Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

BMC Genomics

Heebal Kim¹  Duhak Yoon³  JinYoung Jeong²  Chang-Kyu Lee⁴  Jae Yeon Hwang⁴  Hyeon Jeong Kim¹  Seoae Cho¹  Hyun-Jeong Lee²  Dong-Hyun Shin⁴ 

[1] C&K genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea;Division of Animal Genomics and Bioinformatics, National Institute of Animal science, Rural Development Administration, #564 Omockchun-dong, Suwon 441-706, Korea;Department of Animal Science, Kyungpook National University, Sangju 742-711, Korea;Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea

关键词: Selection signal;    Domestication;    NGS;    Copy Number Variation;    Holstein;    Hanwoo;    Cattle;   

Others  :  1217602
DOI  :  10.1186/1471-2164-15-240

 received in 2013-10-13, accepted in 2014-03-03,  发布年份 2014

【 摘 要 】

Background

Copy number variation (CNV), a source of genetic diversity in mammals, has been shown to underlie biological functions related to production traits. Notwithstanding, there have been few studies conducted on CNVs using next generation sequencing at the population level.

Results

Illumina NGS data was obtained for ten Holsteins, a dairy cattle, and 22 Hanwoo, a beef cattle. The sequence data for each of the 32 animals varied from 13.58-fold to almost 20-fold coverage. We detected a total of 6,811 deleted CNVs across the analyzed individuals (average length = 2732.2 bp) corresponding to 0.74% of the cattle genome (18.6 Mbp of variable sequence). By examining the overlap between CNV deletion regions and genes, we selected 30 genes with the highest deletion scores. These genes were found to be related to the nervous system, more specifically with nervous transmission, neuron motion, and neurogenesis. We regarded these genes as having been effected by the domestication process. Further analysis of the CNV genotyping information revealed 94 putative selected CNVs and 954 breed-specific CNVs.

Conclusions

This study provides useful information for assessing the impact of CNVs on cattle traits using NGS at the population level.

