Barwick SA, Henzell AL. Development successes and issues for the future in deriving and applying selection indexes for beef breeding. Aust J Exp Agric. 2005;45:923. https://doi.org/10.1071/EA05068.
Article
Google Scholar
Utsunomiya YT, do Carmo AS, Carvalheiro R, Neves HH, Matos MC, Zavarez LB, et al. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genet. 2013;14:52. https://doi.org/10.1186/1471-2156-14-52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brito Lopes F, da Silva MC, Magnabosco CU, Goncalves Narciso M, Sainz RD. Selection indices and multivariate analysis show similar results in the evaluation of growth and carcass traits in beef cattle. PLoS One. 2016;11:e0147180. https://doi.org/10.1371/journal.pone.0147180.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meirelles SLC, Mokry FB, Espasandín AC, Dias MAD, Baena MM, de A. Regitano LC. Genetic parameters for carcass traits and body weight using a Bayesian approach in the Canchim cattle. Genet Mol Res. 2016;15. https://doi.org/10.4238/gmr.15027471.
Bourdon RM, Brinks JS. Genetic, environmental and phenotypic relationships among gestation length, birth weight, growth traits and age at first calving in beef cattle. J Anim Sci. 1982;55:543–53. https://doi.org/10.2527/jas1982.553543x.
Article
CAS
PubMed
Google Scholar
Eriksson S, Näsholm A, Johansson K, Philipsson J. Genetic parameters for calving difficulty, stillbirth, and birth weight for Hereford and Charolais at first and later parities1. J Anim Sci. 2004;82:375–83. https://doi.org/10.2527/2004.822375x.
Article
CAS
PubMed
Google Scholar
Cook BR, Tess MW, Kress DD. Effects of selection strategies using heifer pelvic area and sire birth weight expected progeny difference on dystocia in first-calf heifers. J Anim Sci. 1993;71:602–7. https://doi.org/10.2527/1993.713602x.
Article
CAS
PubMed
Google Scholar
Spelman RJ, Huisman AE, Singireddy SR, Coppieters RJ, Arranz J, Georges M, et al. Quantitative trait loci analysis on 17 nonproduction traits in the New Zealand dairy population. J Dairy Sci. 2000;83:370. https://doi.org/10.3168/JDS.S0022-0302(00)74890-9.
Article
CAS
Google Scholar
Kneeland J, Li C, Basarab J, Snelling WM, Benkel B, Murdoch B, et al. 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 taurus1. J Anim Sci. 2004;82:3405–14. https://doi.org/10.2527/2004.82123405x.
Article
CAS
PubMed
Google Scholar
Maltecca C, Weigel KA, 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. 2008:27–34. https://doi.org/10.1111/j.1365-2052.2008.01793.x.
CAS
PubMed
Google Scholar
McClure MC, Morsci NS, Schnabel RD, Kim JW, Yao P, Rolf MM, et al. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim Genet. 2010;41:597–607. https://doi.org/10.1111/j.1365-2052.2010.02063.x.
Article
CAS
PubMed
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. https://doi.org/10.1186/1471-2164-12-408.
Article
PubMed
PubMed Central
Google Scholar
Santiago GG, Siqueira F, Cardoso FF, Regitano LCA, Ventura R, Sollero BP, et al. Genomewide association study for production and meat quality traits in Canchim beef cattle. J Anim Sci. 2017;95:3381–90. https://doi.org/10.2527/jas.2017.1570.
Article
CAS
PubMed
Google Scholar
Saatchi M, Schnabel RD, Taylor JF, Garrick DJ. Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds. BMC Genomics. 2014;15.
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.
Google Scholar
Saatchi M, Schnabel RD, Rolf MM, Taylor JF, Garrick DJ. Accuracy of direct genomic breeding values for nationally evaluated traits in US Limousin and Simmental beef cattle. Genet Sel Evol. 2012;44.
Google Scholar
Saatchi M, Garrick DJ, Tait RG, Mayes MS, Drewnoski M, Schoonmaker J, et al. Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattle a. BMC Genomics. 2013;14.
