A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits

Journal of Dairy Science

Volumn 97, Issue 5, 2014, Pages 3156-3172

  Cole, J B ^a   Waurich, B ^b   Wensch Dorendorf, M ^b   Bickhart, D M ^a   Swalve, H H ^b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

Birth weight; Quantitative trait loci; Selection index; Single nucleotide polymorphism

Indexed keywords

ANIMALIA; BOS; BOS TAURUS;

ANIMAL; BIRTH WEIGHT; BOVINE; FEMALE; GENETIC ASSOCIATION; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; GERMANY; HUMAN; MALE; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

ANIMALS; BIRTH WEIGHT; CATTLE; FEMALE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; GERMANY; HUMANS; MALE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SELECTION, GENETIC; UNITED STATES;

EID: 84899072487     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2013-7409     Document Type: Article

References (113)

1. AIPL (Animal Improvement Programs Laboratory). 2013. Trait evaluations: Calving (calving ease, stillbirth). Accessed Jan. 17, 2013. http://aipl.arsusda.gov/reference/Form_GE_CT_1008.pdf.
2. Ali T.E., Burnside E.B., Schaeffer L.R. Relationship between external body measurements and calving difficulties in Canadian Holstein-Friesian cattle. J. Dairy Sci. 1984, 67:3034-3044.
3. Ark M., Yilmaz N., Yazici G., Kubat H., Aktaş S. Rho-associated protein kinase II (rock II) expression in normal and preeclamptic human placentas. Placenta 2005, 26:81-84. http://dx.doi.org/10.1016/j.placenta.2004.03.012.
4. Berry D.P., Lee J.M., Macdonald K.A., Roche J.R. Body condition score and body weight effects on dystocia and stillbirths and consequent effects on postcalving performance. J. Dairy Sci. 2007, 90:4201-4211.
5. Boldman K.G., Famula T.R. Association of sire dystocia transmitting ability with progeny linear type traits in Holsteins. J. Dairy Sci. 1985, 68:2052-2057.
6. Bradbury P.J., Zhang Z., Kroon D.E., Casstevens T.M., Ramdoss Y., Buckler E.S. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 2007, 23:2633-2635.
7. Brand B., Baes C., Mayer M., Reinsch N., Seidenspinner T., Thaller G., Kühn C. Quantitative trait loci mapping of calving and conformation traits on Bos taurus autosome 18 in the German Holstein population. J. Dairy Sci. 2010, 93:1205-1215.
8. Burrell R.A., McClelland S.E., Endesfelder D., Groth P., Weller M.-C., Shaikh N., Domingo E., Kanu N., Dewhurst S.M., Gronroos E., Chew S.K., Rowan A.J., Schenk A., Sheffer M., Howell M., Kschischo M., Behrens A., Helleday T., Bartek J., Tomlinson I.P., Swanton C. Replication stress links structural and numerical cancer chromosomal instability. Nature 2013, 494:492-496. http://dx.doi.org/10.1038/nature11935.
9. Calo L.L., McDowell R.E., VanVleck L.D., Miller P.D. Genetic aspects of beef production among Holstein-Friesians pedigree selected for milk production. J. Anim. Sci. 1973, 37:676-682.
10. Cameron N.D. Selection Indices and Prediction of Genetic Merit in Animal Breeding 1997, CAB International, New York, NY.
11. Charlier C., Coppieters W., Rollin F., Desmecht D., Agerholm J.S., Cambisano N., Carta E., Dardano S., Dive M., Fasquelle C., Frennet J.-C., Hanset R., Hubin X., Jorgensen C., Karim L., Kent M., Harvey K., Pearce B.R., Simon P., Tama N., Nie H., Vandeputte S., Lien S., Longeri M., Fredholm M., Harvey R.J., Georges M. Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat. Genet. 2008, 40:449-454. http://dx.doi.org/10.1038/ng.96.
12. Chew B.P., Maier L.C., Hillers J.K., Hodgson A.S. Relationship between calf birth weight and dam's subsequent 200- and 305-day yields of milk, fat, and total solids in Holsteins. J. Dairy Sci. 1981, 64:2401-2408.