【 授权许可】

   
2014 Shin et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

【 参考文献 】

• [1]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.
• [2]Liu Y, Qin X, Song X-ZH, Jiang H, Shen Y, Durbin KJ, Lien S, Kent MP, Sodeland M, Ren Y: Bos taurus genome assembly. BMC Genomics 2009, 10(1):180. BioMed Central Full Text
• [3]Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS: A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 2009, 10(4):R42. BioMed Central Full Text
• [4]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.
• [5]Eck SH, Benet-Pagès A, Flisikowski K, Meitinger T, Fries R, Strom TM: Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol 2009, 10(8):R82. BioMed Central Full Text
• [6]Stothard P, Choi J-W, 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. BioMed Central Full Text
• [7]Barendse W, Barendse W, Harrison B, Bunch R, Thomas M, Turner L: Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits. BMC Genomics 2009, 10(1):178. BioMed Central Full Text
• [8]Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM, Lien S: Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science (New York, NY) 2009, 324(5926):528-532.
• [9]Hayes B, Chamberlain A, Maceachern S, Savin K, McPartlan H, MacLeod I, Sethuraman L, Goddard M: A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Anim Genet 2009, 40(2):176-184.
• [10]Mills RE, Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK: Mapping copy number variation by population-scale genome sequencing. Nature 2011, 470(7332):59-65.
• [11]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.
• [12]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(7289):704-712.
• [13]Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Bonnen PE, De Bakker P, Deloukas P, Gabriel SB: Integrating common and rare genetic variation in diverse human populations. Nature 2010, 467(7311):52-58.
• [14]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.
• [15]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.
• [16]She X, Cheng Z, Zöllner S, Church DM, Eichler EE: Mouse segmental duplication and copy number variation. Nat Genet 2008, 40(7):909-914.
• [17]Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellåker C, Goodstadt L, Nicod J, Bhomra A: Sequence-based characterization of structural variation in the mouse genome. Nature 2011, 477(7364):326-329.
• [18]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.
• [19]Fellermann K, Stange DE, Schaeffeler E, Schmalzl H, Wehkamp J, Bevins CL, Reinisch W, Teml A, Schwab M, Lichter P: A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am J Hum Genet 2006, 79(3):439-448.
• [20]le Maréchal C, Masson E, Chen J-M, Morel F, Ruszniewski P, Levy P, Férec C: Hereditary pancreatitis caused by triplication of the trypsinogen locus. Nat Genet 2006, 38(12):1372-1374.
• [21]Stankiewicz P, Lupski JR: Structural variation in the human genome and its role in disease. Annu Rev Med 2010, 61:437-455.
• [22]Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B, Hebert M, Jones KN, Shu Y, Kitzmiller K: Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet 2007, 80(6):1037-1054.
• [23]Zhang F, Gu W, Hurles ME, Lupski JR: Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 2009, 10:451-481.
• [24]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.
• [25]Bae J, Cheong H, Kim L, NamGung S, Park T, Chun J-Y, 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. BioMed Central Full Text
• [26]Fadista J, Thomsen B, Holm L-E, Bendixen C: Copy number variation in the bovine genome. BMC Genomics 2010, 11(1):284. BioMed Central Full Text
• [27]Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'Aquila ME: Analysis of copy number variations among diverse cattle breeds. Genome Res 2010, 20(5):693-703.
• [28]Chen W-K, Swartz JD, Rush LJ, Alvarez CE: Mapping DNA structural variation in dogs. Genome Res 2009, 19(3):500-509.
• [29]Fontanesi L, 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.
• [30]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.
• [31]Kijas JW, Barendse W, Barris W, Harrison B, McCulloch R, McWilliam S, Whan V: Analysis of copy number variants in the cattle genome. Gene 2011, 482(1):73-77.
• [32]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.
• [33]Ramayo-Caldas Y, Castelló A, Pena R, Alves E, Mercadé A, Souza C, Fernández A, Perez-Enciso M, Folch J: Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip. BMC Genomics 2010, 11(1):593. BioMed Central Full Text
