Preprint open access publication

Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds

bioRxiv, Cold Spring Harbor Laboratory,


DOI:10.1101/112979, Dimensions: pub.1085104046,



  1. (1) University of Minnesota, grid.17635.36
  2. (2) University of Copenhagen, grid.5254.6, KU
  3. (3) University of Kentucky, grid.266539.d
  4. (4) University of California, Davis, grid.27860.3b
  5. (5) Centre de Recherches de Jouy-en-Josas, grid.417961.c
  6. (6) Hebrew University of Jerusalem, grid.9619.7
  7. (7) University of Veterinary Medicine Vienna, grid.6583.8
  8. (8) University of Florida, grid.15276.37
  9. (9) University of Veterinary Medicine Hannover, Foundation, grid.412970.9
  10. (10) Technical University of Munich, grid.6936.a
  11. (11) University of Bern, grid.5734.5
  12. (12) University of Sydney, grid.1013.3
  13. (13) University of Louisville, grid.266623.5
  14. (14) Swedish University of Agricultural Sciences, grid.6341.0
  15. (15) University of the Azores, grid.7338.f
  16. (16) University of Illinois at Urbana Champaign, grid.35403.31
  17. (17) Agroscope, grid.417771.3
  18. (18) University of Göttingen, grid.7450.6
  19. (19) Kiel University, grid.9764.c
  20. (20) University of Perugia, grid.9027.c
  21. (21) Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France, 31000


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.

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