CAS
PubMed
PubMed Central
Google Scholar
Pryce JE, Hayes BJ, Bolormaa S, Goddard ME. Polymorphic regions affecting human height also control stature in cattle. Genetics. 2011;187:981–4.
PubMed
PubMed Central
Google Scholar
Gudbjartsson DF, Walters GB, Thorleifsson G, Stefansson H, Halldorsson BV, Zusmanovich P, et al. Many sequence variants affecting diversity of adult human height. Nat Genet. 2008;40:609–15.
CAS
PubMed
Google Scholar
Weedon MN, Lango H, Lindgren CM, Wallace C, Evans DM, Mangino M, et al. Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet. 2008;40:575–83.
CAS
PubMed
PubMed Central
Google Scholar
Pausch H, Flisikowski K, Jung S, Emmerling R, Edel C, Götz KU, et al. Genome-wide association study identifies two major loci affecting calving ease and growth-related traits in cattle. Genetics. 2011;187:289–97.
CAS
PubMed
PubMed Central
Google Scholar
Abo-Ismail MK, Brito LF, Miller SP, Sargolzaei M, Grossi DA, Moore SS, et al. Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle. Genet Sel Evol. 2017;49.
Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, et al. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One. 2009;4:e5350. https://doi.org/10.1371/journal.pone.0005350.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rincon G, Weber KL, Van Eenennaam AL, Golden BL, Medrano JF. Hot topic: performance of bovine high-density genotyping platforms in Holsteins and jerseys. J Dairy Sci. 2011;94:6116–21. https://doi.org/10.3168/JDS.2011-4764.
Article
CAS
PubMed
Google Scholar
VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci. 2008;91:4414–23. https://doi.org/10.3168/JDS.2007-0980.
Article
CAS
PubMed
Google Scholar
Decker JE. Agricultural genomics: commercial applications bring increased basic research power. PLoS Genet. 2015;11:e1005621. https://doi.org/10.1371/journal.pgen.1005621.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012;44:821–4. https://doi.org/10.1038/ng.2310.
Article
CAS
PubMed
PubMed Central
Google Scholar
Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, et al. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat Genet. 2012;44:825–30. https://doi.org/10.1038/ng.2314.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kang HM, Sul JH, Service SK, Zaitlen NA, Kong S, Freimer NB, et al. Variance component model to account for sample structure in genome-wide association studies. Nat Genet. 2010;42:348–54. https://doi.org/10.1038/ng.548.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seabury CM, Oldeschulte DL, Saatchi M, Beever JE, Decker JE, Halley YA, et al. Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. BMC Genomics. 2017;18:386. https://doi.org/10.1186/s12864-017-3754-y.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wellcome Trust Case Control Consortium TWTCC. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007;447:661–78. https://doi.org/10.1038/nature05911.
Article
CAS
Google Scholar
Lee SH, Choi BH, Lim D, Gondro C, Cho YM, Dang CG, et al. Genome-wide association study identifies major loci for carcass weight on BTA14 in Hanwoo (Korean cattle). PLoS One. 2013;8.
CAS
PubMed
PubMed Central
Google Scholar
Utsunomiya YT, Milanesi M, Utsunomiya ATH, Torrecilha RBP, Kim ES, Costa MS, et al. A PLAG1 mutation contributed to stature recovery in modern cattle. Sci Rep. 2017;7.
Fink T, Tiplady K, Lopdell T, Johnson T, Snell RG, Spelman RJ, et al. Functional confirmation of PLAG1 as the candidate causative gene underlying major pleiotropic effects on body weight and milk characteristics. Sci Rep. 2017;7.
Eberlein A, Takasuga A, Setoguchi K, Pfuhl R, Flisikowski K, Fries R, et al. 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;183:951–64.
CAS
PubMed
PubMed Central
Google Scholar
Setoguchi K, Furuta M, Hirano T, Nagao T, Watanabe T, Sugimoto Y, et al. Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-met substitution in NCAPG as a positional candidate. BMC Genet. 2009;10.
