Detection of copy number variations and their effects in Chinese bulls

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Zhang, Liangzhi ^a   Jia, Shangang ^a,d   Yang, Mingjuan ^a   Xu, Yao ^a   Li, Congjun ^b   Sun, Jiajie ^a   Huang, Yongzhen ^a   Lan, Xianyong ^a   Lei, Chuzhao ^a   Zhou, Yang ^a   Zhang, Chunlei ^c   Zhao, Xin ^a   Chen, Hong ^a  

^a NORTHWEST A F UNIVERSITY   (China)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c JIANGSU NORMAL UNIVERSITY   (China)

^d KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

Author keywords

Bos grunniens; Bos taurus; Bubalus bubalis; Copy number variations; Gene expression

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; BOS TAURUS; BULL (MAMMAL); CHINESE; CNVR22 GENE; CNVR310 GENE; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; DOMESTIC ANIMAL; EDA GENE; GENE; GENE EXPRESSION; GENE FUNCTION; GENE LOCUS; GENE LOSS; GENETIC VARIABILITY; GENOME ANALYSIS; GROWTH INHIBITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLA2G2D GENE; QUANTITATIVE TRAIT LOCUS; SLC4A2 GENE; WATER BUFFALO; YAK; ANIMAL; BOVINAE; BREEDING; GENETIC ASSOCIATION; GENOME; QUANTITATIVE TRAIT;

ANIMALS; BREEDING; CATTLE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; GENE EXPRESSION; GENETIC ASSOCIATION STUDIES; GENOME; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE;

EID: 84902302515     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-480     Document Type: Article

References (65)

1. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P. Origins and functional impact of copy number variation in the human genome. Nature 2009, 464:704-712.
2. Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Cáceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE. Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci U S A 2006, 103(21):8006-8011.
3. Cutler G, Marshall LA, Chin N, Baribault H, Kassner PD. Significant gene content variation characterizes the genomes of inbred mouse strains. Genome Res 2007, 17(12):1743-1754.
4. Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM. A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 2007, 3(1):e3.
5. She X, Cheng Z, Zöllner S, Church DM, Eichler EE. Mouse segmental duplication and copy number variation. Nat Genet 2008, 40(7):909-914.
6. Henrichsen CN, Vinckenbosch N, Zöllner S, Chaignat E, Pradervand S, Schütz F, Ruedi M, Kaessmann H, Reymond A. Segmental copy number variation shapes tissue transcriptomes. Nat Genet 2009, 41(4):424-429.
7. Weischenfeldt J, Symmons O, Spitz F, Korbel JO. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet 2013, 14(2):125-138.
8. Reymond A, Henrichsen CN, Harewood L, Merla G. Side effects of genome structural changes. Curr Opin Genet Dev 2007, 17(5):381-386.
9. Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, Mangion J, Roberton-Lowe C, Marshall AJ, Petretto E. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 2006, 439(7078):851-855.
10. Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 2009, 459(7246):569-573.
11. McCarroll SA, Altshuler DM. Copy-number variation and association studies of human disease. Nat Genet 2007, 39:S37-S42.
12. Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M. Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science 2008, 320(5883):1629-1631.
13. Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM. The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res 2009, 19(3):491-499.
14. Li Y, Mei S, Zhang X, Peng X, Liu G, Tao H, Wu H, Jiang S, Xiong Y, Li F. Identification of genome-wide copy number variations among diverse pig breeds by array CGH. BMC Genomics 2012, 13(1):725.
15. Fontanesi L, Beretti F, Riggio V, Dall'Olio S, Davoli R, Russo V, Portolano B. Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors. Cytogenet Genome Res 2009, 126(4):333-347.
16. Metzger J, Philipp U, Lopes MS, da Camara Machado A, Felicetti M, Silvestrelli M, Distl O. Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics 2013, 14(1):487.
17. Fontanesi L, Beretti F, Martelli P, Colombo M, Dall'Olio S, Occidente M, Portolano B, Casadio R, Matassino D, Russo V. A first comparative map of copy number variations in the sheep genome. Genomics 2011, 97(3):158-165.
18. Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'Aquila ME, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LCA, Smith TPL, Song J, Sonstegard TS, Tassell CPV, Ventura M, Eichler EE, McDaneld TG, Keele JW. Analysis of copy number variations among diverse cattle breeds. Genome Res 2010, 20(5):693-703.
19. Fadista J, Thomsen B, Holm LE, Bendixen C. Copy number variation in the bovine genome. BMC Genomics 2010, 11(1):284.
20. Bae J, Cheong H, Kim L, NamGung S, Park T, Chun JY, Kim J, Pasaje C, Lee J, Shin H. Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics 2010, 11(1):232.
21. Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim E, Matukumalli LK, Ventura M, Song J, VanRaden PM. Genomic characteristics of cattle copy number variations. BMC Genomics 2011, 12(1):127.
22. Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res 2012, 22(4):778-790.
23. Jiang L, Jiang J, Yang J, Liu X, Wang J, Wang H, Ding X, Liu J, Zhang Q. Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genomics 2013, 14(1):131.
24. Jiang L, Jiang J, Wang J, Ding X, Liu J, Zhang Q. Genome-wide identification of copy number variations in Chinese Holstein. PLoS ONE 2012, 7(11):e48732.
25. Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS. Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 2011, 12(1):559.
26. Zhan B, Fadista J, Thomsen B, Hedegaard J, Panitz F, Bendixen C. Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping. BMC Genomics 2011, 12(1):557.
27. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TP, Sonstegard TS. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 2009, 4(4):e5350.
28. Sambrook J, Russell D. Molecular cloning: a laboratory manual 2001, Beijing, China: Sicence Press.
29. Liu Y, Qin X, Song XZH, Jiang H, Shen Y, Durbin KJ, Lien S, Kent MP, Sodeland M, Ren Y. Bos taurus genome assembly. BMC Genomics 2009, 10(1):180.
30. Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, Nair P, Brothman AR, Stallings RL. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosom Cancer 2005, 44(3):305-319.
31. Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5(4):557-572.
32. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W. Global variation in copy number in the human genome. Nature 2006, 444(7118):444-454.
33. Hu ZL, Park CA, Wu XL, Reecy JM. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucl Acids Res 2013, 41(D1):D871-D879.
34. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 2006, 34(suppl 2):W293-W297.
35. Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 2010, 26(6):715-721.
36. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative CT method. Nat Protoc 2008, 3(6):1101-1108.
37. Huang Y, He H, Wang J, Li Z, Lan X, Lei C, Zhang E, Zhang C, Wang J, Shen Q. Sequence variants in the bovine nucleophosmin 1 gene, their linkage and their associations with body weight in native cattle breeds in China. Anim Genet 2011, 42(5):556-559.
38. Force A, Lynch M, Pickett FB, Amores A, Yan Y, Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999, 151(4):1531-1545.
39. Wyman MJ, Cutter AD, Rowe L. Gene duplication in the evolution of sexual dimorphism. Evolution 2012, 66(5):1556-1566.
40. Elsik CG, Tellam RL, Worley KC. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009, 324(5926):522-528.
41. Hu Q, Ma T, Wang K, Xu T, Liu J, Qiu Q. The Yak genome database: an integrative database for studying yak biology and high-altitude adaption. BMC Genomics 2012, 13(1):600.
42. Qiu Q, Zhang G, Ma T, Qian W, Wang J, Ye Z, Cao C, Hu Q, Kim J, Larkin DM. The yak genome and adaptation to life at high altitude. Nat Genet 2012, 44(8):946-949.
43. Robin ED, Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J Cell Physiol 1988, 136(3):507-513.
44. Wai T, Ao A, Zhang X, Cyr D, Dufort D, Shoubridge EA. The role of mitochondrial DNA copy number in mammalian fertility. Biol Reprod 2010, 83(1):52-62.
45. May-Panloup P, Chretien MF, Malthiery Y, Reynier P. Mitochondrial DNA in the oocyte and the developing embryo. Curr Top Dev Biol 2007, 77:51-83.
46. Dumollard R, Duchen M, Carroll J. The role of mitochondrial function in the oocyte and embryo. Curr Top Dev Biol 2007, 77:21-49.
47. Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner PA, Eichler EE. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet 2007, 39(11):1361-1368.
48. De Cáceres M, Legendre P, Wiser SK, Brotons L. Using species combinations in indicator value analyses. Methods Ecol Evol 2012, 3(6):973-982.
49. Liu GE, Ventura M, Cellamare A, Chen L, Cheng Z, Zhu B, Li C, Song J, Eichler EE. Analysis of recent segmental duplications in the bovine genome. BMC Genomics 2009, 10(1):571.
50. Drögemüller C, Distl O, Leeb T. Partial deletion of the bovine ED1 gene causes anhidrotic ectodermal dysplasia in cattle. Genome Res 2001, 11(10):1699-1705.
51. Meyers SN, McDaneld TG, Swist SL, Marron BM, Steffen DJ, O'Toole D, O'Connell JR, Beever JE, Sonstegard TS, Smith TP. A deletion mutation in bovine SLC4A2 is associated with osteopetrosis in Red Angus cattle. BMC Genomics 2010, 11(1):337.
52. Guryev V, Saar K, Adamovic T, Verheul M, Van Heesch SA, Cook S, Pravenec M, Aitman T, Jacob H, Shull JD. Distribution and functional impact of DNA copy number variation in the rat. Nat Genet 2008, 40(5):538-545.
53. Golik M, Cohen-Zinder M, Loor JJ, Drackley JK, Band MR, Lewin HA, Weller JI, Ron M, Seroussi E. Accelerated expansion of group IID-like phospholipase A2 genes in Bos taurus. Genomics 2006, 87(4):527-533.
54. Seroussi E, Klompus S, Silanikove M, Krifucks O, Shapiro F, Gertler A, Leitner G. Nonbactericidal secreted phospholipase A2s are potential anti-inflammatory factors in the mammary gland. Immunogenetics 2013, 65(12):861-871.
55. Rutland CS, Polo-Parada L, Ehler E, Alibhai A, Thorpe A, Suren S, Emes RD, Patel B, Loughna S. Knockdown of embryonic myosin heavy chain reveals an essential role in the morphology and function of the developing heart. Development 2011, 138(18):3955-3966.
56. Toydemir RM, Rutherford A, Whitby FG, Jorde LB, Carey JC, Bamshad MJ. Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome. Nat Genet 2006, 38(5):561-565.
57. Niu F, Wang L, Liu X, Wang H, Yang J, Liu Y, Chen L. Genetic diversity of MYH 3 gene associated with growth and carcass traits in Chinese Qinchuan cattle. Mol Biol Rep 2013, 40(10):5635-5643.
58. Kleinjan DA, Van Heyningen V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet 2005, 76(1):8-32.
59. Henrichsen CN, Chaignat E, Reymond A. Copy number variants, diseases and gene expression. Hum Mol Genet 2009, 18(R1):R1-R8.
60. Aldred P, Hollox E, Armour J. Copy number polymorphism and expression level variation of the human α-defensin genes DEFA1 and DEFA3. Hum Mol Genet 2005, 14(14):2045-2052.
61. Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R. Diet and the evolution of human amylase gene copy number variation. Nat Genet 2007, 39:1256-1260.
62. Chen C, Qiao R, Wei R, Guo Y, Ai H, Ma J, Ren J, Huang L. 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, 13(1):733.
63. Seroussi E, Glick G, Shirak A, Yakobson E, Weller JI, Ezra E, Zeron Y. Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs. BMC Genomics 2010, 11(1):673.
64. Hu ZL, Reecy JM. Animal QTLdb: beyond a repository. Mamm Genome 2007, 18:1-4.
65. Sonstegard TS, Garrett WM, Ashwell MS, Bennett GL, Kappes SM, Van Tassell CP. Comparative map alignment of BTA27 and HSA4 and 8 to identify conserved segments of genome containing fat deposition QTL. Mamm Genome 2000, 11(8):682-688.