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Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip

文献类型： 外文期刊

作者： Xu, Chengliang 1 ; Zhang, Wei 1 ; Jiang, Yao 3 ; Zhou, Mei 1 ; Liu, Linqing 1 ; Su, Shiguang 1 ; Li, Xueting 1 ; Wang, Chonglong 1 ;

作者机构： 1.Anhui Acad Agr Sci, Inst Anim Husb & Vet Med, Key Lab Pig Mol Quantitat Genet, Anhui Prov Key Lab Livestock & Poultry Prod Safety, Hefei 230031, Peoples R China

2.Yunnan Agr Univ, Fac Anim Sci & Technol, Kunming 650500, Peoples R China

3.Natl Anim Husb Serv, Beijing 100125, Peoples R China

关键词： copy number variation; Anhui indigenous pig breeds; Western commercial pig breeds; SNP; immune; meat quality

期刊名称：GENES （ 影响因子：3.5； 五年影响因子：3.9 ）

ISSN：

年卷期： 2023 年 14 卷 3 期

页码：

收录情况： SCI

摘要： Copy number variation (CNV) is an important class of genetic variations widely associated with the porcine genome, but little is known about the characteristics of CNVs in foreign and indigenous pig breeds. We performed a genome-wide comparison of CNVs between Anhui indigenous pig (AHIP) and Western commercial pig (WECP) breeds based on data from the Porcine 80K SNP BeadChip. After analysis using the PennCNV software, we detected 3863 and 7546 CNVs in the AHIP and WECP populations, respectively. We obtained 225 (loss: 178, gain: 47) and 379 (loss: 293, gain: 86) copy number variation regions (CNVRs) randomly distributed across the autosomes of the AHIP and WECP populations, accounting for 10.90% and 22.57% of the porcine autosomal genome, respectively. Functional enrichment analysis of genes in the CNVRs identified genes related to immunity (FOXJ1, FOXK2, MBL2, TNFRSF4, SIRT1, NCF1) and meat quality (DGAT1, NT5E) in the WECP population; these genes were a loss event in the WECP population. This study provides important information on CNV differences between foreign and indigenous pig breeds, making it possible to provide a reference for future improvement of these breeds and their production performance.

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