PubMed
PubMed Central
Google Scholar
Lindholm-Perry AK, Kuehn LA, Oliver WT, Sexten AK, Miles JR, Rempel LA, et al. Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain. PLoS One. 2013;8:e80882. https://doi.org/10.1371/journal.pone.0080882.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, Duan X, Chen S, He H, Liu X. NCAPG is differentially expressed during longissimus muscle development and is associated with growth traits in Chinese Qinchuan beef cattle. Genet Mol Biol. 2015;38:450–6.
CAS
PubMed
PubMed Central
Google Scholar
Lyu S, Arends D, Nassar MK, Brockmann GA. Fine mapping of a distal chromosome 4 QTL affecting growth and muscle mass in a chicken advanced intercross line. Anim Genet. 2017;48:295–302.
CAS
PubMed
Google Scholar
Urbinati I, Stafuzza NB, Oliveira MT, Chud TCS, Higa RH, Regitano LC de A, et al. Selection signatures in Canchim beef cattle. J Anim Sci Biotechnol. 2016;7.
Buzanskas ME, Grossi DA, Ventura RV, Schenkel FS, Sargolzaei M, Meirelles SLC, et al. Genome-wide association for growth traits in canchim beef cattle. PLoS One. 2014;9:1–8.
PubMed
PubMed Central
Google Scholar
Mosley JD, Shaffer CM, Van Driest SL, Weeke PE, Wells QS, Karnes JH, et al. A genome-wide association study identifies variants in KCNIP4 associated with ACE inhibitor-induced cough. Pharmacogenomics J. 2016;16:231–7.
CAS
PubMed
Google Scholar
Martínez R, Gómez Y, Martínez-Roch JF. Genome-wide association study on growth traits in Colombian creole breeds and crossbreeds with zebu cattle. Genet Mol Res. 2014;13:6420–32.
PubMed
Google Scholar
Lindholm-Perry AK, Kuehn LA, Smith TPL, Ferrell CL, Jenkins TG, Freetly HC, et al. A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle. Anim Genet. 2012;43:216–9.
CAS
PubMed
Google Scholar
Jepsen MR, Kløverpris S, Mikkelsen JH, Pedersen JH, Füchtbauer EM, Laursen LS, et al. Stanniocalcin-2 inhibits mammalian growth by proteolytic inhibition of the insulin-like growth factor axis. J Biol Chem. 2015;290:3430–9.
CAS
PubMed
Google Scholar
Bolormaa S, Pryce JE, Reverter A, Zhang Y, Barendse W, Kemper K, et al. A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLoS Genet. 2014;10.
PubMed
PubMed Central
Google Scholar
Bouleftour W, Boudiffa M, Wade-Gueye NM, Bouët G, Cardelli M, Laroche N, et al. Skeletal development of mice lacking bone Sialoprotein (BSP) - impairment of long bone growth and progressive establishment of high trabecular bone mass. PLoS One. 2014;9.
PubMed
PubMed Central
Google Scholar
Bellahcene A, Merville M-P, Castronovo V. Expression of Bone Sialoprotein, a Bone Matrix Protein, in Human Breast Cancer. Cancer Res. 1994;54:2823–6.
Cohen-Zinder M, Seroussi E, Larkin DM, Loor JJ. Everts-Van Der wind A, Lee JH, et al. identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle. Genome Res. 2005;15:936–44.
CAS
PubMed
PubMed Central
Google Scholar
An B, Xia J, Chang T, Wang X, Miao J, Xu L, et al. Genome-wide association study identifies loci and candidate genes for internal organ weights in simmental beef cattle. Physiol Genomics. 2018;50:523–31.
CAS
PubMed
Google Scholar
Saunders J, Wisidagama DR, Morford T, Malone CS. Maximal expression of the evolutionarily conserved Slit2 gene promoter requires Sp1. Cell Mol Neurobiol. 2016;36:955–64.
CAS
PubMed
Google Scholar
Holmes G, Niswander L. Expression of slit-2 and slit-3 during chick development. Dev Dyn. 2001;222:301–7. https://doi.org/10.1002/dvdy.1182.