• [34]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.
• [35]Porto Neto LR, Jonsson NN, D’Occhio MJ, Barendse W: Molecular genetic approaches for identifying the basis of variation in resistance to tick infestation in cattle. Vet Parasitol 2011, 180(3):165-172.
• [36]LaFramboise T: Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res 2009, 37(13):4181-4193.
• [37]Lai WR, Johnson MD, Kucherlapati R, Park PJ: Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005, 21(19):3763-3770.
• [38]Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, MacDonald JR, Mills R: Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 2011, 29(6):512-520.
• [39]Winchester L, Yau C, Ragoussis J: Comparing CNV detection methods for SNP arrays. Brief Funct Genomic Proteomic 2009, 8(5):353-366.
• [40]Alkan C, Coe BP, Eichler EE: Genome structural variation discovery and genotyping. Nat Rev Genet 2011, 12(5):363-376.
• [41]Handsaker RE, Korn JM, Nemesh J, McCarroll SA: Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet 2011, 43(3):269-276.
• [42]Winther M, Berezin V, Walmod PS: NCAM2/OCAM/RNCAM: cell adhesion molecule with a role in neuronal compartmentalization. Int J Biochem Cell Biol 2012, 44(3):441-446.
• [43]McIntyre JC, Titlow WB, McClintock TS: Axon growth and guidance genes identify nascent, immature, and mature olfactory sensory neurons. J Neurosci Res 2010, 88(15):3243-3256.
• [44]Xu X-ZS, Wes PD, Chen H, Li H-S, Yu M, Morgan S, Liu Y, Montell C: Retinal targets for calmodulin include proteins implicated in synaptic transmission. J Biol Chem 1998, 273(47):31297-31307.
• [45]Collingridge GL, Lester RA: Excitatory amino acid receptors in the vertebrate central nervous system. Pharmacol Rev 1989, 41(2):143-210.
• [46]Meldrum B, Garthwaite J: Excitatory amino acid neurotoxicity and neurodegenerative disease. Trends Pharmacol Sci 1990, 11(9):379-387.
• [47]Bliss TV, Collingridge GL: A synaptic model of memory: long-term potentiation in the hippocampus. Nature 1993, 361(6407):31-39.
• [48]Cartmell J, Schoepp DD: Regulation of neurotransmitter release by metabotropic glutamate receptors. J Neurochem 2000, 75(3):889-907.
• [49]Yagi T, Takeichi M: Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. Genes Dev 2000, 14(10):1169-1180.
• [50]Davy A, Gale NW, Murray EW, Klinghoffer RA, Soriano P, Feuerstein C, Robbins SM: Compartmentalized signaling by GPI-anchored ephrin-A5 requires the Fyn tyrosine kinase to regulate cellular adhesion. Genes Dev 1999, 13(23):3125-3135.
• [51]Sasaki S, Shionoya A, Ishida M, Gambello MJ, Yingling J, Wynshaw-Boris A, Hirotsune S: A LIS1 < i>/ NUDEL/cytoplasmic dynein heavy chain complex in the developing and adult nervous system. Neuron 2000, 28(3):681-696.
• [52]Brose K, Tessier-Lavigne M: Slit proteins: key regulators of axon guidance, axonal branching, and cell migration. Curr Opin Neurobiol 2000, 10(1):95-102.
• [53]Gleeson JG, Lin PT, Flanagan LA, Walsh CA: Doublecortin is a microtubule-associated protein and is expressed widely by migrating neurons. Neuron 1999, 23(2):257-271.
• [54]Bilimoria PM, Bonni A: Molecular control of axon branching. Neuroscientist 2013, 19(1):16-24.
• [55]Rønn LCB, Hartz B, Bock E: The neural cell adhesion molecule (NCAM) in development and plasticity of the nervous system. Exp Gerontol 1998, 33(7):853-864.
• [56]Hara Y, Nomura T, Yoshizaki K, Frisén J, Osumi N: Impaired Hippocampal neurogenesis and vascular formation in ephrin‒A5‒deficient mice. Stem Cells 2010, 28(5):974-983.
• [57]Litwack ED, Babey R, Buser R, Gesemann M, O'Leary DD: Identification and characterization of two novel brain-derived immunoglobulin superfamily members with a unique structural organization. Mol Cell Neurosci 2004, 25(2):263-274.
• [58]Nemes JP, Benzow KA, Koob MD: The SCA8 transcript is an antisense RNA to a brain-specific transcript encoding a novel actin-binding protein (KLHL1). Hum Mol Genet 2000, 9(10):1543-1551.
• [59]Itoh A, Miyabayashi T, Ohno M, Sakano S: Cloning and expressions of three mammalian homologues of < i > Drosophila slit suggest possible roles for < i > Slit in the formation and maintenance of the nervous system. Mol Brain Res 1998, 62(2):175-186.
• [60]Yoneyama M, Kawada K, Shiba T, Ogita K: Endogenous nitric oxide generation linked to ryanodine receptors activates cyclic GMP/protein kinase G pathway for cell proliferation of neural stem/progenitor cells derived from embryonic hippocampus. J Pharmacol Sci 2011, 115(2):182-195.
