Genome-wide mapping of copy number variations in commercial hybrid pigs using a high-density SNP genotyping array

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• 作者：L. S. Zhou ; J. Li ; J. Yang ; C. L. Liu ; X. H. Xie ; Y. N. He…
• 关键词：copy number variation ; SNP arrays ; commercial hybrid pig
• 刊名：Russian Journal of Genetics
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：52
• 期：1
• 页码：85-92
• 全文大小：301 KB
• 参考文献：1.Lankin, V.S., Genotypic and modification variability of passive-defensive behavior toward humans in domestic pigs, Russ. J. Genet: Appl. Res., 2014, vol. 4, no. 1, pp. 60–73.CrossRef
  2.Nikitin, S.V., Knyazev, S.P., and Ermolaev, V.I., Model of genetic control of the number and location of nipples in domestic pig, Russ. J. Genet., 2012, vol. 48, no. 11, pp. 1128–1140.CrossRef
  3.Stankiewicz, P. and Lupski J.R., Structural variation in the human genome and its role in disease, Annu. Rev. Med., 2010, vol. 61, pp. 437–455.CrossRef PubMed
  4.Conrad, D.F., Dalila, P., Richard, R., et al., Origins and functional impact of copy number variation in the human genome, Nature, 2010, vol. 464, no. 7289, pp. 704–712.CrossRef PubMed PubMedCentral
  5.Srivastava, P.P., Kar, P.K., Awasthi, A.K., and Urs, S.R., Identification and association of ISSR markers for thermal stress in polyvoltine silkworm Bombyx mori, Russ. J. Genet., 2007, vol. 43, no. 8. pp. 858–864.CrossRef
  6.Li, W., Zhang, D.F., Wei, Y.M., et al., Genetic diversity of Triticum turgidum L. based on microsatellite markers, Russ. J. Genet., 2006, vol. 42, no. 3, pp. 311–316.CrossRef
  7.Terman, A. and Kumalska, M., The effect of a SNP in ESR gene on the reproductive performance traits in Polish sows, Russ. J. Genet., 2012, vol. 48, no. 12, pp. 1260–1263.CrossRef
  8.Henrichsen, C.N., Chaignat, E., and Reymond, A., Copy number variants, diseases and gene expression, Hum. Mol. Genet., 2009, vol. 18, no. R1, pp R1–8.CrossRef PubMed
  9.Zhang, F. and Gu, W.M., Copy number variation in human health, disease, and evolution, Annu. Rev. Genomics Hum. Genet., 2009, vol. 10, pp. 451–481.CrossRef
  10.Victor, G., Kathrin, S., Tatjana, A., et al., Distribution and functional impact of DNA copy number variation in the rat, Nat. Genet., 2008, vol. 40, no. 5, pp. 538–545.CrossRef
  11.Nicholas, T.J., Cheng, Z., Ventura, M., et al., The genomic architecture of segmental duplications and associated copy number variants in dogs, Genome Res., 2009, vol. 19, no. 3, pp. 491–499.CrossRef PubMed PubMedCentral
  12.Griffin, D.K., Robertson, L.B., Tempest, H.G., et al., Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution, BMC Genomics, 2008, vol. 9, p. 168.CrossRef PubMed PubMedCentral
  13.Hou, Y., Liu, G.E., Bickhart, D.M., et al., Genomic characteristics of cattle copy number variations, BMC Genomics, 2011, vol. 12, p. 127.CrossRef PubMed PubMedCentral
  14.Doan, R., Identification of copy number variants in horses, Genome Res., 2012, vol. 22, no. 5, pp. 899–907.CrossRef PubMed PubMedCentral
  15.Kirov, G., The role of copy number variation in schizophrenia, Expert Rev. Neurother., 2010, vol. 10, no. 1, pp. 25–32.CrossRef PubMed
  16.Sha, B.Y., Yang, T.L., Zhao, L.J., et al., Genome-wide association study suggested copy number variation may be associated with body mass index in the Chinese population, J. Hum. Genet., 2009, vol. 54, no. 4, pp. 199–202.CrossRef PubMed PubMedCentral
  17.Harteveld, C.L. and Higgs, D.R., Alpha-thalassaemia, Orphanet J. Rare Dis., 2010, vol. 5, p. 13.CrossRef PubMed PubMedCentral
  18.Xudong, L., Linghan, G., Aman, Z., et al., Identification of duplication downstream of BMP2 in a Chinese family with brachydactyly type A2 (BDA2), PLoS One, 2014, vol. 9, no. 4. e94201CrossRef
  19.Wright, D., Boije, H., Meadows, et al., Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens, PLoS Genet., 2009, vol. 5, no. 6. e1000512CrossRef PubMed PubMedCentral
  20.Rosengren, P.G., Golovko, A., Sundstrom, E., et al., A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse, Nat. Genet., 2008, vol. 40, no. 8, pp. 1004–1009.CrossRef
  21.Fontanesi, L., Beretti, F., Riggio, V., et al., Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors, Cytogenet. Genome Res., 2009, vol. 126, no. 4, pp. 333–347.CrossRef PubMed
  22.Johansson, A., Pielberg, G., Andersson, L., and Edfors-Lilja, I., Polymorphism at the porcine Dominant white/KIT locus influence coat colour and peripheral blood cell measures, Anim. Genet., 2005, vol. 36, no. 4, pp. 288–296.CrossRef PubMed
  23.Pielberg, G., Olsson, C., Syvanen, A.C., and Andersson, L., Unexpectedly high allelic diversity at the KIT locus causing dominant white color in the domestic pig, Genetics, 2002, vol. 160, no. 1, pp. 305–311.PubMed PubMedCentral
  24.Ramayo-Caldas, Y., Castelló, A., Pena, R.N., et al., Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip, BMC Genomics, 2010, vol. 11, p. 593.CrossRef PubMed PubMedCentral
  25.Chen, C., Qiao, R., Wei, R., et al., 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, 2012, vol. 13, p. 733.CrossRef PubMed PubMedCentral
