Identification of Genome-Wide Copy Number Variations among Diverse Pig Breeds Using SNP Genotyping Arrays

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Wang, Jiying ^a,b   Wang, Haifei ^a   Jiang, Jicai ^a   Kang, Huimin ^a   Feng, Xiaotian ^a   Zhang, Qin ^a   Liu, Jian Feng ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b SHANDONG PEANUT RESEARCH INSTITUTE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREED; CONTROLLED STUDY; COPY NUMBER VARIATION; DISEASE PREDISPOSITION; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME; GENOTYPE; NONHUMAN; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; WILD BOAR;

ANIMALS; BREEDING; DNA COPY NUMBER VARIATIONS; GENOME; GENOTYPING TECHNIQUES; POLYMORPHISM, SINGLE NUCLEOTIDE; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SUS SCROFA;

EID: 84880730380     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068683     Document Type: Article

References (45)

1. Liu GE, Bickhart DM (2012) Copy number variation in the cattle genome. Funct Integr Genomics: 609-624.
2. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470: 59-65.
3. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
4. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
5. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
6. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, et al. (2010) Diversity of human copy number variation and multicopy genes. Science 330: 641-646.
7. Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, et al. (2010) Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 42: 400-405.
8. Henrichsen CN, Chaignat E, Reymond A, (2009) Copy number variants, diseases and gene expression. Hum mol genet 18: R1-8.
9. Zhang F, Gu W, Hurles ME, Lupski JR, (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10: 451-481.
10. Feuk L, Carson AR, Scherer SW, (2006) Structural variation in the human genome. Nat Rev Genet 7: 85-97.
11. Gamazon ER, Nicolae DL, Cox NJ, (2011) A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. PLoS Genet 7: e1001292.
12. Marklund S, Kijas J, Rodriguez-Martinez H, Rönnstrand L, Funa K, et al. (1998) Molecular basis for the dominant white phenotype in the domestic pig. Genome res 8: 826-833.
13. Giuffra E, Törnsten A, Marklund S, Bongcam-Rudloff E, Chardon P, et al. (2002) A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Mamm Genome 13: 569-577.
14. Pielberg GR, Golovko A, Sundström E, Curik I, Lennartsson J, et al. (2008) A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse. Nat genet 40: 1004-1009.
15. Seroussi E, Glick G, Shirak A, Yakobson E, Weller JI, et al. (2010) Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs. BMC genomics 11: 673.
16. Clop A, Vidal O, Amills M, (2012) Copy number variation in the genomes of domestic animals. Anim Genet 43: 503-517.
17. Alkan C, Coe BP, Eichler EE, (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12: 363-376.
18. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, et al. (2006) High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome res 16: 1136-1148.
19. Winchester L, Yau C, Ragoussis J, (2009) Comparing CNV detection methods for SNP arrays. Brief Funct Genomic Proteomic 8: 353-356.
20. Meurens F, Summerfield A, Nauwynck H, Saif L, Gerdts V, (2012) The pig: a model for human infectious diseases. Trends in Microbiol 20: 50-57.
21. Li Y, Mei S, Zhang X, Peng X, Liu G, et al. (2012) Identification of genome-wide copy number variations among diverse pig breeds by array CGH. BMC genomics 13: 725.
22. Fadista J, Nygaard M, Holm LE, Thomsen B, Bendixen C, (2008) A snapshot of CNVs in the pig genome. PLoS One 3: e3916.
23. Wang J, Jiang J, Fu W, Jiang L, Ding X, et al. (2012) A genome-wide detection of copy number variations using SNP genotyping arrays in swine. BMC genomics 13: 273.
24. Chen C, Qiao R, Wei R, Guo Y, Ai H, et al. (2012) A comprehensive survey of copy number variation in 18 diverse pig populations and identification of candidate copy number variable genes associated with complex traits. BMC genomics 13: 733.
25. Ramayo-Caldas Y, Castelló A, Pena RN, Alves E, Mercadé A, et al. (2010) Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip. BMC genomics 11: 593.
26. Rubin CJ, Megens HJ, Barrio AM, Maqbool K, Sayyab S, et al. (2012) Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A. 109: 19529-19536.
27. Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, et al. (2009) The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome res 19: 491-499.
28. Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, et al. (2011) Genomic characteristics of cattle copy number variations. BMC genomics 12: 127.
29. Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, et al. (2010) Analysis of copy number variations among diverse cattle breeds. Genome res 20: 693-703.
30. Zhang C, Plastow G, (2011) Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock. Curr Genomics 12: 138-146.
31. Zhang ZG, Li B, Chen X (1986) Pig breeds in China. Shanghai: Shanghai Scientific and Technical Publisher. 17-24.
32. Wang K, Li M, Hadley D, Liu R, Glessner J, et al. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome res 17: 1665-1674.
33. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. Nat genet 25: 25-29.
34. Hall MA, Norman PJ, Thiel B, Tiwari H, Peiffer A, et al. (2002) Quantitative-trait loci on chromosomes 1, 2, 3, 4, 8, 9, 11, 12, and 18 control variation in levels of T and B lymphocyte subpopulations. Am J Hum Genet 70: 1172-1182.
35. Ballester M, Castelló A, Ibáñez E, Sánchez A, Folch JM, (2004) Real-time quantitative PCR-based system for determining transgene copy number in transgenic animals. Biotechniques 37: 610-613.
36. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-[Delta][Delta] CT method. Methods 25: 402-408.
37. Ramos AM, Crooijmans R, Affara NA, Amaral AJ, Archibald AL, et al. (2009) Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4: e6524.
38. Matsuzaki H, Wang PH, Hu J, Rava R, Fu GK, (2009) High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians. Genome biol 10: R125.
39. Jiang L, Jiang J, Wang J, Ding X, Liu J, et al. (2012) Genome-Wide Identification of Copy Number Variations in Chinese Holstein. PLoS One 7: e48732.
40. Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, et al. (2008) High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genet 4: e1000249.
41. Nozawa M, Nei M, (2008) Genomic drift and copy number variation of chemosensory receptor genes in humans and mice. Cytogenet Genome Res 123: 263-269.
42. Nguyen D, Lee K, Choi H, Choi M, Le M, et al. (2012) The complete swine olfactory subgenome: expansion of the olfactory gene repertoire in the pig genome. BMC genomics 13: 584.
43. Guan F, Gu J, Hu F, Zhu Y, Wang W, (2012) Association between α1-antichymotrypsin signal peptide-15A/T polymorphism and the risk of Alzheimer's disease: a meta-analysis. Mol biol rep 39: 6661-6669.
44. Ortega L, Balboa F, González L, (2010) alpha(1)-Antichymotrypsin deficiency associated with liver cirrhosis. Pediatr Int 52: 147-149.
45. De Smith AJ, Walters RG, Froguel P, Blakemore AJ, (2008) Human genes involved in copy number variation: Mechanisms of origin, functional effects and implications for disease. Cytogenet Genome Res 123: 17-26.