstract

摘要： 旨在通过全基因组选择信号分析揭示剑白香猪和从江香猪的遗传差异,提高对从江香猪和剑白香猪种群的保护状况、遗传多样性、群体结构和和适应性进化的认识。本研究随机选取2岁龄从江香猪和剑白香猪各5头,并分为两组。通过全基因组重测序对从江香猪和剑白香猪测序,将测序数据利用bwa软件比对到猪参考基因组Sscrofa 11.1上,随后使用GATK软件进行变异检测和SNP、INDEL过滤提取。同时,利用Plink和SNeP软件进行群体遗传多样性分析,包括群体有效大小、多态位点比例、观测杂合度、期望杂合度。使用vcftools软件分析群体选择信号,并通过KEGG和GO分析受选择区域基因。经过SNP和INDEL分析,发现从江香猪和剑白香猪群体共有的SNPs位点数为16 158 002个,从江香猪特有的为6 863 992个,剑白香猪特有的为4 275 660个;共有的INDEls位点数为3 275 375个,从江香猪特有的为1 674 081个,剑白香猪特有的为1 114 248个。从采样起算,从江香猪和剑白香猪的群体在13代前的有效大小均为18头。其中,从江香猪的多态性位点比例更高,达到了0.875 7,而二者群体的观测杂合度均高于期望杂合度。剑白香猪和从江香猪的核苷酸多样性均小于0.5%,群体内选择检验Tajima's D值均大于0,ROD值为0.553 1,Fst值为0.736 2。KEGG和GO富集分析表明,剑白香猪和从江香猪的遗传差异涉及多种通路和基因功能。包括涉及轴突引导、ECM与受体的相互作用、局部粘附、PI3K-Akt信号通路、硫辛酸代谢、cGMP-PKG信号通路、MAPK信号传导途径、核苷酸切除修复、阿佩林信号通路、心律失常性右室心肌病等通路。剑白香猪和从江香猪群体之间存在一定的群体多态性损失,群体分歧度较高,两亚群间存在明显的种群分化,并且二者基因组内存在大量的中等频率等位基因,需要提高从江香猪和剑白香猪群体内的遗传多样性,减少外来血缘引入导致纯种度降低的风险。

关键词: 全基因组, 选择信号, 香猪, 遗传差异

Abstract: The purpose was to unveil the genetic disparities between the Jianbai and Congjiang Xiang pigs breeds, enhance the understanding of their conservation status, genetic diversity, population structure, and adaptive evolution through whole-genome selection signal analysis. The 2-year-old Congjiang and Jianbai Xiang pigs were randomly selected and divided into two groups of 5 pigs each. Whole-genome resequencing was performed on Jianbai and Congjiang Xiang pigs, and the sequencing data was aligned to the pig reference genome Sscrofa 11.1 using the bwa software. Subsequently, the GATK software was used for variant detection and filtering of SNPs and INDELs. Additionally, population genetic diversity analysis, including effective population size, proportion of polymorphic loci, observed heterozygosity, and expected heterozygosity, was carried out using Plink and SNeP software. The population selection signals were analyzed using the vcftools software, and the selected genomic regions were subjected to KEGG and GO pathway analyses. After SNP and INDEL analysis, it was found that there were 16 158 002 common SNPs in the populations of Jianbai and Congjiang Xiang pigs, with 6 863 992 SNPs unique to Congjiang and 4 275 660 unique to Jianbai. The common INDELs were 3 275 375, with 1 674 081 INDELs unique to Congjiang and 1 114 248 unique to Jianbai. Starting from the sampling time point, the effective population size of both Congjiang and Jianxiang pig populations could be traced back to 18 individuals 13 generations ago. The Congjiang breed displayed a higher proportion of polymorphic loci, with a value of 0.875 7, whereas both populations had observed heterozygosity values exceeding the expected heterozygosity.Nucleotide diversity was less than 0.5% for both breeds, and Tajima's D was greater than 0, with ROD values of 0.553 1 and Fst values of 0.736 2. KEGG and GO enrichment analyses showed that the genetic differences between Jianbai and Congjiang Xiang pigs involved multiple pathways and gene functions, including axon guidance, ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway, lipoic acid metabolism, cGMP-PKG signaling pathway, MAPK signaling pathway, nucleotide excision repair, aspirin signaling pathway, and arrhythmogenic right ventricular cardiomyopathy. There are a certain loss of population polymorphism and a high degree of population divergence between the Jianbai and Congjiang pig populations. There is clear population differentiation between the two breeds, and both genomes exhibit a substantial number of alleles at intermediate frequencies. It is necessary to enhance the genetic diversity within the Congjiang and Jianbai Xiang pig populations and reduce the risk of decreased purity due to the introduction of foreign lineages.

Key words: whole genome, selection signals, Xiang pig, genetic differences

中图分类号:

S828.2

袁巍, 毕欢, 张雨丹, 张依裕, 顾晓龙, 杨红文, 陈伟. 全基因组选择信号解析剑白香猪和从江香猪的遗传差异[J]. 畜牧兽医学报, 2023, 54(9): 3631-3641.

YUAN Wei, BI Huan, ZHANG Yudan, ZHANG Yiyu, GU Xiaolong, YANG Hongwen, CHEN Wei. Deciphering Genome-wide Selection Signals Reveals Genetic Differences between Jianbai and Congjiang Xiang Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3631-3641.

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全基因组选择信号解析剑白香猪和从江香猪的遗传差异

Deciphering Genome-wide Selection Signals Reveals Genetic Differences between Jianbai and Congjiang Xiang Pigs

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