Mee JF. Prevalence and risk factors for dystocia in dairy cattle: a review. Vet J. 2008;176:93–101.
Article
CAS
PubMed
Google Scholar
de Maturana EL, Ugarte E, González-Recio O. Impact of calving ease on functional longevity and herd amortization costs in Basque Holsteins using survival analysis. J Dairy Sci. 2007;90:4451–7.
Article
Google Scholar
de Maturana EL, Wu X-L, Gianola D, Weigel KA, Rosa GJM. Exploring biological relationships between calving traits in primiparous cattle with a Bayesian recursive model. Genetics. 2009;181:277–87.
Article
PubMed
PubMed Central
Google Scholar
Meyer CL, Berger PJ, Koehler KJ, Thompson JR, Sattler CG. Phenotypic trends in incidence of stillbirth for Holsteins in the United States. J Dairy Sci. 2001;84:515–23.
Article
CAS
PubMed
Google Scholar
Bicalho RC, Galvão KN, Cheong SH, Gilbert RO, Warnick LD, Guard CL. Effect of stillbirths on dam survival and reproduction performance in Holstein dairy cows. J Dairy Sci. 2007;90:2797–803.
Article
CAS
PubMed
Google Scholar
Eaglen SA, Coffey MP, Woolliams JA, Mrode R, Wall E. Phenotypic effects of calving ease on the subsequent fertility and milk production of dam and calf in UK Holstein-Friesian heifers. J Dairy Sci. 2011;94:5413–23.
Article
CAS
PubMed
Google Scholar
Zaborski D, Grzesiak W, Szatkowska I, Dybus A, Muszynska M, Jedrzejczak M. Factors affecting dystocia in cattle. Reprod Domest Anim. 2009;44:540–51.
Article
CAS
PubMed
Google Scholar
Eaglen SA, Coffey MP, Woolliams JA, Wall E. Direct and maternal genetic relationships between calving ease, gestation length, milk production, fertility, type, and lifespan of Holstein-Friesian primiparous cows. J Dairy Sci. 2013;96:4015–25.
Article
CAS
PubMed
Google Scholar
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. Nucleic Acids Res. 2013;41:871–9.
Article
Google Scholar
Cole JB, Goodling RC, Wiggans GR, Vanraden PM. Genetic evaluation of calving ease for Brown Swiss and Jersey bulls from purebred and crossbred calvings. J Dairy Sci. 2005;88:1529–39.
Article
CAS
PubMed
Google Scholar
Olson KM, Cassell BG, McAllister AJ, Washburn SP. Dystocia, stillbirth, gestation length, and birth weight in Holstein, Jersey, and reciprocal crosses from a planned experiment. J Dairy Sci. 2009;92:6167–75.
Article
CAS
PubMed
Google Scholar
McClintock S, Poole R, Beard K, Goddard M. Cross breeding in dairy cattle: the effect on calving ease. Interbull Bulletin. 2004;32:113–7.
McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008;9:356–69.
Article
CAS
PubMed
Google Scholar
Wiggans GR, Vanraden PM, Cooper TA. The genomic evaluation system in the United States: past, present, future. J Dairy Sci. 2011;94:3202–11.
Article
CAS
PubMed
Google Scholar
Cooper TA, Wiggans GR, Null DJ, Hutchison JL, Cole JB. Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle. J Dairy Sci. 2014;97:3878–82.
Article
CAS
PubMed
Google Scholar
Goddard M. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica. 2009;136:245–57.
Article
PubMed
Google Scholar
de Roos AP, Hayes BJ, Spelman RJ, Goddard ME. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics. 2008;179:1503–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
VanRaden PM, Van Tassell CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF, et al. Invited review: reliability of genomic predictions for North American Holstein bulls. J Dairy Sci. 2009;92:16–24.
Article
CAS
PubMed
Google Scholar
Parker Gaddis KL, Cole JB, Clay JS, Maltecca C. Genomic selection for producer-recorded health event data in US dairy cattle. J Dairy Sci. 2014;97:3190–9.
Article
CAS
PubMed
Google Scholar
de Roos AP, Hayes BJ, Goddard ME. Reliability of genomic predictions across multiple populations. Genetics. 2009;183:1545–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hayes BJ, Bowman PJ, Chamberlain AC, Verbyla K, Goddard ME. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet Sel Evol. 2009;41:51.
Article
PubMed
PubMed Central
Google Scholar
Benfey PN, Mitchell-Olds T. From genotype to phenotype: systems biology meets natural variation. Science. 2008;320:495–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hudson NJ, Dalrymple BP, Reverter A. Beyond differential expression: the quest for causal mutations and effector molecules. BMC Genomics. 2012;13:356.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hudson NJ, Reverter A, Dalrymple BP. A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol. 2009;5:e1000382.