13. Chu T., Dufort I., Sirard M.-A. Effect of ovarian stimulation on oocyte gene expression in cattle. Theriogenology 2012, 77:1928-1938.
14. Coffey M.P., Hickey J., Brotherstone S. Genetic aspects of growth of Holstein-Friesian dairy cows from birth to maturity. J. Dairy Sci. 2006, 89:322-329.
15. Cole J.B., Goodling R.C., Wiggans G.R., VanRaden P.M. Genetic evaluation of calving ease for Brown Swiss, Jersey, and Holstein bulls from purebred and crossbred calvings. J. Dairy Sci. 2005, 88:1529-1539.
16. Cole, J. B., P. M. VanRaden, and Multi-State Project S-1040. 2009a. Net merit as a measure of lifetime profit: 2010 revision. AIPL Research Report NM$4. Accessed Jan. 18, 2013. http://aipl.arsusda.gov/reference/nmcalc.htm.
17. Cole J.B., VanRaden P.M., O'Connell J.R., Van Tassell C.P., Sonstegard T.S., Schnabel R.D., Taylor J.F., Wiggans G.R. Distribution and location of genetic effects for dairy traits. J. Dairy Sci. 2009, 92:2931-2946.
18. Cole J.B., Wiggans G.R., Ma L., Sonstegard T.S., Lawlor T.J., Crooker B.A., Van Tassell C.P., Yang J., Wang S., Matukumalli L.K., Da Y. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. BMC Genomics 2011, 12:408. http://dx.doi.org/10.1186/1471-2164-12-408.
19. Cole J.B., Wiggans G.R., VanRaden P.M. Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model. J. Dairy Sci. 2007, 90:2480-2488.
20. Corsi J.-M., Rouer E., Girault J.-A., Enslen H. Organization and post-transcriptional processing of focal adhesion kinase gene. BMC Genomics 2006, 7:198. http://dx.doi.org/10.1186/1471-2164-7-198.
21. Cue R.I., Monardes H.G., Hayes J.F. Relationships of calving ease with type traits. J. Dairy Sci. 1990, 73:3586-3590.
22. Dadati E., Kennedy B.W., Burnside E.B. Relationships between conformation and reproduction in Holstein cows: Type and calving performance. J. Dairy Sci. 1985, 68:2639-2645.
23. Davis, G. P., D. J. S. Hetzel, N. J. Corbet, S. Scacheri, S. Lowden, J. Renaud, C. Mayne, R. Stevenson, S. S. Moore, and K. Byrne. 1998. The mapping of quantitative trait loci for birth weight in tropical beef herd. Pages 441-444 in Proc. 6th World Congr. Genet. Appl. Livest. Prod., Armidale, NSW, Australia.
24. Dennis G., Sherman B.T., Hosack D.A., Yang J., Gao W., Lane H.C., Lempicki R.A. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol. 2003, 4:P3.
25. Du M., Zhao J.X., Yan X., Huang Y., Nicodemus L.V., Yue W., McCormick R.J., Zhu M.J. Fetal muscle development, mesenchymal multipotent cell differentiation, and associated signaling pathways. J. Anim. Sci. 2011, 89:583-590. http://dx.doi.org/10.2527/jas.2010-3386.
26. Eaglen S.A.E., Coffey M.P., Woolliams J.A., Wall E. Evaluating alternate models to estimate genetic parameters of calving traits in United Kingdom Holstein Friesian dairy cattle. Genet. Sel. Evol. 2012, 44:23.
27. Eberlein A., Takasuga A., Setoguchi K., Pfuhl R., Flisikowski K., Fries R., Klopp N., Fürbass R., Weikard R., Kühn C. Dissection of genetic factors modulating fetal growth in cattle indicates a substantial role of the non-SMC condensin I complex, subunit G (NCAPG) gene. Genetics 2009, 183:951-964.
28. Eichler E.E. Masquerading repeats: Paralogous pitfalls of the human genome. Genome Res. 1998, 8:758-762.
29. Ellenberger T., Tomkinson A.E. Eukaryotic DNA ligases: Structural and functional insights. Annu. Rev. Biochem. 2008, 77:313-338.
