Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Samples and Genotyping
2.3. Genome-Wide Detection of CNVs and CNVRs
2.4. Gene Contents and Functional Annotation
3. Results
3.1. Genome-Wide Detection of CNVs
3.2. Analysis of Genes within AHIPs and WECPs CNVR
3.3. Enrichment Analysis of Candidate Genes in WECPs and AHIPs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Group | Sample Size | Total Number of CNV | Unique Number of CNVR | Gain | Loss | Average Size (kb) | Max Size (kb) | Median Size (kb) | Min Size (kb) |
---|---|---|---|---|---|---|---|---|---|
AHIPs | 170 | 3863 | 225 | 47 | 178 | 1187.45 | 6400.56 | 774.74 | 25.44 |
WECPs | 150 | 7546 | 379 | 86 | 293 | 1459.32 | 9761.85 | 901.97 | 4.85 |
Total | 320 | 11409 | 604 | 133 | 471 | 1358.04 | 9761.85 | 4.85 |
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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
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 StyleXu, 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 StyleXu, 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