Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #340281

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Meta-analysis of genome wide association studies for the stature of cattle reveals numerous common genes that regulate size in mammals

Author
item Bouwman, Aniek - Wageningen Ur
item Daetwyler, Hans - Collaborator
item Chamberlain, Amanda - Collaborator
item Ponce, Carla - University Of Melbourne
item Sargolzaei, Mehdi - University Of Guelph
item Schenke, Flavio - University Of Guelph
item Sahana, Goutam - Aarhus University
item Govignon-gion, Armelle - Agro Paris Tech
item Boitard, Simon - Agro Paris Tech
item Dolezal, Marlies - University Of Veterinary Medicine
item Pausch, Hubert - Technische Universitat Munchen
item Brondum, Rasmus - Aarhus University
item Bowman, Phil - Collaborator
item Thomsen, Bo - Aarhus University
item Guldbrandtsen, Bernt - Aarhus University
item Lund, Mogens - Aarhus University
item Servin, Bertrand - University Of Toulouse
item Garrick, Dorian - Iowa State University
item Reecy, James - Iowa State University
item Vilkki, Johanna - Natural Resources Institute Finland (LUKE)
item Bagnato, Alessandro - University Of Milan
item Wang, Min - La Trobe University
item Hoff, Jesse - University Of Missouri
item Schnabel, Robert - University Of Missouri
item Taylor, Jerry - University Of Missouri
item Vinkhuyzen, Anna - University Of Queensland
item Panitz, Frank - Aarhus University
item Bendixen, Christian - Aarhus University
item Holm, Lars-erik - Aarhus University
item Gredler, Birgit - Collaborator
item Hoze, Chris - Agro Paris Tech
item Boussaha, Mekki - Agro Paris Tech
item Sanchez, Marie-pierre - University Of Queensland
item Rocha, Dominique - Agro Paris Tech
item Capitan, Aurelien - Agro Paris Tech
item Tribout, Thierry - Agro Paris Tech
item Barbat, Anne - Agro Paris Tech
item Croiseau, Pascal - Agro Paris Tech
item Drogemuller, Cord - University Of Bern
item Jagannathan, Vidhya - University Of Bern
item Jagt, Christy - Collaborator
item Crowley, John - Collaborator
item Intergenomics, Consortium - Collaborator
item Bieber, Anna - Collaborator
item Purfield, Deirdre - Collaborator
item Berry, Donagh - Collaborator
item Emmerling, Reiner - Collaborator
item Gotz, Kay-uwe - Collaborator
item Frischknecht, Mirjam - Collaborator
item Russ, Ingolf - Collaborator
item Solkner, Johann - University Of Natural Resources & Applied Life Sciences - Austria
item Van Tassell, Curtis - Curt
item Fries, Ruedi - Technische Universitat Munchen
item Stothard, Paul - University Of Alberta
item Veerkamp, Roel - Wageningen Ur
item Boichard, Didier - Agro Paris Tech
item Goddard, Mik - University Of Melbourne
item Hayes, Ben - University Of Queensland

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/3/2018
Publication Date: 2/19/2018
Citation: Bouwman, A.C., Daetwyler, H.D., Chamberlain, A.J., Ponce, C.H., Sargolzaei, M., Schenke, F.S., Sahana, G., Govignon-Gion, A., Boitard, S., Dolezal, M., Pausch, H., Brondum, R., Bowman, P.J., Thomsen, B., Guldbrandtsen, B., Lund, M.S., Servin, B., Garrick, D.J., Reecy, J., Vilkki, J., Bagnato, A., Wang, M., Hoff, J.L., Schnabel, R.D., Taylor, J.F., Vinkhuyzen, A.A., Panitz, F., Bendixen, C., Holm, L., Gredler, B., Hoze, C., Boussaha, M., Sanchez, M., Rocha, D., Capitan, A., Tribout, T., Barbat, A., Croiseau, P., Drogemuller, C., Jagannathan, V., Jagt, C.V., Crowley, J.J., Intergenomics, C., Bieber, A., Purfield, D.C., Berry, D.P., Emmerling, R., Gotz, K., Frischknecht, M., Russ, I., Solkner, J., Van Tassell, C.P., Fries, R., Stothard, P., Veerkamp, R.F., Boichard, D., Goddard, M., Hayes, B.J. 2018. Meta-analysis of genome wide association studies for the stature of cattle reveals numerous common genes that regulate size in mammals. Nature Genetics. 50(3):362-367. https://doi.org/10.1038/s41588-018-0056-5.
DOI: https://doi.org/10.1038/s41588-018-0056-5

Interpretive Summary: A person’s height has been shown to be affected by a large number of genetic difference or polymorphisms, each having a small effect in height. In contrast, genetic variation for the analogous trait, stature, in dogs, even within breeds, is mostly influenced by differences in six genes. In this study, we used data from cattle to compare the genetic mechanisms of stature to that in humans and dogs. We conducted an across-experiment analysis, or meta-analysis, for stature using 58,265 cattle from 17 populations with 25.4 million inferred whole genome sequence variants. Results revealed that; genetic mechanism of stature in cattle is more similar to that in humans than dogs, as 163 statistically significant genomic regions (P<.0000005) explained at most 13.8% of the phenotypic variation. But, difference in stature between miniature cattle and standard cattle of the same breed can be predicted by the lead variants. Many of the differences likely arose prior to domestication as 23% were variable in an pre-domesticated cow, the Auroch, genome. Most of the regions associated with the biggest differences did not code for changes in protein sequence, including changes that were associated with gene expression differences. There were many genes that affected the stature in humans and other mammals. Differences in gene frequencies were strongly influenced by selection.

Technical Abstract: Stature is affected by many polymorphisms of small effect in humans but in contrast variation in dogs, even within breeds is largely due to variants in six genes. Here we use data from cattle to compare genetic architecture of stature to that 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 revealed that; genetic architecture of stature in cattle is more similar to that in humans than dogs, as lead variants in 163 significant genomic regions (p<5×10e^-8) explained at most 13.8% of the phenotypic variance; difference in stature between miniature cattle and standard cattle of the same breed can be predicted by the lead variants; many of the variants likely arose prior to domestication as 23% were heterozygous in an Auroch genome; most lead variants were non-coding, including variants that were also eQTL and in ChIP-seq peaks; significant overlap existed in loci for stature with humans and other mammals; and allele frequencies of these variants are strongly influenced by selection.