Article
PubMed
PubMed Central
Google Scholar
Fortes MRS, DeAtley KL, Lehnert SA, Burns BM, Reverter A, Hawken RJ, et al. Genomic regions associated with fertility traits in male and female cattle: advances from microsatellites to high-density chips and beyond. Anim Reprod Sci. 2013;141:1.
Article
CAS
PubMed
Google Scholar
Fortes MRS, Reverter A, Zhang Y, Collis E, Nagaraj SH, Jonsson NN, et al. Association weight matrix for the genetic dissection of puberty in beef cattle. Proc Natl Acad Sci. 2010;107:13642–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van Tassell CP, Wiggans GR, Misztal I. Implementation of a sire-maternal grandsire model for evaluation of calving ease in the United States. J Dairy Sci. 2003;86:3366–73.
Article
CAS
PubMed
Google Scholar
Norman HD, Wright JR, Kuhn MT, Hubbard SM, Cole JB, VanRaden PM. Genetic and environmental factors that affect gestation length in dairy cattle. J Dairy Sci. 2009;92:2259–69.
Article
CAS
PubMed
Google Scholar
Wiggans GR, Gengler N, Wright JR. Type trait (co)variance components for five dairy breeds. J Dairy Sci. 2004;87:2324–30.
Article
CAS
PubMed
Google Scholar
Tsuruta S, Misztal I, Aguilar I, Lawlor TJ. Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins. J Dairy Sci. 2011;94:4198–204.
Article
CAS
PubMed
Google Scholar
Garrick DJ, Taylor JF, Fernando RL. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet Sel Evol. 2009;41:55.
Article
PubMed
PubMed Central
Google Scholar
Tiezzi F, Maltecca C. Accounting for trait architecture in genomic predictions of US Holstein cattle using a weighted realized relationship matrix. Genet Sel Evol. 2015;47:1–13.
Article
CAS
Google Scholar
Fernando R, Garrick D. GenSel-user manual for a portfolio of genomic selection related analyses. Ames: Animal Breeding and Genetics, Iowa State University; 2008. p. 0–24.
Google Scholar
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 2009;10:R42.
Article
PubMed
PubMed Central
Google Scholar
Reverter A, Chan EKF. Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Bioinformatics. 2008;24:2491–7.
Article
CAS
PubMed
Google Scholar
R Development Core Team. R: a language and environment for statisitical computing. Vienna: R Foundation for Statistical Computing; 2012.
Google Scholar
Kalinka AT. The probability of drawing intersections: extending the hypergeometric distribution. arXiv:1305.0717v5 [math.FA]; 2014. p. 1–15.
Google Scholar
Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst. 2006;1695:1.
Google Scholar
Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics. 2007;23:257–8.
Article
CAS
PubMed
Google Scholar
Storey JD. The positive false discovery rate: a Bayesian interpretation and the q-value. Ann Stat. 2003;31:2013–35.
Article
Google Scholar
Supek F, Bošnjak M, Škunca N, Šmuc T. Revigo summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6:e21800.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schlicker A, Domingues FS, Rahnenführer J, Lengauer T. A new measure for functional similarity of gene products based on gene ontology. BMC Bioinf. 2006;7:302.
Article
Google Scholar
Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, J-SS K, et al. A novel signaling pathway impact analysis. Bioinformatics. 2008;25:75–82.
Article
PubMed
PubMed Central
Google Scholar
Saatchi M, McClure MC, McKay SD, Rolf MM, Kim J, Decker JE, et al. Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation. Genet Sel Evol. 2011;43:40.
Article
PubMed
PubMed Central
Google Scholar
VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci. 2008;91:4414–23.
Article
CAS
PubMed
Google Scholar
Cole JB, VanRaden PM, O’Connell JR, Van Tassell CP, Sonstegard TS, Schnabel RD, et al. Distribution and location of genetic effects for dairy traits. J Dairy Sci. 2009;92:2931–46.
Article
CAS
PubMed
Google Scholar
Sahana G, Guldbrandtsen B, Lund MS. Genome-wide association study for calving traits in Danish and Swedish Holstein cattle. J Dairy Sci. 2011;94:479–86.
Article
CAS
PubMed
Google Scholar
Höglund JK, Guldbrandtsen B, Lund MS, Sahana G. Analyzes of genome-wide association follow-up study for calving traits in dairy cattle. BMC Genet. 2012;13:71.
