基于填充测序数据的荣昌猪群体遗传结构和选择信号分析

doi:10.11843/j.issn.0366-6964.2025.01.014

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (1): 147-158.doi: 10.11843/j.issn.0366-6964.2025.01.014

基于填充测序数据的荣昌猪群体遗传结构和选择信号分析

吴平先¹^,²(), 王俊戈¹, 刁淑琪¹^,², 柴捷¹^,², 查琳⁴, 郭宗义¹^,², 陈红跃³, 龙熙¹^,²^,*()

1. 重庆市畜牧科学院, 重庆 402460
2. 国家生猪技术创新中心, 重庆 402460
3. 重庆市畜牧技术推广总站, 重庆 401120
4. 内江市农业科学院, 内江 641000

收稿日期:2024-08-09 出版日期:2025-01-23 发布日期:2025-01-18
通讯作者: 龙熙 E-mail:wupingxianxian@163.com;981568078@qq.com
作者简介:吴平先(1993-)，男，四川雅安人，副研究员，博士，主要从事猪遗传育种研究，E-mail: wupingxianxian@163.com
基金资助:
重庆市博士后特别资助项目(22327)；国家生猪技术创新中心先导科技项目(22601)；重庆市现代农业产业技术体系创新团队项目(23319)

Analysis of Genetic Architecture Characteristics and Selection Signature by Imputed Whole Genome Sequencing Data in Rongchang Pigs

WU Pingxian¹^,²(), WANG Junge¹, DIAO Shuqi¹^,², CHAI Jie¹^,², ZHA Lin⁴, GUO Zongyi¹^,², CHEN Hongyue³, LONG Xi¹^,²^,*()

1. Chongqing Academy of Animal Sciences, Chongqing 402460, China
2. National Center of Technology Innovation for Pigs, Chongqing 402460, China
3. Chongqing Animal Husbandry Technology Extension Station, Chongqing 401120, China
4. Neijiang Academy of Agricultural Sciences, Neijiang 641000, China

Received:2024-08-09 Online:2025-01-23 Published:2025-01-18
Contact: LONG Xi E-mail:wupingxianxian@163.com;981568078@qq.com

摘要/Abstract

摘要：

旨在基于填充序列数据，通过选择信号分析挖掘荣昌猪重要经济性状相关的候选基因，探究其在人工和自然选择过程中的受选择情况。本研究选取591头荣昌猪进行猪50K基因分型，随机选取其中120头进行全基因组测序，以全基因组重测序数据为填充参考模板对50K基因数据进行填充，基于填充序列数据开展遗传结构、Tajima’D和CLR分析。基因型填充后，基因型填充正确率为0.942，质控后保留了8 823 367个高质量SNPs(填充正确率为1.00)。遗传结构分析显示，荣昌猪群体不存在明显的群体分层，且绝大部分个体间遗传距离>0.1，分子亲缘系数 < 0.1。CLR检验筛选到226个潜在受选择区域，基因注释发现与繁殖、生长、胴体等性状相关的候选基因(CDK9、SLC2A8、IGF1R、GSK3B等基因)。利用Tajima’D检验检测到225个潜在受选择区域，基因注释发现与毛长度(CFAP299)、毛色或耳聋(MITF、ZNF532)、脂肪沉积(GSK3B)、繁殖(FOXP1)等性状相关的基因。进一步整合不同方法分析结果，发现11个相同的潜在受选择区域和123个候选基因，包括MITF、ZNF532、GSK3B等与耳聋和白化病、繁殖等经济性状相关的基因，并且发现1条显著的GO条目和KEGG通路(P < 0.05)与黑色素生成、视觉发育等通路相关。本研究根据富集分析结果和基因分子生物学功能，筛选出MITF、ZNF532、GSK3B、FOXP1、SLC2A8、CDK9、IGF1R、TBC1D4等8个重要候选基因可能参与调控荣昌猪毛色、耳聋、脂肪沉积、繁殖性能、生长性能等经济性状相关。该结果从全基因组水平探究了荣昌猪的遗传结构和选择信号特征，筛选出的重要候选基因为后续荣昌猪保种育种和特色性状的遗传机制解析提供了重要的理论参考。

关键词: 荣昌猪, 全基因组测序, 基因型填充, 遗传结构, 选择信号

Abstract:

This study aimed to identify the candidate genes associated with important economic traits of Rongchang pigs in the process of artificial and natural selection by selection signal analysis based on the imputed sequence data. In this study, a total of 591 Rongchang pigs were genotyped by porcine 50K SNP chip, among these, 120 pigs were randomly selected to perform whole genome sequencing. The whole genome resequencing data was used as reference template to imputed 50K SNP data. Then genetic structure analysis, Tajima'D and CLR tests were conducted based on the imputed sequence data. After genotype imputation, the imputation accuracy was 0.942, and 8 823 367 high-quality SNPs were retained after quality control (the imputation accuracy was 1.00). The genetic structure analysis showed that there was no obvious population stratification in Rongchang pig, and the genetic distance among most individuals was greater than 0.1, and the numerator relationship was less than 0.1. The CLR test detected 226 potential selected regions and found candidate genes (CDK9, SLC2A8, IGF1R, GSK3B) related to reproduction, growth and carcass traits through gene annotation. The Tajima'D test detected 225 potential selected regions, and gene annotation found that genes associated with hair length (CFAP299), hair color or deafness (MITF, ZNF532), fat deposition (GSK3B), and reproduction (FOXP1). Further analysis, a total of 11 same potential selected regions between the results of CLR and Tajima'D test were found, and 123 candidate genes related to important economic traits such as reproduction (ZNF532 and GSK3B), deafness and albinism(MITF)were screened. Moreover, a significant GO term and KEGG pathway (P < 0.05) related to melanin generation and ocular vision development was found. In this study, according to the results of enrichment analysis and molecular biological functions of genes, 8 important candidate genes, including MITF, ZNF532, GSK3B, FOXP1, SLC2A8, CDK9, IGF1R and TBC1D4, were suggested as the candidate genes for hair color and deafness, fat deposit, reproductive performance and growth performance in Rongchang pigs. These results explored the genetic structure and selection signature characteristics of Rongchang pigs at the whole genome level, the identified candidate genes associated with important economic traits provided an important theoretical reference for future breeding and genetic mechanism analysis of characteristic traits in Rongchang pigs.

Key words: Rongchang pig, whole genome sequencing, genotype imputation, genetic architecture, selection signature

中图分类号:

S828.2

吴平先, 王俊戈, 刁淑琪, 柴捷, 查琳, 郭宗义, 陈红跃, 龙熙. 基于填充测序数据的荣昌猪群体遗传结构和选择信号分析[J]. 畜牧兽医学报, 2025, 56(1): 147-158.

WU Pingxian, WANG Junge, DIAO Shuqi, CHAI Jie, ZHA Lin, GUO Zongyi, CHEN Hongyue, LONG Xi. Analysis of Genetic Architecture Characteristics and Selection Signature by Imputed Whole Genome Sequencing Data in Rongchang Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(1): 147-158.

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染色体 Chromosome	候选区域/Mb Region	基因 Gene
1	107.68~108.42	CSNK1G1、PPIB、SNX22、SNX1、CIAO2A、DAPK2、HERC1、FBXL22、USP3
1	159.7~162.25	CDH20、MC4R、PMAIP1、CCBE1、LMAN1、CPLX4、RAX、GRP、SEC11C、ZNF532、MALT1、ALPK2
4	80.05~80.31	SPIDR
6	37.25~40.23	NETO2、DNAJA2、GPT2、C16orf87、MYLK3、ORC6、VPS35、SHCBP1、UQCRFS1、VSTM2B、POP4、PLEKHF1、C19orf12、URI1
11	46.28~48.45	TBC1D4、UCHL3、LMO7
11	49.03~49.85	KCTD12、ACOD1、CLN5、FBXL3、MYCBP2、SCEL、SLAIN1
13	34.25~34.97	TWF2、PPM1M、WDR82、MIRLET7G、GLYCTK、MIR135A1、DNAH1、BAP1、PHF7等
13	46.11~54.30	MITF、GSK3B、FOXP1、ADAMTS9、MAGI1、SLC25A26、LRIG1、KBTBD8、SUCLG2、ARL6IP5、LMOD3、FRMD4B等
13	139.98~141.27	GPR156、NR1I2、CFAP91、COX17、POPDC2、PLA1A、ADPRH、CD80等
15	51.75~51.96	—
15	89.48~90.07	ZNF804A

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基于填充测序数据的荣昌猪群体遗传结构和选择信号分析

Analysis of Genetic Architecture Characteristics and Selection Signature by Imputed Whole Genome Sequencing Data in Rongchang Pigs

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