1. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
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Phil J. Bowman, Johanna Vilkki, Mehdi Sargolzaei, Robert D. Schnabel, Didier Boichard, Frank Panitz, Chris Hozé, Kay Uwe Götz, D. C. Purfield, Christian Bendixen, Lars-Erik Holm, Carla Hurtado Ponce, Ben J. Hayes, Alessandro Bagnato, J. J. Crowley, Cord Drögemüller, Jeremy F. Taylor, Aniek C. Bouwman, Aurélien Capitan, Jesse L. Hoff, Marie Pierre Sanchez, Thierry Tribout, Hubert Pausch, Dorian J. Garrick, Michael E. Goddard, Mekki Boussaha, Min Wang, Anna A. E. Vinkhuyzen, Ruedi Fries, Hans D. Daetwyler, Roel F. Veerkamp, Curtis P. Van Tassell, Ingolf Russ, Amanda J. Chamberlain, Reiner Emmerling, R.F. Brøndum, Mirjam Frischknecht, Vidhya Jagannathan, Marlies Dolezal, Paul Stothard, Bo Thomsen, Bertrand Servin, Simon Boitard, Donagh P. Berry, James M. Reecy, Dominique Rocha, Anna Bieber, Birgit Gredler, Johann Sölkner, Mogens Sandø Lund, Christy J. Vander Jagt, Pascal Croiseau, Goutam Sahana, Anne Barbat, Armelle Govignon-Gion, Flavio S Schenkel, Bernt Guldbrandtsen, Department of Agriculture, Food and the Marine, Ireland, Science Foundation Ireland, German Federal Ministry of Education and Research, Deutsche Forschungsgemeinschaft, Breed4Food, European Commission, Dairy Futures Cooperative Research Centre, Genome Canada project, 11/S/112, 14/IA/2576, 0315527B, PA 2789/1-1, BO-22.04-011-001-ASG-LR, Wageningen University and Research Centre (WUR), Dept Econ Dev Jobs Transport & Resources, La Trobe University, University of Melbourne, University of Guelph, Semex Alliance, Partenaires INRAE, Aarhus University [Aarhus], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Veterinary Medicine [Vienna] (Vetmeduni), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), ETH, Dept Anim Sci, University Fed Rural Semi Arido, Natural Resources Institute Finland (LUKE), Dept Vet Med, University of California [Davis] (UC Davis), University of California-University of California, Div Anim Sci, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Inst Mol Biosci, Karl-Franzens-Universität [Graz, Autriche], University of Queensland [Brisbane], Qualitas AG, Allice, Inst Genet, University of Bern, Canadian Beef Breeds Council, Research Institute of Organic Agriculture - Forschungsinstitut für biologischen Landbau (FiBL), Teagasc Agriculture and Food Development Authority (Teagasc), Bavarian State Res Ctr Agr, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), USDA-ARS : Agricultural Research Service, University of Alberta, and AgriBio
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0301 basic medicine ,[SDV]Life Sciences [q-bio] ,Genome-wide association study ,Conserved Sequence ,condition score ,Mammals ,2. Zero hunger ,Genetics ,04 agricultural and veterinary sciences ,Body size ,plag1 ,Phenotype ,Animal Breeding & Genomics ,Cattle stature ,Quantitative Trait Loci ,selection ,Genomics ,Quantitative trait locus ,Biology ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,milk-yield ,Genetic variation ,Animals ,Humans ,Life Science ,Dairy cattle ,[INFO]Computer Science [cs] ,Human height ,Fokkerij & Genomica ,Genetic Association Studies ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,missense mutation ,0402 animal and dairy science ,Genetic Variation ,Beef cattle ,weight ,040201 dairy & animal science ,Body Height ,Genetic architecture ,Breeding and genetics ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,030104 developmental biology ,human height ,Expression quantitative trait loci ,genome-wide association studies ,angus ,Cattle ,Human genome ,hereford ,Genome-Wide Association Study - Abstract
peer-reviewed H.D.D., A.J.C., P.J.B. and B.J.H. would like to acknowledge the Dairy Futures Cooperative Research Centre for funding. H.P. and R.F. acknowledge funding from the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr ‘Synbreed—Synergistic Plant and Animal Breeding’ (grant 0315527B). H.P., R.F., R.E. and K.-U.G. acknowledge the Arbeitsgemeinschaft Süddeutscher Rinderzüchter, the Arbeitsgemeinschaft Österreichischer Fleckviehzüchter and ZuchtData EDV Dienstleistungen for providing genotype data. A. Bagnato acknowledges the European Union (EU) Collaborative Project LowInputBreeds (grant agreement 222623) for providing Brown Swiss genotypes. Braunvieh Schweiz is acknowledged for providing Brown Swiss phenotypes. H.P. and R.F. acknowledge the German Holstein Association (DHV) and the Confederación de Asociaciones de Frisona Española (CONCAFE) for sharing genotype data. H.P. was financially supported by a postdoctoral fellowship from the Deutsche Forschungsgemeinschaft (DFG) (grant PA 2789/1-1). D.B. and D.C.P. acknowledge funding from the Research Stimulus Fund (11/S/112) and Science Foundation Ireland (14/IA/2576). M.S. and F.S.S. acknowledge the Canadian Dairy Network (CDN) for providing the Holstein genotypes. P.S. acknowledges funding from the Genome Canada project entitled ‘Whole Genome Selection through Genome Wide Imputation in Beef Cattle’ and acknowledges WestGrid and Compute/Calcul Canada for providing computing resources. J.F.T. was supported by the National Institute of Food and Agriculture, US Department of Agriculture, under awards 2013-68004-20364 and 2015-67015-23183. A. Bagnato, F.P., M.D. and J.W. acknowledge EU Collaborative Project Quantomics (grant 516 agreement 222664) for providing Brown Swiss and Finnish Ayrshire sequences and genotypes. A.C.B. and R.F.V. acknowledge funding from the public–private partnership ‘Breed4Food’ (code BO-22.04-011- 001-ASG-LR) and EU FP7 IRSES SEQSEL (grant 317697). A.C.B. and R.F.V. acknowledge CRV (Arnhem, the Netherlands) for providing data on Dutch and New Zealand Holstein and Jersey bulls. Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018