30. Fleischer J., Breer H., Strotmann J. Mammalian olfactory receptors. Front. Cell. Neurosci. 2009, 3:9. http://dx.doi.org/10.3389/neuro.03.009.2009.
31. Garrick D.J., Taylor J.F., Fernando R.L. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet. Sel. Evol. 2009, 41:55. http://dx.doi.org/10.1186/1297-9686-41-55.
32. Gaynor E.C., Mondésert G., Grimme S.J., Reed S.I., Orlean P., Emr S.D. MCD4 encodes a conserved endoplasmic reticulum membrane protein essential for glycosylphosphatidylinositol anchor synthesis in yeast. Mol. Biol. Cell 1999, 10:627-648.
33. Groeneveld, E., M. Kovač and N. Mielenz. 2010. VCE User's Guide and Reference Manual. Version 6.0. Accessed July 15, 2013. ftp://ftp.tzv.fal.de/pub/latest_vce/doc/vce6-manual-3.1-LETTER.pdf.
34. Haines B.P., Wheldon L.M., Summerbell D., Heath J.K., Rigby P.W.J. Regulated expression of FLRT genes implies a functional role in the regulation of FGF signalling during mouse development. Dev. Biol. 2006, 297:14-25.
35. Hansen M., Lund M.S., Pedersen J., Christensen L.G. Gestation length in Danish Holsteins has weak genetic associations with stillbirth, calving difficulty, and calf size. Livest. Prod. Sci. 2004, 91:23-33.
36. Hattori K., Naguro I., Runchel C., Ichijo H. The roles of ASK family proteins in stress responses and diseases. Cell Commun. Signal. 2009, 7:9. http://dx.doi.org/10.1186/1478-811X-7-9.
37. Heins B.J., Hansen L.B., Hazel A.R., Seykora A.J., Johnson D.G., Linn J.G. Birth traits of pure Holstein calves versus Montbeliarde-sired crossbred calves. J. Dairy Sci. 2010, 93:2293-2299.
38. Hofmann C., Shepelev M., Chernoff J. The genetics of Pak. J. Cell Sci. 2004, 117:4343-4354. http://dx.doi.org/10.1242/jcs.01392.
39. Holmberg M., Andersson-Eklund L. Quantitative trait loci affecting fertility and calving traits in Swedish dairy cattle. J. Dairy Sci. 2006, 89:3664-3671.
40. Holstein Association USA. 2011. Linear type evaluations. Accessed Apr. 27, 2011. http://holstein.com/genetic_evaluations/ss_linear.html.
41. Horikoshi M., Yaghootkar H., Mook-Kanamori D.O., Sovio U., Taal H.R., Hennig B.J., Bradfield J.P., St.Pourcain B., Evans D.M., Charoen P., Kaakinen M., Cousminer D.L., Lehtimäki T., Kreiner-Møller E., Warrington N.M., Bustamante M., Feenstra B., Berry D.J., Thiering E., Pfab T., Barton S.J., Shields B.M., Kerkhof M., van Leeuwen E.M., Fulford A.J., Kutalik Z., Zhao J.H., den Hoed M., Mahajan A., Lindi V., Goh L.-K., Hottenga J.-J., Wu Y., Raitakari O.T., Harder M.N., Meirhaeghe A., Ntalla I., Salem R.M., Jameson K.A., Zhou K., Monies D.M., Lagou V., Kirin M., Heikkinen J., Adair L.S., Alkuraya F.S., Al-Odaib A., Amouyel P., Andersson E.A., Bennett A.J., Blakemore A.I.F., Buxton J.L., Dallongeville J., Das S., de Geus E.J.C., Estivill X., Flexeder C., Froguel P., Geller F., Godfrey K.M., Gottrand F., Groves C.J., Hansen T., Hirschhorn J.N., Hofman A., Hollegaard M.V., Hougaard D.M., Hyppönen E., Inskip H.M., Isaacs A., Jørgensen T., Kanaka-Gantenbein C., Kemp J.P., Kiess W., Kilpeläinen T.O., Klopp N., Knight B.A., Kuzawa C.W., McMahon G., Newnham J.P., Niinikoski H., Oostra B.A., Pedersen L., Postma D.S., Ring S.M., Rivadeneira F., Robertson N.R., Sebert S., Simell O., Slowinski T., Tiesler C.M.T., Tönjes A., Vaag A., Viikari J.S., Vink J.M., Vissing N.H., Wareham N.J., Willemsen G., Witte D.R., Zhang H., Zhao J., Wilson J.F., Stumvoll M., Prentice A.M., Meyer B.F., Pearson E.R., Boreham C.A.G., Cooper C., Gillman M.W., Dedoussis G.V., Moreno L.A., Pedersen O., Saarinen M., Mohlke K.L., Boomsma D.I., Saw S.