Article
PubMed
PubMed Central
Google Scholar
Cole JB, Wiggans GR, Ma L, Sonstegard TS, Lawlor TJ, Crooker BA, et al. 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.
Article
PubMed
PubMed Central
Google Scholar
Maltecca C, Gray KA, Weigel KA, Cassady JP, Ashwell M. A genome-wide association study of direct gestation length in US Holstein and Italian Brown populations. Anim Genet. 2011;42:585–91.
Article
CAS
PubMed
Google Scholar
Cole JB, Waurich B, Wensch-Dorendorf M, Bickhart DM, Swalve HH. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. J Dairy Sci. 2014;97:3156–72.
Article
CAS
PubMed
Google Scholar
Brand B, Baes C, Mayer M, Reinsch N, Seidenspinner T, Thaller G, et al. Quantitative trait loci mapping of calving and conformation traits on Bos taurus autosome 18 in the German Holstein population. J Dairy Sci. 2010;93:1205–15.
Article
CAS
PubMed
Google Scholar
Seidenspinner T, Bennewitz J, Reinhardt F, Thaller G. Need for sharp phenotypes in QTL detection for calving traits in dairy cattle. J Anim Breed Genet. 2009;126:455–62.
Article
CAS
PubMed
Google Scholar
Kühn C, Bennewitz J, Reinsch N, Xu N, Thomsen H, Looft C, et al. Quantitative trait loci mapping of functional traits in the German Holstein cattle population. J Dairy Sci. 2003;86:360–8.
Article
PubMed
Google Scholar
Schrooten C, Bovenhuis H, Coppieters W, Van Arendok JAM. Whole genome scan to detect quantitative trait loci for conformation and functional traits in dairy cattle. J Dairy Sci. 2000;83:795–806.
Article
CAS
PubMed
Google Scholar
Raven L-A, Cocks BG, Hayes BJ. Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle. BMC Genomics. 2014;15:62.
Article
PubMed
PubMed Central
Google Scholar
Guo J, Jorjani H, Carlborg Ö. A genome-wide association study using international breeding-evaluation data identifies major loci affecting production traits and stature in the Brown Swiss cattle breed. BMC Genet. 2012;13:82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morris CA, Pitchford WS, Cullen NG, Esmailizadeh AK, Hickey SM, Hyndman D, et al. Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot. Anim Genet. 2009;40:648–54.
Article
CAS
PubMed
Google Scholar
Barabási A-L, Oltvai ZN. Network biology: understanding the cell’s functional organization. Nat Rev Genet. 2004;5:101–13.
Article
PubMed
Google Scholar
Nielsen E, Cheung AY, Ueda T. The regulatory RAB and ARF GTPases for vesicular trafficking. Plant Physiol. 2008;147:1516–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Campa F, Randazzo PA. Arf GTPase-activating proteins and their potential role in cell migration and invasion. Cell Adhes Migr. 2008;2:258–62.
Article
Google Scholar
Donaldson JG, Jackson CL. ARF family G proteins and their regulators: roles in membrane transport, development and disease. Nat Rev Mol Cell Biol. 2011;12:362–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sancho D, Vicente-Manzanares M, Mittelbrunn M, Montoya MC, Gordón-Alonso M, Serrador JM, et al. Regulation of microtubule-organizing center orientation and actomyosin cytoskeleton rearrangement during immune interactions. Immunol Rev. 2002;189:84–97.
Article
CAS
PubMed
Google Scholar
Albrecht E, Lembcke C, Wegner J, Maak S. Prenatal muscle fiber development and bundle structure in beef and dairy cattle. J Anim Sci. 2013;91:3666–73.
Article
CAS
PubMed
Google Scholar
Duarte MS, Paulino PVR, Das AK, Wei S, Serão NVL, Fu X, et al. Enhancement of adipogenesis and fibrogenesis in skeletal muscle of Wagyu compared with Angus cattle. J Anim Sci. 2013;91:2938–46.
Article
CAS
PubMed
Google Scholar
Nayeri S, Sargolzaei M, Abo-Ismail MK, May N, Miller SP, Schenkel F, et al. Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle. BMC Genet. 2016;17:75.
Article
PubMed
PubMed Central
Google Scholar
Parker Gaddis KL, Null DJ, Cole JB. Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits. J Dairy Sci. 2016;99:6420–35.
Article
CAS
PubMed
Google Scholar
Snelling WM, Cushman RA, Keele JW, Maltecca C, Thomas MG, Fortes MRS, et al. Breeding and genetics symposium: networks and pathways to guide genomic selection. J Anim Sci. 2013;91:537–52.
Article
CAS
PubMed
Google Scholar