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Volume 14
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10.3390/genes14030654
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Article

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

by
Chengliang Xu
1,2,†,
Wei Zhang
1,†,
Yao Jiang
3,
Mei Zhou
1,
Linqing Liu
1,
Shiguang Su
1,
Xueting Li
1 and
Chonglong Wang
1,*
1
Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
2
Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650500, China
3
National Animal Husbandry Service, Beijing 100125, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2023, 14(3), 654; https://doi.org/10.3390/genes14030654
Submission received: 19 January 2023 / Revised: 27 February 2023 / Accepted: 1 March 2023 / Published: 5 March 2023
(This article belongs to the Special Issue Recent Advances in Pig Molecular Genetics and Breeding)
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Abstract

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.
Keywords: copy number variation; Anhui indigenous pig breeds; Western commercial pig breeds; SNP; immune; meat quality copy number variation; Anhui indigenous pig breeds; Western commercial pig breeds; SNP; immune; meat quality

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MDPI and ACS Style

Xu, C.; Zhang, W.; Jiang, Y.; Zhou, M.; Liu, L.; Su, S.; Li, X.; Wang, C. Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip. Genes 2023, 14, 654. https://doi.org/10.3390/genes14030654

AMA Style

Xu C, Zhang W, Jiang Y, Zhou M, Liu L, Su S, Li X, Wang C. Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip. Genes. 2023; 14(3):654. https://doi.org/10.3390/genes14030654

Chicago/Turabian Style

Xu, Chengliang, Wei Zhang, Yao Jiang, Mei Zhou, Linqing Liu, Shiguang Su, Xueting Li, and Chonglong Wang. 2023. "Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip" Genes 14, no. 3: 654. https://doi.org/10.3390/genes14030654

APA Style

Xu, C., Zhang, W., Jiang, Y., Zhou, M., Liu, L., Su, S., Li, X., & Wang, C. (2023). Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip. Genes, 14(3), 654. https://doi.org/10.3390/genes14030654

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