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 MachadoJames 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

Research output: Contribution to journalArticlepeer-review

47 Scopus citations

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.

Original languageEnglish (US)
Article number565
JournalBMC Genomics
Volume18
Issue number1
DOIs
StatePublished - Jul 27 2017

Bibliographical note

Funding Information:
These genomic tools are the result of a collaborative effort that involved a number of laboratories within the equine genetics community, many of which provided support or insight at various steps for this community resource. We would like to acknowledge Chad Dow from Affymetrix for the support he and his team provided while designing the MNEc2M array. Funding Support for the generation of whole genome sequence came from the following sources: ? USDA NIFA project 2012-67,015-19,432 and Minnesota Agricultural Experiment Station Multistate project MIN-62-090. ? The National Animal Genome Project (NRSP8) through the equine genome coordinator: USDA-NRSP8 (2013-2018) horse-technical-committee coordinator funds. ? The Danish Council for Independent Research, Natural Sciences (Grant 4002-00152B); the Danish National Research Foundation (Grant DNRF94); Initiative d'Excellence Chaires d'attractivit?, Universit? de Toulouse (OURASI), and; the European Research Council (ERC-CoG-2015-681,605). ? The Bavarian Ministry State Ministry for Food and Agriculture, and Forestry (A/13/39). ? The Laboratory of Molecular Evolution, The Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Israel) for contributing pure-bred Arabian whole-genomes on behalf of The Israel Science Foundation (ISF) grant #1365/10. ? The Swedish Research Council Formas (221-2013-1661) and the Swedish Research Council VR (621-2012-4666). Funding sources played no role in the design of this study or the collection, analysis, and the interpretation of data and in writing the manuscript.

Publisher Copyright:
© 2017 The Author(s).

Copyright:
Copyright 2018 Elsevier B.V., All rights reserved.

Keywords

  • Equine genomics
  • Linkage disequilibrium
  • SNP chip
  • SNP discovery
  • SNP informativeness
  • SNP validation
  • SNP-tagging
  • Variant recalibration
  • Whole genome sequence

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