五指山猪和杜洛克猪全基因组选择信号差异分析

doi:10.11843/j.issn.0366-6964.2022.12.005

Abstract

Abstract: The purpose of this study was to investigate the selection signature differences of immune and lipid metabolic related genes between Wuzhishan pig and Duroc pig. The ear tissues were sampled from 30 individuals of 4 months old healthy Wuzhishan pig (10 boar and 20 sows) from Hainan National Conservation Farm of Wuzhishan Pig and performed whole genome sequencing (WGS), and the Duroc WGS data was download from the NCBI database (SRA: PRJNA378496). The single nucleotide polymorphisms (SNPs) of the WGS data of 59 samples were analyzed by bioinformatics methods. The SNPs were filtered, located in the genome, their structural characteristics, genotype frequency were analyzed, the functions of corresponding genes were annotated. The strongly selected regions of the Wuzhishan pig genome were screened using the XP-CLR method, and the functional differences of genes in related pathways of the two breeds was analyzed. The results showed that each Wuzhishan pig had 36 961 902 SNPs, and intron region had the largest number of 16 729 364 SNPs, taking account of 45.26%, and the coding region (start, end codons) had 2 073 SNPs. The selected signal regions screened by XP-CLR was focus on the immune response, metabolic, and neurological functions related pathways. In the immune response pathway, there was only one kind of mutation homozygous genotype in Wuzhishan pigs in the functional region SNPs of 9 genes (TGFBR2, IL26, IL15, BMPR2, TNFSF15, TNFSF4, TNFSF8, ACKR4, TNFRSF11B), while in Duroc, there are three kinds of genotypes (wild homozygous genotype, heterozygous, mutant homozygous genotype) in most individuals, among which the wild homozygous genotype had the highest proportion. In the lipid metabolism pathway, the genotype frequencies of key regulatory genes IRS2, PRKG1, and ADCY5 were similar to those of immune response genes. The proportion of mutant homozygous genotypes in Wuzhishan pigs was 100%, and the proportion of wild homozygous genotypes in Duroc pigs was 48%-93% (14/29-27/29). In this study, 9 candidate genes related to immune response and 3 candidate genes related to lipid metabolism were screened out in Wuzhishan pigs, and the candidate genes related to immune response, metabolic, and neurological functions showed stronger selection signature in Wuzhishan pig than that in Duroc pig, which provide a reference for revealing the molecular mechanism of the formation of characteristic traits of Wuzhishan pigs.

Key words: Wuzhishan pig, whole genome sequencing, single nucleotide polymorphisms (SNPs), XP-CLR selective signal, inflammatory factors, lipid metabolism

CLC Number:

S828.2

REN Yuwei, WANG Feng, WANG Cheng, ZHANG Yan, SUN Ruiping, LIU Hailong, QIAO Chuanmin, XING Manping, HUANG Lili, CAO Zongxi, CHAO Zhe. The Whole-Genome Selection Signature Differences between Wuzhishan Pig and Duroc Pig[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(12): 4172-4182.

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The Whole-Genome Selection Signature Differences between Wuzhishan Pig and Duroc Pig

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