Article
CAS
PubMed
Google Scholar
Dallol A, Da Silva NF, Viacava P, Minna JD, Bieche I, Maher ER, et al. SLIT2, a human homologue of the Drosophila Slit2 gene, has tumor suppressor activity and is frequently inactivated in lung and breast cancers. Cancer Res. 2002;62:5874–80 http://www.ncbi.nlm.nih.gov/pubmed/12384551.
CAS
PubMed
Google Scholar
Yang J, Siqueira MF, Behl Y, Alikhani M, Graves DT. The transcription factor ST18 regulates proapoptotic and proinflammatory gene expression in fibroblasts. FASEB J. 2008;22:3956–67.
CAS
PubMed
PubMed Central
Google Scholar
Han YJ, Chen Y, Liu Y, Liu XL. Sequence variants of the LCORL gene and its association with growth and carcass traits in Qinchuan cattle in China. J Genet. 2017;96:9–17. https://doi.org/10.1007/s12041-016-0732-0.
Article
CAS
PubMed
Google Scholar
Al-Mamun HA, Kwan P, Clark SA, Ferdosi MH, Tellam R, Gondro C. Genome-wide association study of body weight in Australian merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genet Sel Evol. 2015;47.
Michot P, Chahory S, Marete A, Grohs C, Dagios D, Donzel E, et al. A reverse genetic approach identifies an ancestral frameshift mutation in RP1 causing recessive progressive retinal degeneration in European cattle breeds. Genet Sel Evol. 2016;48.
Do DN, Bissonnette N, Lacasse P, Miglior F, Sargolzaei M, Zhao X, et al. Genome-wide association analysis and pathways enrichment for lactation persistency in Canadian Holstein cattle. J Dairy Sci. 2017;100:1955–70.
CAS
PubMed
Google Scholar
Abo-Ismail MK, Vander Voort G, Squires JJ, Swanson KC, Mandell IB, Liao X, et al. Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle. BMC Genet. 2014;15:14. https://doi.org/10.1186/1471-2156-15-14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patel K, Scrimieri F, Ghosh S, Zhong J, Kim M-S, Ren YR, et al. FAM190A deficiency creates a cell division defect. Am J Pathol. 2013;183:296–303. https://doi.org/10.1016/j.ajpath.2013.03.020.
Article
CAS
PubMed
PubMed Central
Google Scholar
Siddiqui IJ, Pervaiz N, Abbasi AA. The Parkinson disease gene SNCA: evolutionary and structural insights with pathological implication. Sci Rep. 2016;6.
Doxakis E. Post-transcriptional regulation of α-synuclein expression by mir-7 and mir-153. J Biol Chem. 2010;285:12726–34.
CAS
PubMed
PubMed Central
Google Scholar
Brito LF, Kijas JW, Ventura RV, Sargolzaei M, Porto-Neto LR, Cánovas A, et al. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics. 2017;18:1–20.
Kuemmerle JM, Theiss F, Okoniewski MJ, Weber FA, Hemmi S, Mirsaidi A, et al. Identification of novel equine (Equus caballus) tendon markers using RNA sequencing. Genes (Basel). 2016;7:1–14.
PubMed Central
Google Scholar
Round J, Stein E. Netrin signaling leading to directed growth cone steering. Curr Opin Neurobiol. 2007;17:15–21. https://doi.org/10.1016/j.conb.2007.01.003.
Article
CAS
PubMed
Google Scholar
Sugimoto M, Gotoh Y, Kawahara T, Sugimoto Y. Molecular effects of polymorphism in the 3’UTR of unc-5 homolog C associated with conception rate in Holsteins. PLoS One. 2015;10.
PubMed
PubMed Central
Google Scholar
Lapinski PE, Oliver JA, Bodie JN, Marti F, King PD. The T-cell-specific adapter protein family: TSAd, ALX, and SH2D4A/SH2D4B. Immunol Rev. 2009;232:240–54.