  26.Li, Y., Mei, S.Q., Zhang, X.Y., et al., Identification of genome-wide copy number variations among diverse pig breeds by array CGH, BMC Genomics, 2012, vol. 13, p. 725.CrossRef PubMed PubMedCentral
  27.Carl-Johan, Rubin, Hendrik Jan, et al., Strong signatures of selection in the domestic pig genome, Proc. Natl. Acad. Sci. U.S.A., 2012, vol. 109, no. 48, pp. 19529–19536.CrossRef
  28.Wang, J., Jiang, J., Fu, W., et al., A genome-wide detection of copy number variations using SNP genotyping arrays in swine, BMC Genomics, 2012, vol. 13, p. 273.CrossRef PubMed PubMedCentral
  29.Paudel, Y., Madsen, O., Megens, H.J., et al., Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication, BMC Genomics, 2013, vol. 14, p. 449.CrossRef PubMed PubMedCentral
  30.Jiying, W., Haifei, W., Jicai, J., et al., Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays, PLoS One, 2013, vol. 8, no. 7. e68683CrossRef
  31.Wang, L., Liu, X., Zhang, L., et al., Genome-wide copy number variations inferred from SNP genotyping arrays using a Large White and Minzhu intercross population, PLoS One, 2013, vol. 8, no. 10. e74879CrossRef PubMed PubMedCentral
  32.Wang, J., Jiang, J., Wang, et al., Enhancing genomewide copy number variation identification by high density array CGH using diverse resources of pig breeds, PLoS One, 2014, vol. 9, no. 1. e87571CrossRef PubMed PubMedCentral
  33.Wang, K., Li, M., Hadley, D., et al., PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data, Genome Res., 2007, vol. 17, no. 11, pp. 1665–1674.CrossRef PubMed PubMedCentral
  34.Redon, R., Ishikawa, S., Fitch, K.R., et al., Global variation in copy number in the human genome, Nature, 2006, vol. 444, no. 7118, pp. 444–454.CrossRef PubMed PubMedCentral
  35.Livak, K.J. and Schmittgen, T.D., Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method, Methods, 2001, vol. 25, no. 4, pp. 402–408.CrossRef PubMed
  36.Ballester, M., Castelló, A., Ibánez, E., et al., Real-time quantitative PCR-based system for determining transgene copy number in transgenic animals, Biotechniques, 2004, vol. 37, no. 4, pp. 610–613.PubMed
  37.Ramos, A.M., Crooijmans, R.P.M.A., Affara, N.A., et al., Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology, PLoS One, 2009, vol. 4, no. 8. e6524CrossRef PubMed PubMedCentral
  38.Liu, G.E., Hou, Y.B., Cardone, M.F., et al., Analysis of copy number variations among diverse cattle breeds, Genome Res., 2010, vol. 20, no. 5, pp. 693–703.CrossRef PubMed PubMedCentral
  39.Winchester, L., Yau, C., and Ragoussis, J., Comparing CNV detection methods for SNP arrays, Briefings Funct. Genomics Proteomics, 2009, vol. 8, no. 5, pp. 353–366.CrossRef
  40.Diskin, S.J., Li, M., Hou, C., et al., Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms, Nucleic Acids Res., 2008, vol. 36, no. 19, p. 126.CrossRef
  41.Fadista, J., Nygaard, M., Holm, L.E., et al., A snapshot of CNVs in the pig genome, PLoS One, 2008, vol. 3, no. 12. e3916CrossRef PubMed PubMedCentral
  42.De Smith, A.J., Walters, R.G., Froguel, P., and Blakemore, A.I., Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease, Cytogenet. Genome Res., 2008, vol. 123, nos. 1–4, pp. 17–26.CrossRef PubMed
  43.Young, J.M., Endicott, R.M., Parghi, S.S., et al., Extensive copy-number variation of the human olfactory receptor gene family, Am. J. Hum. Genet., 2008, vol. 83, no. 2, pp. 228–242.CrossRef PubMed PubMedCentral
  44.Hussain, A., Saraiva, L.R., and Korsching, S.I., Positive Darwinian selection and the birth of an olfactory receptor clade in teleosts, Proc. Natl. Acad. Sci. U.S.A., 2009, vol. 106, no. 11, pp. 4313–4318.CrossRef PubMed PubMedCentral
  45.Gaur, U., Xiong, Y., Luo, Q., et al., Breed-specific transcriptome response of spleen from six to eight week old piglet after infection with Streptococcus suis type 2, Mol. Biol. Rep., 2014, pp. 1–9.
  46.Li, B. and Trueb, B., DRG represents a family of two closely related GTP-binding proteins, Biochim. Biophys. Acta, Gene Struct. Expression, 2000, vol. 1491, no. 1, pp. 196–204.CrossRef
  47.Grötsch, H., Kunert, M., Mooslenhner, K.A., et al., RWDD1 interacts with the ligand binding domain of the androgen receptor and acts as a coactivator of androgen-dependent transactivation, Mol. Cell. Endocrinol., 2012, vol. 358, no. 1, pp. 53–62.CrossRef PubMed
  48.Victoria, A., Payne, Neil, et al., The human lipodystrophy gene BSCL2/seipin may be essential for normal adipocyte differentiation, Diabetes, 2008, vol. 57, no. 8, pp. 2055–2060.CrossRef
  49.Zayed, H., Chao, R., Moshrefi, A., et al., A maternally inherited chromosome 18q22.1 deletion in a male with late-presenting diaphragmatic hernia and microphthalmia-evaluation of DSEL as a candidate gene for the diaphragmatic defect, Am. J. Med. Genet., 2010, vol. 152A, no. 4, pp. 916–923.CrossRef PubMed PubMedCentral
  50.Chao, R., Nevin, L., Agarwal, P., et al., A male with unilateral microphthalmia reveals a role for TMX3 in eye development, PLoS One, 2010, vol. 5, no. 5. e10565CrossRef PubMed PubMedCentral
  51.Hulsen, J. and Scheepens, K., Pig Signals: Look Think and Act, Jan Hulsen, V., Ed., ROODBONT, 2006.
  