-M., Lakka T.A., Körner A., Loos R.J.F., Ong K.K., Vollenweider P., van Duijn C.M., Koppelman G.H., Hattersley A.T., Holloway J.W., Hocher B., Heinrich J., Power C., Melbye M., Guxens M., Pennell C.E., Bønnelykke K., Bisgaard H., Eriksson J.G., Widén E., Hakonarson H., Uitterlinden A.G., Pouta A., Lawlor D.A., Smith G.D., Frayling T.M., McCarthy M.I., Grant S.F., Jaddoe V.W.V., Jarvelin M.-R., Timpson N.J., Prokopenko I., Freathy R.M. And the Early Growth Genetics (EGG) Consortium, New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism. Nat. Genet. 2013, 45:76-82. The Meta-Analyses of Glucose- and Insulin-related traits Consortium (MAGIC), http://dx.doi.org/10.1038/ng.2477.
42. Hou Y., Liu G.E., Bickhart D.M., Cardone M.F., Wang K., Kim E.-S., Matukumalli L.K., Ventura M., Song J., VanRaden P.M., Sonstegard T.S., Van Tassell C.P. Genomic characteristics of cattle copy number variations. BMC Genomics 2011, 12:127. http://dx.doi.org/10.1186/1471-2164-12-127.
43. Houmani J.L., Davis C.I., Ruf I.K. Growth-promoting properties of Epstein-Barr virus EBER-1 RNA correlate with ribosomal protein L22 binding. J. Virol. 2009, 83:9844-9853. http://dx.doi.org/10.1128/JVI.01014-09.
44. Huang D.W., Sherman B.T., Lempicki R.A. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37:1-13.
45. Jamrozik J., Fatehi J., Kistemaker G.J., Schaeffer L.R. Estimates of genetic parameters for Canadian Holstein female reproduction traits. J. Dairy Sci. 2005, 88:2199-2208.
46. Janssens V., Goris J. Protein phosphatase 2A: A highly regulated family of serine/threonine phosphatases implicated in cell growth and signalling. Biochem. J. 2001, 353:417-439.
47. Johanson J.M., Berger P.J. Birth weight as a predictor of calving ease and perinatal mortality in Holstein cattle. J. Dairy Sci. 2003, 86:3745-3755.
48. Johanson J.M., Berger P.J., Tsuruta S., Misztal I. A Bayesian threshold-linear model evaluation of perinatal mortality, dystocia, birth weight, and gestation length in a Holstein herd. J. Dairy Sci. 2011, 94:450-460.
49. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Haussler D. The Human Genome Browser at UCSC. Genome Res. 2002, 12:996-1006. http://dx.doi.org/10.1101/gr.229102.
50. Kneeland J., Li C., Basarab J., Snelling W.M., Benkel B., Murdoch B., Hansen C., Moore S.S. Identification and fine mapping of quantitative trait loci for growth traits on bovine chromosomes 2, 6, 14, 19, 21, and 23 within one commercial line of Bos taurus. J. Anim. Sci. 2004, 82:3405-3414.
51. Koenen E.P.C., Groen A.F. Genetic analysis of growth patterns of black and white dairy heifers. J. Dairy Sci. 1996, 79:495-501.
52. Kolbehdari D., Wang Z., Grant J.R., Murdoch B., Prasad A., Xiu Z., Marques E., Stothard P., Moore S.S. A whole-genome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls. J. Dairy Sci. 2008, 91:2844-2856.