CAS
PubMed
Google Scholar
Qrafli M, Asekkaj I, Bourkadi JE, El Aouad R, Sadki K. New variant identified in major susceptibility locus to tuberculosis on chromosomal region 8q12-q13 in Moroccan population: A case control study. BMC Infect Dis. 2017;17.
Gérard A, Ségéral E, Naughtin M, Abdouni A, Charmeteau B, Cheynier R, et al. The Integrase cofactor LEDGF/p75 associates with Iws1 and Spt6 for Postintegration silencing of HIV-1 gene expression in latently infected cells. Cell Host Microbe. 2015;17:107–17.
PubMed
Google Scholar
Khatib H, Zaitoun I, Wiebelhaus-Finger J, Chang YM, Rosa GJM. The association of bovine PPARGC1A and OPN genes with milk composition in two independent Holstein cattle populations. J Dairy Sci. 2007;90:2966–70.
CAS
PubMed
Google Scholar
Weikard R, Kuhn C, Goldammer T, Freyer G, Schwerin M. The bovine PPARGC1A gene: molecular characterization and association of an SNP with variation of milk fat synthesis. Physiol Genomics. 2005:1–13.
CAS
PubMed
Google Scholar
Holt LJ, Siddle K. Grb10 and Grb14: enigmatic regulators of insulin action - and more? Biochem J. 2005;388:393–406.
CAS
PubMed
PubMed Central
Google Scholar
Hazra A, Kraft P, Lazarus R, Chen C, Chanock SJ, Jacques P, et al. Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway. Hum Mol Genet. 2009;18:4677–87.
CAS
PubMed
PubMed Central
Google Scholar
Iyengar L, Rajalakshmi K. Effect of folic acid supplement on birth weights of infants. Am J Obstet Gynecol. 1975;122:332–6.
CAS
PubMed
Google Scholar
Pulukuri SMK, Knost JA, Estes N, Rao JS. Small interfering RNA-directed knockdown of uracil DNA glycosylase induces apoptosis and sensitizes human prostate cancer cells to genotoxic stress. Mol Cancer Res. 2009;7:1285–93.
CAS
PubMed
PubMed Central
Google Scholar
Liu Y-J, Liu X-G, Wang L, Dina C, Yan H, Liu J-F, et al. Genome-wide association scans identified CTNNBL1 as a novel gene for obesity. Hum Mol Genet. 2008;17:1803–13. https://doi.org/10.1093/hmg/ddn072.
Article
CAS
PubMed
PubMed Central
Google Scholar
Labeit S, Fautel M, Lakey A, Trinick J. Towards a molecular understanding of titin. EMBO J. 1992;11:1711–6.
CAS
PubMed
PubMed Central
Google Scholar
Linke WA, Stockmeier MR, Ivemeyer M, Hosser H, Mundel P. Characterizing titin’s I-band Ig domain region as an entropic spring. J Cell Sci. 1998:1567–74.
Neagoe C, Kulke M, Del Monte F, Gwathmey JK, De Tombe PP, Hajjar RJ, et al. Titin isoform switch in ischemic human heart disease. Circulation. 2002;106:1333–41.
PubMed
Google Scholar
Liu L, Gudas LJ. Disruption of the lecithin:retinol acyltransferase gene makes mice more susceptible to vitamin A deficiency. J Biol Chem. 2005;280:40226–34.
CAS
PubMed
Google Scholar
Wang B, Nie W, Fu X, de Avila JM, Ma Y, Zhu MJ, et al. Neonatal vitamin A injection promotes cattle muscle growth and increases oxidative muscle fibers. J Anim Sci Biotechnol. 2018;9.
Harris CL, Wang B, Deavila JM, Busboom JR, Maquivar M, Parish SM, et al. Vitamin A administration at birth promotes calf growth and intramuscular fat development in Angus beef cattle. J Anim Sci Biotechnol. 2018;9.
West KP, LeClerq SC, Shrestha SR, Wu LS-F, Pradhan EK, Khatry SK, et al. Effects of vitamin A on growth of vitamin A-deficient children: field studies in Nepal. J Nutr. 1997;127:1957–65.
