利用全基因组选择信号方法鉴别影响猪肉滴水损失的候选基因

doi:10.11843/j.issn.0366-6964.2022.05.006

畜牧兽医学报 ›› 2022, Vol. 53 ›› Issue (5): 1373-1383.doi: 10.11843/j.issn.0366-6964.2022.05.006

利用全基因组选择信号方法鉴别影响猪肉滴水损失的候选基因

陶伟^1,2, 侯黎明^1,2, 王彬彬^1,2, 刘航^1,2, 李开军^1,2, 尹彦镇^1,2, 郭皓^1,2, 牛培培², 张总平², 李强³, 黄瑞华^1,2,4*, 李平华^1,2,4*

1. 南京农业大学养猪研究所, 南京 210095;
2. 南京农业大学淮安研究院, 淮安 223001;
3. 淮安市淮阴新淮种猪场, 淮安 223322;
4. 江苏现代农业 (生猪) 产业体系集成创新中心, 南京 210095

收稿日期:2021-09-09 出版日期:2022-05-23 发布日期:2022-05-25
通讯作者: 李平华,主要从事猪健康生产学与遗传育种学研究,E-mail:lipinghua718@njau.edu.cn;黄瑞华,主要从事猪健康生产学与遗传育种学研究,E-mail:rhhuang@njau.edu.cn
作者简介:陶伟(1997-),男,山东菏泽人,硕士生,主要从事猪数量遗传学研究,E-mail:1994829469@qq.com
基金资助:
国家自然科学基金(U1904115)；农业品种改良提升专项(19210387)；江苏省农业重大新品种创制项目(PZCZ201732)；2017年度“淮上英才计划”创新创业领军人才项目

Identification of Candidate Genes Affecting Drip Loss in Pork by Genome-wide Selection Signal Method

TAO Wei^1,2, HOU Liming^1,2, WANG Binbin^1,2, LIU Hang^1,2, LI Kaijun^1,2, YIN Yanzhen^1,2, GUO Hao^1,2, NIU Peipei², ZHANG Zongping², LI Qiang³, HUANG Ruihua^1,2,4*, LI Pinghua^1,2,4*

1. Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China;
2. Huai'an Academy, Nanjing Agricultural University, Huai'an 223001, China;
3. Huaiyin Xinhuai Pig Breeding Farm of Huai'an City, Huai'an 223322, China;
4. Industrial Technology System Integration Innovation Center of Jiangsu Modern Agriculture (Pig), Nanjing 210095, China

Received:2021-09-09 Online:2022-05-23 Published:2022-05-25

摘要/Abstract

摘要： 旨在鉴定影响猪群体滴水损失变异的相关候选基因，为猪肉质选育奠定基础。本研究利用478头体质健康，平均日龄为237.95 d的苏淮猪个体，其中阉公猪290头，母猪188头。采集所有个体的背最长肌样本后，采用吊袋法测定滴水损失(drip loss, DL)表型，计算群体滴水损失估计育种值(estimated breeding value, EBV)，选择其中EBV极高(N=48)和极低(N=48)各10% 的个体进行猪80K芯片基因分型。借助群体分化指数(fixation index, Fst)和基于单倍型信息的单倍型积分值(integrated haplotype score, iHS)方法对苏淮猪进行全基因组选择信号检测，选择 iHS值在前5%，同时Fst值≥0.15的SNP位点作为受选择的位点，接着对受选择SNP上、下游各50 kb的区域进行基因注释，并对所有基因进行KEGG和GO富集分析，鉴别与猪滴水损失相关的候选基因。通过对芯片分型数据质控后，96个样本的51 705个有效SNPs用于后续分析。通过Fst和iHS选择信号合并分析，共筛选出175个受选择的SNPs，主要位于1、6、7、11号染色体上，其中仅有27个SNPs位于已报道的影响猪滴水损失的QTL区域上。对受选择SNP 位点附近区域进行基因注释显示，175个SNPs涉及到 73 个基因，其中多个基因被报道与肌肉发育以及细胞氧化应激等功能相关，包括PACRG、EZR、MRTFA、LCP1和VKORC1L1基因，这5个基因都是新发现的功能上与猪滴水损失有关的候选基因。选择3个位于功能候选基因上，同时又位于QTL区域内的SNPs进行苏淮猪全群分型，并与滴水损失进行关联性分析。结果发现，位于MRTFA 基因上的rs340037952位点与苏淮猪群体滴水损失存在显著关联(P<0.05)，位于VKORC1L1基因上的rs320624660与苏淮猪群体滴水损失存在极显著关联(P<0.01)。本研究通过选择信号分析找到175个受选择的SNPs，基因功能注释鉴别到5个影响滴水损失的候选基因，还分别在MRTFA和VKORC1L1基因上鉴别到与苏淮猪群体的滴水损失存在显著关联的位点：rs340037952和rs320624660，为后续猪滴水损失性状的选育提供了前期基础。