53. Koshkoih, A. E., W. S. Pitchford, C. D. K. Bottema, A. P. Verbyla, and A. R. Gilmour. 2006. Mapping multiple QTL for birth weight using a mixed model approach. Comm. 20-17 in Proc. 8th World Congr. Genet. Appl. Livest. Prod., Belo Horizonte, MG, Brazil.
54. Kühn C., Bennewitz J., Reinsch N., Xu N., Thomsen H., Looft C., Brockmann G.A., Schwerin M., Weimann C., Hiendleder S., Erhardt G., Medjugorac I., Förster M., Brenig B., Reinhardt F., Reents R., Russ I., Averdunk G., Blümel J., Kalm E. Quantitative trait loci mapping of functional traits in the German Holstein cattle population. J. Dairy Sci. 2003, 86:360-368.
55. Lee J.-H., Paull T.T. Activation and regulation of ATM kinase activity in response to DNA double-strand breaks. Oncogene 2007, 26:7741-7748.
56. Legault C.R., Touchberry R.W. Heritability of birth weight and its relationship with production in dairy cattle. J. Dairy Sci. 1962, 45:1226-1233.
57. Lin L., Lesnick T.G., Maraganore D.M., Isacson O. Axon guidance and synaptic maintenance: Preclinical markers for neurodegenerative disease and therapeutics. Trends Neurosci. 2009, 32:142-149. http://dx.doi.org/10.1016/j.tins.2008.11.006.
58. López de Maturana E., Wu X.-L., Gianola D., Weigel K.A., Rosa G.J.M. Exploring biological relationships between calving traits in primiparous cattle with a Bayesian recursive model. Genetics 2009, 181:277-287.
59. Maltecca C., Gray K.A., Weigel K.A., Cassady J.P., Ashwell M. A genome-wide association study of direct gestation length in US Holstein and Italian Brown populations. Anim. Genet. 2011, 42:585-591. http://dx.doi.org/10.1111/j.1365-2052.2011.02188.x.
60. Maltecca C., Weigel K.A., Khatib H., Cowan M., Bagnato A. Whole-genome scan for quantitative trait loci associated with birth weight, gestation length and passive immune transfer in a Holstein × Jersey crossbred population. Anim. Genet. 2008, 40:27-34.
61. Maltecca C., Weigel K.A., Khatib H., Cowan M., Bagnato A. Whole-genome scan for quantitative trait loci associated with birth weight, gestation length and passive immune transfer in a Holstein × Jersey crossbred population. Anim. Genet. 2009, 40:27-34.
62. Maydan G., Noyman I., Har-Zahav A., Ben Neriah Z., Pasmanik-Chor M., Yeheskel A., Albin-Kaplanski A., Maya I., Magal N., Birk E., Simon A.J., Halevy A., Rechavi G., Shohat M., Straussberg R., Basel-Vanagaite L. Multiple congenital anomalies-hypotonia-seizures syndrome is caused by a mutation in PIGN. J. Med. Genet. 2011, 48:383-389. http://dx.doi.org/10.1111/j.1365-2052.2011.02188.x.
63. McDermott J.J., Allen O.B., Martin S.W., Alves D.M. Patterns of stillbirth and dystocia in Ontario cow-calf herds. Can. J. Vet. Res. 1992, 56:47-55.
64. Meijering A. Dystocia and stillbirth in cattle-A review of causes, relations and implications. Livest. Prod. Sci. 1984, 11:143-177.
65. Meyer C.L., Berger P.J., Thompson J.R., Sattler C.G. Genetic evaluation of Holstein sires and maternal grandsires in the United States for perinatal survival. J. Dairy Sci. 2001, 84:1246-1254.
66. Miesenberger, J. 1997. Zuchtzieldefinition und Indexselektion für die österreichische Rinderzucht [Definition of the aggregate genotype and a selection index for the Austrian cattle]. PhD Diss. Universität für Bodenkultur, Vienna, Austria.