• [61]Nagae S, Tanoue T, Takeichi M: Temporal and spatial expression profiles of the Fat3 protein, a giant cadherin molecule, during mouse development. Dev Dyn 2007, 236(2):534-543.
• [62]Hu Z-L, Fritz ER, Reecy JM: AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Res 2007, 35(suppl 1):D604-D609.
• [63]Yamada T, Sasaki S, Sukegawa S, Yoshioka S, Takahagi Y, Morita M, Murakami H, Morimatsu F, Fujita T, Miyake T: Association of a single nucleotide polymorphism in titin gene with marbling in Japanese Black beef cattle. BMC Res Notes 2009, 2(1):78. BioMed Central Full Text
• [64]Heinola T, de Grauw J, Virkki L, Kontinen A, Raulo S, Sukura A, Konttinen Y: Bovine chronic osteoarthritis causes minimal change in synovial fluid. J Comp Pathol 2013, 148(4):335-344.
• [65]Cole J, Wiggans G, Ma L, Sonstegard T, Lawlor T, Crooker B, Van Tassell C, Yang J, Wang S, Matukumalli L: Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary US Holstein cows. BMC Genomics 2011, 12(1):408. BioMed Central Full Text
• [66]Pipes G, Bauman T, Brooks J, Comfort J, Turner C: Effect of season, sex and breed on the thyroxine secretion rate of beef cattle and a comparison with dairy cattle. J Anim Sci 1963, 22(2):476-480.
• [67]Fukuda T, Sugita S, Inatome R, Yanagi S: CAMDI, a novel disrupted in schizophrenia 1 (DISC1)-binding protein, is required for radial migration. J Biol Chem 2010, 285(52):40554-40561.
• [68]Mohammad MA, Hadsell DL, Haymond MW: Gene regulation of UDP-galactose synthesis and transport: potential rate-limiting processes in initiation of milk production in humans. Am J Physiol Endocrinol Metab 2012, 303(3):E365-E376.
• [69]Perez R, Cañón J, Dunner S: Genes associated with long-chain omega-3 fatty acids in bovine skeletal muscle. J Appl Genet 2010, 51(4):479-487.
• [70]Moore TM, Garg R, Johnson C, Coptcoat MJ, Ridley AJ, Morris JD: PSK, a novel STE20-like kinase derived from prostatic carcinoma that activates the c-Jun N-terminal kinase mitogen-activated protein kinase pathway and regulates actin cytoskeletal organization. J Biol Chem 2000, 275(6):4311-4322.
• [71]Fluckey JD, Knox M, Smith L, Dupont-Versteegden EE, Gaddy D, Tesch PA, Peterson CA: Insulin-facilitated increase of muscle protein synthesis after resistance exercise involves a MAP kinase pathway. Am J Physiol Endocrinol Metab 2006, 290(6):E1205-E1211.
• [72]Aspenström P: A Cdc42 target protein with homology to the non-kinase domain of FER has a potential role in regulating the actin cytoskeleton. Curr Biol 1997, 7(7):479-487.
• [73]Yin H-Q, Kim M, Kim J-H, Kong G, Kang K-S, Kim H-L, Yoon B-I, Lee M-O, Lee B-H: Differential gene expression and lipid metabolism in fatty liver induced by acute ethanol treatment in mice. Toxicol Appl Pharmacol 2007, 223(3):225-233.
• [74]Sun H, Tonks NK: The coordinated action of protein tyrosine phosphatases and kinases in cell signaling. Trends Biochem Sci 1994, 19(11):480-485.
• [75]Rodrigues GA, Falasca M, Zhang Z, Ong SH, Schlessinger J: A novel positive feedback loop mediated by the docking protein Gab1 and phosphatidylinositol 3-kinase in epidermal growth factor receptor signaling. Mol Cell Biol 2000, 20(4):1448-1459.
• [76]Lannon CL, Sorensen PHB: ETV6-NTRK3: a chimeric protein tyrosine kinase with transformation activity in multiple cell lineages. Semin. Cancer Biol 2005, 15:215-223.
• [77]Takada Y, Ye X, Simon S: The integrins. Genome Biol 2007, 8(5):215. BioMed Central Full Text
• [78]Veit G, Kobbe B, Keene DR, Paulsson M, Koch M, Wagener R: Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain. J Biol Chem 2006, 281(6):3494-3504.
• [79]Rosato R, Veltmaat JM, Groffen J, Heisterkamp N: Involvement of the tyrosine kinase fer in cell adhesion. Mol Cell Biol 1998, 18(10):5762-5770.
• [80]Senetar MA, Moncman CL, McCann RO: Talin2 is induced during striated muscle differentiation and is targeted to stable adhesion complexes in mature muscle. Cell Motil Cytoskeleton 2007, 64(3):157-173.
• [81]Vidal F, Baudoin C, Miquel C, Galliano M-F, Christiano AM, Uitto J, Ortonne J-P, Meneguzzi G: Cloning of the laminin α3 chain gene (LAMA3) and identification of a homozygous deletion in a patient with Herlitz junctional epidermolysis bullosa. Genomics 1995, 30(2):273-280.
• [82]Runswick SK, O'Hare MJ, Jones L, Streuli CH, Garrod DR: Desmosomal adhesion regulates epithelial morphogenesis and cell positioning. Nat Cell Biol 2001, 3(9):823-830.
• [83]Halbleib JM, Nelson WJ: Cadherins in development: cell adhesion, sorting, and tissue morphogenesis. Genes Dev 2006, 20(23):3199-3214.
