BMC Genomics (Jul 2017)
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
- Robert J. Schaefer,
- Mikkel Schubert,
- Ernest Bailey,
- Danika L. Bannasch,
- Eric Barrey,
- Gila Kahila Bar-Gal,
- Gottfried Brem,
- Samantha A. Brooks,
- Ottmar Distl,
- Ruedi Fries,
- Carrie J. Finno,
- Vinzenz Gerber,
- Bianca Haase,
- Vidhya Jagannathan,
- Ted Kalbfleisch,
- Tosso Leeb,
- Gabriella Lindgren,
- Maria Susana Lopes,
- Núria Mach,
- Artur da Câmara Machado,
- James N. MacLeod,
- Annette McCoy,
- Julia Metzger,
- Cecilia Penedo,
- Sagi Polani,
- Stefan Rieder,
- Imke Tammen,
- Jens Tetens,
- Georg Thaller,
- Andrea Verini-Supplizi,
- Claire M. Wade,
- Barbara Wallner,
- Ludovic Orlando,
- James R. Mickelson,
- Molly E. McCue
Affiliations
- Robert J. Schaefer
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota
- Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
- Ernest Bailey
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky
- Danika L. Bannasch
- School of Veterinary Medicine, University of California-Davis
- Eric Barrey
- Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA, Université Paris-Saclay
- Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University
- Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna
- Samantha A. Brooks
- Department of Animal Science, University of Florida
- Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine
- Ruedi Fries
- Lehrstuhl für Tierzucht der Technischen Universität München
- Carrie J. Finno
- School of Veterinary Medicine, University of California-Davis
- Vinzenz Gerber
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, and Agroscope
- Bianca Haase
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney
- Vidhya Jagannathan
- Institute of Genetics, University of Bern
- Ted Kalbfleisch
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Louisville
- Tosso Leeb
- Institute of Genetics, University of Bern
- Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
- Maria Susana Lopes
- Biotechnology Centre of Azores, University of Azores
- Núria Mach
- Unité de Génétique Animale et Biologie Intégrative- UMR1313, INRA, Université Paris-Saclay
- Artur da Câmara Machado
- Biotechnology Centre of Azores, University of Azores
- James N. MacLeod
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky
- Annette McCoy
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine
- Cecilia Penedo
- Veterinary Genetics Laboratory, University of California Davis
- Sagi Polani
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University
- Stefan Rieder
- Agroscope, Swiss National Stud Farm
- Imke Tammen
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney
- Jens Tetens
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel
- Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel
- Andrea Verini-Supplizi
- Department of Veterinary Medicine - Sport Horse Research Centre, University of Perugia
- Claire M. Wade
- School of Life and Environmental Sciences, Faculty of Veterinary Science, University of Sydney
- Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
- James R. Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota
- Molly E. McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota
- DOI
- https://doi.org/10.1186/s12864-017-3943-8
- Journal volume & issue
-
Vol. 18,
no. 1
pp. 1 – 18
Abstract
Abstract Background To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. Results Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation. Conclusions Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.
Keywords