67. Misztal, I., S. Tsuruta, T. Strabel, B. Auvray, T. Druet, and D. H. Lee. 2002. BLUPF90 and related programs (BGF90). Comm. No. 28-07 in Proc. 7th World Congr. Genet. Appl. Livest. Prod., Montpellier, France.
68. Müller P.-S., Schulz R., Maretto S., Costello I., Srinivas S., Bikoff E., Robertson E. The fibronectin leucine-rich repeat transmembrane protein Flrt2 is required in the epicardium to promote heart morphogenesis. Development 2011, 138:1297-1308. http://dx.doi.org/10.1242/dev.059386.
69. Muntoni F., Torelli S., Ferlini A. Dystrophin and mutations: One gene, several proteins, multiple phenotypes. Lancet Neurol. 2003, 2:731-740.
70. Nakashiba T., Ikeda T., Nishimura S., Tashiro K., Honjo T., Culotti J.G., Itohara S. Netrin-G1: A novel glycosyl phosphatidylinositol-linked mammalian netrin that is functionally divergent from classical netrins. J. Neurosci. 2000, 20:6540-6550.
71. Norman H.D., Wright J.R., Kuhn M.T., Hubbard S.M., Cole J.B., VanRaden P.M. Genetic and environmental factors that affect gestation length in dairy cattle. J. Dairy Sci. 2009, 92:2259-2269.
72. Olson K.M., Cassell B.G., McAllister A.J., Washburn S.P. Dystocia, stillbirth, gestation length, and birth weight in Holstein, Jersey, and reciprocal crosses from a planned experiment. J. Dairy Sci. 2009, 92:6167-6175.
73. Pausch H., Flisikowski K., Jung S., Emmerling R., Edel C., Götz K.-U., Fries R. Genome-wide association study identifies two major loci affecting calving ease and growth-related traits in cattle. Genetics 2011, 187:289-297.
74. Pfaeffle R.W., Hunter C.S., Savage J.J., Duran-Prado M., Mullen R.D., Neeb Z.P., Eiholzer U., Hesse V., Haddad N.G., Stobbe H.M., Blum W.F., Weigel J.F.W., Rhodes S.J. Three novel missense mutations within the LHX4 gene are associated with variable pituitary hormone deficiencies. J. Clin. Endocrinol. Metab. 2008, 93:1062-1071. http://dx.doi.org/10.1210/jc.2007-1525.
75. Pfeffer P.L., Sisco B., Donnison M., Somers J., Smith C. Isolation of genes associated with developmental competency of bovine oocytes. Theriogenology 2007, 68(Suppl. 1):S84-S90. http://dx.doi.org/10.1016/j.theriogenology.2007.03.016.
76. Philipsson J., Foulley J.L., Lederer J., Liboriussen T., Osinga A. Sire evaluation standards and breeding strategies for limiting dystocia and stillbirth. Report of an E.E.C./E.A.A.P. working group. Livest. Prod. Sci. 1979, 6:111-127.
77. Pryce J.E., Hayes B.J., Bolormaa S., Goddard M.E. Polymorphic regions affecting human height also control stature in cattle. Genetics 2011, 187:981-984. http://dx.doi.org/10.1534/genetics.110.123943.
78. Purfield D.C., Bradley D.G., Kearney J.F., Berry D.P. Genome-wide association study for calving traits in Holstein-Friesian dairy cattle. Animal 2014, 8:224-235. http://dx.doi.org/10.1017/S175173111300195X.
79. Qanbari S., Gianola D., Hayes B., Schenkel F., Miller S., Moore S., Thaller G., Simianer H. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics 2011, 12:318. http://dx.doi.org/10.1186/1471-2164-12-318.
80. Quinlan A.R., Hall I.M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842.
81. R: A Language and Environment for Statistical Computing 2010, R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria.
82. Ren G., Chen H., Zhang L.Z., Lan X.Y., Wei T.B., Li M.J., Jing Y.J., Lei C.Z., Wang J.Q. A coding SNP of LHX4 gene is associated with body weight and body length in bovine. Mol. Biol. Rep. 2010, 37:417-422. http://dx.doi.org/10.1007/s11033-009-9486-6.
