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

摘要/Abstract

摘要： 旨在探究五指山猪和杜洛克猪免疫和脂质代谢相关基因的选择信号差异。本研究从海南国家级五指山猪保种场采集30头4月龄健康(10公，20母)五指山猪的耳组织进行全基因组重测序(whole genome sequencing,WGS)，从NCBI数据库下载29头杜洛克猪全基因组重测序数据(SRA：PRJNA378496)；通过生物信息学方法分析59个样本WGS数据的单核苷酸多态性(single nucleotide polymorphism，SNPs)，进行SNPs过滤，定位SNPs在基因组的位置，分析其结构特征和基因型频率，并注释对应基因的功能；使用XP-CLR方法筛选五指山猪基因组受到强烈选择的区域，分析两个品种相关通路基因的功能差异。结果表明，五指山猪平均每个样本共筛选到36 961 902个SNPs位点，内含子区域分布最多，平均每个样本16 729 364个，约占45.26%，编码区(起始、终止密码子)平均有2 073个SNPs；五指山猪受选择的基因组区域主要集中在免疫、代谢和神经功能相关通路；免疫反应通路中，9个基因(TGFBR2、IL26、IL15、BMPR2、TNFSF15、TNFSF4、TNFSF8、ACKR4、TNFRSF11B)功能区域SNPs位点在五指山猪中只存在一种突变纯合基因型，而在杜洛克猪大部分个体中存在3种基因型(野生纯合基因型、杂合子、突变纯合基因型)，其中野生纯合基因型比例最高；脂类代谢通路中，关键调节基因IRS2、PRKG1、ADCY5的基因型频率与免疫反应基因类似。在五指山猪中突变纯合基因型比例为100%，在杜洛克猪中野生纯合基因型所占比例为48%~93%(14/29-27/29)。本研究筛选出与五指山猪免疫性状相关的候选基因9个、与脂类代谢相关的候选基因3个，发现五指山猪免疫、代谢和神经功能相关基因的受选择程度强于杜洛克猪，为揭示五指山猪特色性状形成的分子机制提供参考。

关键词: 五指山猪, 全基因组重测序, 单核苷酸多态性, XP-CLR选择信号, 炎症因子, 脂类代谢

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

中图分类号:

S828.2

任钰为, 王峰, 王成, 张艳, 孙瑞萍, 刘海隆, 乔传民, 邢漫萍, 黄丽丽, 曹宗喜, 晁哲. 五指山猪和杜洛克猪全基因组选择信号差异分析[J]. 畜牧兽医学报, 2022, 53(12): 4172-4182.

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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