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

Abstract

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

CLC Number:

S828.2

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.

Figures/Tables 7

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References 44

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

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