83. Sahana G., Guldbrandtsen B., Lund M.S. Genome-wide association study for calving traits in Danish and Swedish Holstein cattle. J. Dairy Sci. 2011, 94:479-486.
84. Schnabel R.D., Sonstegard T.S., Taylor J.F., Ashwell M.S. Whole-genome scan to detect QTL for milk production, fertility and functional traits in two US Holstein families. Anim. Genet. 2005, 36:408-416.
85. Schutz M.M. Genetic evaluation of somatic cell scores for United States dairy cattle. J. Dairy Sci. 1994, 77:2113-2129.
86. Seidenspinner T., Tetens J., Habier D., Bennewitz J., Thaller G. The placental growth factor (PGF)-A positional and functional candidate gene influencing calving ease and stillbirth in German dairy cattle. Anim. Genet. 2011, 42:22-27.
87. Simmons D., Seed B. Isolation of a cDNA encoding CD33, a differentiation antigen of myeloid progenitor cells. J. Immunol. 1988, 141:2797-2800.
88. Smith S.B., Qu H.-Q., Taleb N., Kishimoto N.Y., Scheel D.W., Lu Y., Patch A.-M., Grabs R., Wang J., Lynn F.C., Miyatsuka T., Mitchell J., Seerke R., Désir J., Eijnden S.V., Abramowicz M., Kacet N., Weill J., Renard M.-É., Gentile M., Hansen I., Dewar K., Hattersley A.T., Wang R., Wilson M.E., Johnson J.D., Polychronakos C., German M.S. Rfx6 directs islet formation and insulin production in mice and humans. Nature 2010, 463:775-780. http://dx.doi.org/10.1038/nature08748.
89. Smith S.L., Everts R.E., Sung L.-Y., Du F., Page R.L., Henderson B., Rodriguez-Zas S.L., Nedambale T.L., Renard J.-P., Lewin H.A., Yang X., Tian X.C. Gene expression profiling of single bovine embryos uncovers significant effects of in vitro maturation, fertilization and culture. Mol. Reprod. Dev. 2009, 76:38-47.
90. Sokal R.R., Rohlf F.J. Biometry: The Principles and Practice of Statistics in Biological Research 1995, W. H. Freeman and Co., New York, NY. 3rd.
91. Swali A., Wathes D.C. Influence of the dam and sire on size at birth and subsequent growth, milk production and fertility in dairy heifers. Theriogenology 2006, 66:1173-1184.
92. Thomasen J.R., Guldbrandtsen B., Sørensen P., Thomsen B., Lund M.S. Quantitative trait loci affecting calving traits in Danish Holstein cattle. J. Dairy Sci. 2008, 91:2098-2105.
93. Thompson J.R., Freeman A.E., Berger P.J. Relationship of dystocia transmitting ability with type and production transmitting ability in Holstein bulls. J. Dairy Sci. 1980, 63:1462-1464.
94. Uitto J. The gene family of ABC transporters-Novel mutations, new phenotypes. Trends Mol. Med. 2005, 11:341-343.
95. Utsunomiya Y.T., do Carmo A.S., Carvalheiro R., Neves H.H.R., Matos M.C., Zavarez L.B., Pérez O'Brien A.M., Sölkner J., McEwan J., Cole J.B., Van Tassell C.P., Schenkel F.S., da Silva M.V.G.B., Porto Neto L.R., Sonstegard T.S., Garcia J.F. Genome-wide association study for birth weight in Brazilian Nellore cattle (Bos taurus indicus) points to previously described orthologous genes affecting human and bovine height. BMC Genet. 2013, 14:52. http://dx.doi.org/10.1186/1471-2156-14-52.
96. Van Tassell C.P., Wiggans G.R., Misztal I. Implementation of a sire-maternal grandsire model for evaluation of calving ease in the United States. J. Dairy Sci. 2003, 86:3366-3373.
97. VanRaden P.M. Efficient methods to compute genomic predictions. J. Dairy Sci. 2008, 91:4414-4423.
98. VanRaden P.M., O'Connell J.R., Wiggans G.R., Weigel K.A. Genomic evaluations with many more genotypes. Genet. Sel. Evol. 2011, 43:10.
