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

Abstract

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

CLC Number:

S828

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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Detection of Genome-wide Copy Number Variation Using Porcine 50K SNP Beadchips in Longlin Pigs

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