• [84]Marthiens V, Gavard J, Lambert M, Mège RM: Cadherin‒based cell adhesion in neuromuscular development. Biol Cell 2002, 94(6):315-326.
• [85]Mitsui K, Nakajima D, Ohara O, Nakayama M: Mammalian fat3: a large protein that contains multiple cadherin and EGF-like motifs. Biochem Biophys Res Commun 2002, 290(4):1260-1266.
• [86]Baik M, Etchebarne B, Bong J, VandeHaar M: Gene expression profiling of liver and mammary tissues of lactating dairy cows. Asian Austral J Animal Sci 2009, 6:871-884.
• [87]Winters SJ, Moore JP: PACAP, an autocrine/paracrine regulator of gonadotrophs. Biol Reprod 2011, 84(5):844-850.
• [88]Connor E, Siferd S, Elsasser T, Evock-Clover C, Van Tassell C, Sonstegard T, Fernandes V, Capuco A: Effects of increased milking frequency on gene expression in the bovine mammary gland. BMC Genomics 2008, 9(1):362. BioMed Central Full Text
• [89]Casey T, Plaut K: LACTATION BIOLOGY SYMPOSIUM: Circadian clocks as mediators of the homeorhetic response to lactation. J Anim Sci 2012, 90(3):744-754.
• [90]Li H, Wang Z, Moore SS, Schenkel FS, Stothard P: Genome-wide scan for positional and functional candidate genes affecting milk production traits in Canadian Holstein cattle. Leipzig, Germany: Proc. 9th WCGALP; 2010. http://www.kongressband.de/wcgalp2010/assets/pdf/0535.pdf webcite Accessed Nov, 2010. 26: p
• [91]Dostaler-Touchette V, Bédard F, Guillemette C, Pothier F, Chouinard P, Richard F: Cyclic adenosine monophosphate (cAMP)-specific phosphodiesterase is functional in bovine mammary gland. J Dairy Sci 2009, 92(8):3757-3765.
• [92]Bionaz M, Periasamy K, Rodriguez-Zas SL, Hurley WL, Loor JJ: A novel dynamic impact approach (DIA) for functional analysis of time-course omics studies: validation using the bovine mammary transcriptome. PLoS One 2012, 7(3):e32455.
• [93]D’Alessandro A, Zolla L, Scaloni A: The bovine milk proteome: cherishing, nourishing and fostering molecular complexity. An interactomics and functional overview. Mol Biosyst 2011, 7(3):579-597.
• [94]Sadkowski T, Jank M, Zwierzchowski L, Oprządek J, Motyl T: Comparison of skeletal muscle transcriptional profiles in dairy and beef breeds bulls. J Appl Genet 2009, 50(2):109-123.
• [95]Watanabe N, Satoh Y, Fujita T, Ohta T, Kose H, Muramatsu Y, Yamamoto T, Yamada T: Distribution of allele frequencies at TTN g. 231054C > T, RPL27A g. 3109537C > T and AKIRIN2 c.* 188G > A between Japanese Black and four other cattle breeds with differing historical selection for marbling. BMC Res Notes 2011, 4(1):10. BioMed Central Full Text
• [96]Ramos A, Megens H, Crooijmans R, Schook L, Groenen M: Identification of high utility SNPs for population assignment and traceability purposes in the pig using high‒throughput sequencing. Anim Genet 2011, 42(6):613-620.
• [97]Robinson GE, Fernald RD, Clayton DF: Genes and social behavior. Science 2008, 322(5903):896-900.
• [98]Niimura Y, Nei M: Extensive gains and losses of olfactory receptor genes in mammalian evolution. PLoS One 2007, 2(8):e708.
• [99]Seroussi E, Glick G, Shirak A, Yakobson E, Weller J, Ezra E, Zeron Y: Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs. BMC Genomics 2010, 11(1):673. BioMed Central Full Text
• [100]Lee K, Nguyen DT, Choi M, Cha S-Y, Kim J-H, Dadi H, Seo HG, Seo K, Chun T, Park C: Analysis of cattle olfactory subgenome: the first detail study on the characteristics of the complete olfactory receptor repertoire of a ruminant. BMC Genomics 2013, 14(1):596. BioMed Central Full Text
• [101]Youn H-D, Grozinger CM, Liu JO: Calcium regulates transcriptional repression of myocyte enhancer factor 2 by histone deacetylase 4. J Biol Chem 2000, 275(29):22563-22567.
• [102]Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359.
• [103]McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M: The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303.
• [104]Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S: Ensembl 2012. Nucleic Acids Res 2012, 40(D1):D84-D90.
• [105]Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A: BioMart–biological queries made easy. BMC Genomics 2009, 10(1):22. BioMed Central Full Text
• [106]da Wei Huang BTS, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2008, 4(1):44-57.
• [107]Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000, 155(2):945-959.
• [108]Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19(12):1572-1574.
• [109]Wright S: The genetical structure of populations. Ann Eugen 1949, 15(1):323-354.