99. VanRaden P.M., Olson K.M., Wiggans G.R., Cole J.B., Tooker M.E. Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss. J. Dairy Sci. 2011, 94:5673-5682.
100. VanRaden P.M., Sanders A.H., Tooker M.E., Miller R.H., Norman H.D., Kuhn M.T., Wiggans G.R. Development of a national genetic evaluation for cow fertility. J. Dairy Sci. 2004, 87:2285-2292.
101. VanRaden P.M., Wiggans G.R. Productive life evaluations: Calculation, accuracy, and economic value. J. Dairy Sci. 1995, 78:631-638.
102. Varki A., Angata T. Siglecs-The major subfamily of I-type lectins. Glycobiology 2006, 1:1R-27R. http://dx.doi.org/10.1093/glycob/cwj008.
103. Venables J.P., Vernet C., Chew S.L., Elliott D.J., Cowmeadow R.B., Wu J., Cooke H.J., Artzt K., Eperon I.C. T-STAR/ÉTOILE: A novel relative of SAM68 that interacts with an RNA-binding protein implicated in spermatogenesis. Hum. Mol. Genet. 1999, 8:959-969.
104. Villa A., Strina D., Frattini A., Faranda S., Macchi P., Finelli P., Bozzi F., Susani L., Archidiacono N., Rocchi M., Vezzoni P. The ZNF75 zinc finger gene subfamily: Isolation and mapping of the four members in humans and great apes. Genomics 1996, 35:312-320.
105. vit. 2013. Estimation of breeding values for milk production traits, somatic cell score, conformation, productive life and reproduction traits in German dairy cattle. Accessed Jan. 17, 2013. http://www.vit.de/fileadmin/user_upload/vit-fuers-rind/zuchtwertschaetzung/milchrinder-zws-online/Zws_Bes_eng.pdf.
106. Vitelli F., Piccini M., Caroli F., Franco B., Malandrini A., Pober B., Jonsson J., Sorrentino V., Renieri A. Identification and characterization of a highly conserved protein absent in the Alport syndrome (A), mental retardation (M), midface hypoplasia (M), and elliptocytosis (E) contiguous gene deletion syndrome (AMME). Genomics 1999, 55:335-340.
107. Waurich, B., M. Wensch-Dorendorf, J. B. Cole, and H. H. Swalve. 2011. Genetic evaluations for birth weight: A comparison of continuous and discrete definitions of birth weight under varying accuracies of recording. Session 36:2, S. 217 in Proc. Annu. Mtg. EAAP, Stavanger, Norway. Wageningen Academic Publishers, Wageningen, the Netherlands.
108. Waurich, B., M. Wensch-Dorendorf, R. Schafberg, B. Rudolphi, and H. H. Swalve. 2010. Relationships between conformation traits and traits of the calving complex in dairy cows. Paper no. 0386 in Proc. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany.
109. Wei L., Roberts W., Wang L., Yamada M., Zhang S., Zhao Z., Rivkees S.A., Schwartz R.J., Imanaka-Yoshida K. Rho kinases play an obligatory role in vertebrate embryonic organogenesis. Development 2001, 128:2953-2962.
110. Wickham H. ggplot2: Elegant Graphics for Data Analysis 2009, Springer, New York, NY.
111. Yu J., Pressoir G., Briggs W.H., Bi I.V., Yamasaki M., Doebley J.F., McMullen M.D., Gaut B.S., Nielsen D.M., Holland J.B., Kresovich S., Buckler E.S. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 2006, 38:203-208.
112. Zhang R., Yao F., Gao F., Abou-Samra A.B. Nrac, a novel nutritionally-regulated adipose and cardiac-enriched gene. PLoS ONE 2012, 7:e46254. http://dx.doi.org/10.1371/journal.pone.0046254.
113. Zimin A.V., Delcher A.L., Florea L., Kelley D.R., Schatz M.C., Puiu D., Hanrahan F., Pertea G., Van Tassell C.P., Sonstegard T.S., Marçais G., Roberts M., Subramanian P., Yorke J.A., Salzberg S.L. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 2009, 10:R42. http://dx.doi.org/10.1186/gb-2009-10-4-r42.