• 作者单位：L. S. Zhou (1)
  J. Li (1)
  J. Yang (1)
  C. L. Liu (1)
  X. H. Xie (1)
  Y. N. He (1)
  X. X. Liu (1)
  W. S. Xin (1)
  W. C. Zhang (1)
  J. Ren (1)
  J. W. Ma (1)
  L. S. Huang (1)
  
  1. State Key Laboratory for Pig Genetics and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Biomedicine
  Human Genetics
  Animal Genetics and Genomics
  Microbial Genetics and Genomics
  Russian Library of Science
  
• 出版者：MAIK Nauka/Interperiodica distributed exclusively by Springer Science+Business Media LLC.
• ISSN：1608-3369

文摘

Copy number variations (CNVs) are important forms of structural variation in human and animals and can be considered as a major genetic component of phenotypic diversity. Here we used the Illumina PorcineSNP60 BeadChip V2 and a DLY [Duroc × (Large White × Landrace)] commercial hybrid population to identify 272 CNVs belonging to 165 CNV regions (CNVRs), of which 66 are new. As CNVRs are specific to origin of population, our DLY-specific data is an important complementary to the existing CNV map in the pig genome. Eight CNVRs were selected for validation by quantitative real-time PCR (qRT-PCR) and the accurate rate was high (87.25%). Gene function analysis suggested that a common CNVR may play an important role in multiple traits, including growth rate and carcass quality. Keywords copy number variation SNP arrays commercial hybrid pig