<scp>IMAGE001</scp> : A new livestock multispecies <scp>SNP</scp> array to characterize genomic variation in European livestock gene bank collections
Molecular genetic characterization of genetic resources is essential to study biodiversity. Whereas whole genome sequencing is still relatively expensive, low density SNP arrays offer a cost-effective and standardized solution. However, most of the current arrays are species specific. Their high SNP density often exceeds diversity mapping requirements and remains too costly for many genetic resource managers. The IMAGE H2020 project aimed at developing a low-cost multispecies SNP array to facilitate mapping of the genetic diversity in samples stored in gene banks and in vivo (on farm) traditional populations. This farm animal multispecies array contains approximately 10 K SNPs per species. The species included are cattle, sheep, goat, horse, pig, and chicken. We developed and tested this array on many samples from each of the six species. We describe here the SNP coverage and informativity across 253 breeds. We show that the array can be used to cluster local breeds according to history and genetic diversity. We illustrate its use for parentage testing. The array is publicly available at a reasonable price if ordered in multiples of 384 samples, leading to an overall cost of genotyping of approximately 15 euros per sample.
Authors
- Michèle Tixier‐Boichard (ORCID: https://orcid.org/0000-0001-5944-7884)
- Nathalie Peynot
- Elisa Somenzi (ORCID: https://orcid.org/0000-0003-3238-0004)
- R.P.M.A. Crooijmans (ORCID: https://orcid.org/0000-0001-8108-9972)
- Gábor Mészáros (ORCID: https://orcid.org/0000-0002-5937-0060)
- Martien A. M. Groenen (ORCID: https://orcid.org/0000-0003-0484-4545)
- Marcello Del Corvo (ORCID: https://orcid.org/0000-0002-8039-4155)
- Ludovic Orlando (ORCID: https://orcid.org/0000-0003-3936-1850)
- Dirkjan Schokker (ORCID: https://orcid.org/0000-0001-6082-7227)
- Paolo Ajmone‐Marsan (ORCID: https://orcid.org/0000-0003-3165-4579)
- Mario Barbato (ORCID: https://orcid.org/0000-0002-7203-1549)
- Gwenola Tosser‐Klopp (ORCID: https://orcid.org/0000-0003-0550-4673)
- Licia Colli (ORCID: https://orcid.org/0000-0002-7221-2905)
- Molly E. McCue (ORCID: https://orcid.org/0000-0002-6807-0318)
- Steffen Weigend (ORCID: https://orcid.org/0000-0002-5670-2808)
- Gwendal Restoux (ORCID: https://orcid.org/0000-0001-7771-9476)
- Daniel G. Bradley (ORCID: https://orcid.org/0000-0001-7335-7092)
- S.J. Hiemstra
- R. Gonzalez Prendes
- Barbara C. Wallner
- Alessandra Stella
Institutions
- Università Cattolica del Sacro Cuore (IT)
- University of Messina (IT)
- Centre National de la Recherche Scientifique (FR)
- University of Minnesota (US)
- Friedrich-Loeffler-Institut (DE)
- Université Toulouse III - Paul Sabatier (FR)
- University of Veterinary Medicine Vienna (AT)
- École Nationale Vétérinaire de Toulouse (FR)
- Université Fédérale de Toulouse Midi-Pyrénées (FR)
- Trinity College Dublin (IE)
- AgroParisTech (FR)
- Université Paris-Saclay (FR)
- University of Minnesota System (US)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Institute of Agricultural Biology and Biotechnology (IT)
- Génétique Physiologie et Systèmes d'Elevage (FR)
- National Research Council (IT)
- Deleted Institution
- Wageningen University & Research (NL)
- BOKU University (AT)
Publication Details
- Journal
- Animal Genetics
- Published
- 2025-09-18
- DOI
- https://doi.org/10.1111/age.70039
- Citations
- 1
- Primary Topic
- Genetic and phenotypic traits in livestock
- Type
- article
- Field-Weighted Citation Impact
- 1.82
Funders
- Horizon 2020 Framework Programme