CAS
PubMed
Google Scholar
Lominadze D, Tsakadze N, Sen U, Falcone JC, D’Souza SE. Fibrinogen and fragment D-induced vascular constriction. Am J Physiol - Hear Circ Physiol. 2005;288(3):57–3.
Google Scholar
Paterson J, Forcherio C, Larson B, Samford M, Kerley M. The effects of fescue toxicosis on beef cattle productivity. J Anim Sci. 1995;73:889–98.
CAS
PubMed
Google Scholar
Wong M-L, Arcos-Burgos M, Liu S, Vélez JI, Yu C, Baune BT, et al. The PHF21B gene is associated with major depression and modulates the stress response. Mol Psychiatry. 2017;22:1015–25. https://doi.org/10.1038/mp.2016.174.
Article
CAS
PubMed
Google Scholar
Bertonha FB, Barros Filho Mde C, Kuasne H, dos Reis PP, da Costa Prando E, JJAM M, et al. PHF21B as a candidate tumor suppressor gene in head and neck squamous cell carcinomas. Mol Oncol. 2015;9:450–62. https://doi.org/10.1016/j.molonc.2014.09.009.
Article
CAS
PubMed
Google Scholar
Endelman JB. Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome. 2011;4:250–5.
Google Scholar
R Core Team. R: The R Project for Statistical Computing. R Foundation for Statistical 844 Computing. 2017. https://www.r-project.org/.
PRISM. Climate Group. PRISM. 2011; http://prism.oregonstate.edu/. .
Leutner B, Horning N. Tools for Remote Sensing Data Analysis [R package RStoolbox version 0.1.10]. 2017. https://cran.r-project.org/web/packages/RStoolbox/index.html. Accessed 27 Aug 2019.
R Core Team. R: The R Project for Statistical Computing. 2013. https://www.r-project.org/. Accessed 27 Aug 2019.
Hennig C. CRAN - package fpc. 2013. https://cran.r-project.org/web/packages/fpc/index.html.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75. https://doi.org/10.1086/519795.
Article
CAS
PubMed
PubMed Central
Google Scholar
Loh P-R, Danecek P, Palamara PF, Fuchsberger C, Reshef YA, Finucane HK, et al. Reference-based phasing using the Haplotype Reference Consortium panel. Nat Genet. 2016;48:1443–8. https://doi.org/10.1038/ng.3679.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27:2987–93. https://doi.org/10.1093/bioinformatics/btr509.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 2007;39:906–13. https://doi.org/10.1038/ng2088.
Article
CAS
PubMed
Google Scholar
Zhou X, Stephens M. Efficient multivariate linear mixed model algorithms for genome-wide association studies. Nat Methods. 2014;11:407–9. https://doi.org/10.1038/nmeth.2848.
Article
CAS
PubMed
PubMed Central
Google Scholar
Neibergs HL, Seabury CM, Wojtowicz AJ, Wang Z, Scraggs E, Kiser JN, et al. Susceptibility loci revealed for bovine respiratory disease complex in pre-weaned Holstein calves. BMC Genomics. 2014;15:1164. https://doi.org/10.1186/1471-2164-15-1164.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davis BW, Seabury CM, Brashear WA, Li G, Roelke-Parker M, Murphy WJ. Mechanisms underlying mammalian hybrid sterility in two feline interspecies models. Mol Biol Evol. 2015;32:2534–46. https://doi.org/10.1093/molbev/msv124.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hyun MK, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, et al. Efficient control of population structure in model organism association mapping. Genetics. 2008;178:1709–23.
Google Scholar
Vihjal B. "mixmogam" 2012. https://github.com/bvilhjal/mixmogam/tree/a40f3e2c95aa17d22243ae2865aee6176ae821a6.
Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. GenABEL: an R library for genome-wide association analysis. Bioinformatics. 2007;23:1294–6. https://doi.org/10.1093/bioinformatics/btm108.
Article
CAS
PubMed
Google Scholar