关键词: 猪, 滴水损失, 选择信号, Fst, iHS, 候选基因

Abstract: The purpose of this study was to identify candidate genes affecting drip loss of pork, and to lay a foundation for meat quality breeding of pigs. The experimental population in this study was 478 healthy Suhuai pigs with an average age of 237.95 days, including 290 castrated boars and 188 sows. The longissimus dorsi muscle samples of all individuals were collected, and then the drip loss (DL) phenotype data were measured by hanging bag method to calculate the estimated breeding value (EBV) of drip loss, and Suhuai pigs with top 10% (N=48) and bottom 10% (N=48) of EBV_DL were selected for genotyping using the GeneSeek GGP-Porcine 80 K SNP BeadChip (Illumnia). The fixation index (Fst) and integrated haplotype score (iHS) were used to detect the whole genome selection signals of Suhuai pigs. We selected SNP sites with iHS value in the top 5% and Fst ≥ 0.15 as the selected SNPs, then gene annotation was performed within the region of 50 kb upstream and downstream of the selected SNPs, and all genes were analyzed for KEGG and GO enrichment to identify candidate genes associated with drip loss of pork. After the quality control of chip typing data, 51 705 valid SNPs from 96 samples were used for subsequent analysis. A total of 175 SNPs were screened by Fst and iHS selective signal analysis, they were mainly located on chromosome 1, 6, 7 and 11, of which only 27 SNPs were located in the QTL regions that have been reported to affect the drip loss of pork. Gene annotations of the area around the selected SNPs showed that 175 significant SNPs were involved 73 genes. Among these genes, several genes have been reported to be related to muscle development and cell oxidative stress, including PACRG, EZR, MRTFA, LCP1 and VKORC1L1. The 5 genes were newly discovered functional candidate genes that were related to the drip loss of pork. Then, we genotyped 3 SNPs located on the intron of the functional candidate genes and on the QTL region, and analyzed the correlation between genotypes of the 3 SNPs and the drip loss in the whole Suhuai pig population. The results showed that rs340037952 located on the MRTFA gene was significantly associated with drip loss in Suhuai pig population (P<0.05), and rs320624660 located on the VKORC1L1 gene was extremely significantly associated with drip loss in Suhuai pig population (P<0.01). In this study, 175 selected SNPs were found through selection signal analysis, 5 candidate genes affecting drip loss were identified by gene function annotation, and 2 SNPs (rs340037952 and rs320624660) significantly associated with drip loss in Suhuai pigs population were identified on MRTFA and VKORC1L1 genes, which provided a preliminary basis for the breeding of drip loss in pigs.

Key words: pig, drip loss, selection signals, Fst, iHS, candidate genes

中图分类号:

S828.2

陶伟, 侯黎明, 王彬彬, 刘航, 李开军, 尹彦镇, 郭皓, 牛培培, 张总平, 李强, 黄瑞华, 李平华. 利用全基因组选择信号方法鉴别影响猪肉滴水损失的候选基因[J]. 畜牧兽医学报, 2022, 53(5): 1373-1383.

TAO Wei, HOU Liming, WANG Binbin, LIU Hang, LI Kaijun, YIN Yanzhen, GUO Hao, NIU Peipei, ZHANG Zongping, LI Qiang, HUANG Ruihua, LI Pinghua. Identification of Candidate Genes Affecting Drip Loss in Pork by Genome-wide Selection Signal Method[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(5): 1373-1383.

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利用全基因组选择信号方法鉴别影响猪肉滴水损失的候选基因

Identification of Candidate Genes Affecting Drip Loss in Pork by Genome-wide Selection Signal Method

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