利用中芯一号SNP芯片检测隆林猪全基因组拷贝数变异

doi:10.16431/j.cnki.1671-7236.2022.01.003

摘要/Abstract

摘要： [目的] 检测隆林猪的全基因组拷贝数变异。[方法] 采集33头隆林猪的耳组织样本，通过酚-氯仿法提取DNA后，使用猪中芯一号50K SNP芯片进行基因分型，得到的原始数据通过Genomestudio软件和Linux系统进行处理，使用CNVPartition和PennCNV软件分别检测拷贝数变异（copy number variation，CNV），并利用Bedtools软件将CNV合并为拷贝数变异区域（copy number variation region，CNVR），使用Biomart对CNVR进行基因定位，利用David网站对定位到的基因进行GO和KEGG富集分析，使用猪QTL数据库对共同CNVR进行QTL注释。[结果] CNVPartition软件共检测到260个CNVs，合并为47个CNVRs，其中缺失型40个、获得型5个、混合型2个，共定位到84个基因，显著富集到13条信号通路；PennCNV软件共检测到96个CNVs，合并为15个CNVRs，其中缺失型9个、获得型1个、混合型5个，共定位到8个基因，显著富集到8条信号通路；2个软件检测结果定位到的基因主要富集在嗅觉相关通路和G-蛋白偶联相关通路中，其中INPP5B、NEURL1和GAPDHS基因显著富集到精子活力通路；2个软件获得了3个共同CNVRs，其中缺失型、获得型和混合型均为1个，共定位到8个基因，显著富集到涉及嗅觉感官知觉的化学刺激检测通路、嗅觉受体活性通路、嗅觉转导通路、G-蛋白偶联受体活性通路、G-蛋白偶联受体信号通路、膜整体组件通路和质膜通路共7条信号通路；共有130个QTLs与3个共同CNVRs重叠，其中与背膘厚、肉质和乳头数相关的QTLs分别有11、9和6个。[结论] 隆林猪CNV可能与嗅觉功能、繁殖性能、背膘厚、肉质和乳头数性状相关。

关键词: 隆林猪; 猪中芯一号50K SNP芯片; 拷贝数变异; 拷贝数变异区域

Abstract: [Objective] The genome-wide copy number variation in Longlin pigs was detected. [Method] Ear tissue samples from 33 Longlin pigs were collected. After extracting DNA by phenol-chloroform methods, the porcine 50K SNP beadchip was used to genotype. The raw dates were analyzed by Genomestudio software and Linux system. The copy number variation (CNV) was detected by CNVPartition and PennCNV softwares, then the Bedtools software was used to merge the CNVs as copy number variation region (CNVR). The Biomart was used to identify the genes in CNVR. The GO and KEGG enrichment analysis were completed by David website. The pig QTL database was used to annotate the QTL in common CNVR. [Result] 260 CNVs and 47 CNVRs were detected by CNVPartition, including 40 deletions, 5 duplications and 2 mixed. 84 genes were located, which were significantly enriched into 13 signal pathways. A total of 96 CNVs and 15 CNVRs were detected by PennCNV, including 9 deletions, 1 duplications and 5 mixed. 8 genes were located, which were significantly enriched into 8 signal pathways. The genes detected by the 2 software were mainly enriched in olfactory pathway and G-protein coupling pathway. INPP5B, NEURL1 and GAPDHS genes were significantly enriched in sperm motility pathway. 3 common CNVRs were obtained by Bedtools software, including 1 deletions, 1 duplications and 1 mixed. A total of 8 genes were located and significantly enriched into 7 signal pathways, including detection of chemical stimulus involved in sensory perception of smell pathway, olfactory receptor activity pathway, G-protein coupled receptor activity pathway, G-protein coupled receptor signaling pathway, olfactory transduction pathway, plasma membrane and integral component of membran pathway. A total of 130 QTLs were overlaid with 3 common CNVRs, including 11 backfat thickness QTLs, 9 meat quality QTLs and 6 teat number QTLs. [Conclusion] The CNV of Longlin pigs might be related to the olfactory function, reproduction ability, backfat thickness, meat quality and teat number.

Key words: Longlin pigs; porcine 50K SNP beadchip; CNV; CNVR

中图分类号:

S828

路玉洁, 莫家远, 朱思燃, 杨丽丽, 陈奎蓉, 吕冬玲, 李月月, 刘笑笑, 梁靓, 兰干球, 梁晶. 利用中芯一号SNP芯片检测隆林猪全基因组拷贝数变异[J]. 中国畜牧兽医, 2022, 49(1): 23-31.

LU Yujie, MO Jiayuan, ZHU Siran, YANG Lili, CHEN Kuirong, LYU Dongling, LI Yueyue, LIU Xiaoxiao, LIANG Liang, LAN Ganqiu, LIANG Jing. Detection of Genome-wide Copy Number Variation Using Porcine 50K SNP Beadchips in Longlin Pigs[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(1): 23-31.

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