Omneity® Pellets
All-In-One Vitamin & Mineral Pellet
IMAGE001: A new livestock multispecies SNP array to characterize genomic variation in European livestock gene bank collections.
Abstract: 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.
© 2025 The Author(s). Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.
Publication Date: 2025-09-18 PubMed ID: 40965185PubMed Central: PMC12445162DOI: 10.1111/age.70039Google Scholar: Lookup The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
Summary
This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.
Overview
- This research article presents the development and validation of a cost-effective, low-density SNP array designed for multiple livestock species to facilitate genomic characterization and biodiversity studies in European gene bank collections.
Background and Need
- Genetic characterization of livestock biodiversity is crucial for conserving and managing genetic resources effectively.
- Whole genome sequencing, though comprehensive, remains expensive for large-scale applications across multiple species.
- Low-density SNP arrays offer a more affordable and standardized alternative but are typically species-specific and often have more SNPs than necessary, increasing costs unnecessarily.
- Managing livestock genetic diversity, especially in gene banks and traditional on-farm populations, requires cost-effective tools that can handle multiple species simultaneously.
The IMAGE Project Goals
- The European Union-funded IMAGE H2020 project aimed to develop a low-cost SNP array that works across multiple livestock species.
- Focus was on six key livestock species: cattle, sheep, goats, horses, pigs, and chickens.
- The array is designed to include approximately 10,000 SNP markers per species, balancing sufficient genomic coverage and cost efficiency.
Development and Testing
- The array was developed by selecting SNPs that are informative for each species, capturing relevant genetic variation.
- It was extensively tested on numerous samples across the six species to ensure accuracy and reliability.
- The study included analysis across 253 breeds, representing a broad spectrum of genetic backgrounds.
Performance and Applications
- The array demonstrated strong capability to cluster local breeds according to their historical and genetic relationships, validating its effectiveness in population structure analysis.
- It can be used for parentage testing, an important tool in breeding management and conservation.
- The genomic coverage and informativity of the SNP set are sufficient for mapping genetic diversity, helping researchers and managers make informed decisions.
Availability and Cost
- The IMAGE multispecies SNP array is publicly available, offering an economical genotyping solution for livestock genetic resource management.
- When ordering in batches of 384 samples, the cost per sample is approximately 15 euros, making it accessible for large-scale studies.
- This cost efficiency encourages its adoption by gene banks and breeding organizations to enhance the characterization and conservation of European livestock diversity.
Cite This Article
APA
Crooijmans RPMA, Gonzalez Prendes R, Colli L, Del Corvo M, Barbato M, Somenzi E, Tosser-Klopp G, Meszaros G, Ajmone-Marsan P, Weigend S, Wallner B, McCue ME, Orlando L, Bradley D, Hiemstra SJ, Schokker D, Peynot N, Stella A, Restoux G, Groenen MAM, Tixier-Boichard M.
(2025).
IMAGE001: A new livestock multispecies SNP array to characterize genomic variation in European livestock gene bank collections.
Anim Genet, 56(5), e70039.
https://doi.org/10.1111/age.70039 Publication
Researcher Affiliations
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
- Facoltà di Scienze Agrarie, Alimentari e Ambientali/DIANA Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy.
- Facoltà di Scienze Agrarie, Alimentari e Ambientali/DIANA Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
- Facoltà di Scienze Agrarie, Alimentari e Ambientali/DIANA Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
- Dipartimento di Scienze Veterinarie, Università Degli Studi di Messina, Messina, Italy.
- Facoltà di Scienze Agrarie, Alimentari e Ambientali/DIANA Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France.
- Universität für Bodenkultur, Wien, Austria.
- Facoltà di Scienze Agrarie, Alimentari e Ambientali/DIANA Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
- Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics, Neustadt-Mariensee, Germany.
- Department of Biomedical Sciences and Pathobiology, Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria.
- University of Minnesota College of Veterinary Medicine, St Paul, Minnesota, USA.
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Toulouse, France.
- Trinity College Dublin, University of Dublin, Dublin, Ireland.
- Centre for Genetic Resources, the Netherlands (CGN) of Wageningen University & Research, Wageningen, The Netherlands.
- Wageningen Bioveterinary Research, Lelystad, The Netherlands.
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
- Institute of Agricultural Biology and Biotechnology, National Research Council (IBBA-CNR), Milan, Italy.
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
MeSH Terms
- Animals
- Polymorphism, Single Nucleotide
- Livestock / genetics
- Europe
- Goats / genetics
- Genetic Variation
- Breeding
- Genomics
- Horses / genetics
- Chickens / genetics
- Cattle / genetics
- Sheep / genetics
Grant Funding
- 677353 / Horizon 2020 Framework Programme
- 101071707 / European Research Council
- 681605 / European Research Council
Conflict of Interest Statement
None of the authors of this paper has a financial or personal relationship with other people or organizations that could inappropriately influence or bias the content of this paper.
References
This article includes 32 references
- Ajmone‐Marsan P, Colli L, Ginja C, Kantanen J, Lenstra JA. Genomic characterization of animal genetic resources. FAO Animal Production and Health Guidelines No. 32.
- Ali AO, Stear A, Fairlie‐Clarke K, Brujeni GN, Isa NM, Salisi MS. The genetic architecture of the MHC class II region in British Texel sheep. Immunogenetics 69, 157–163.
- . BovineHD DNA Analysis Kit. 2022.
- . BovineSNP50 DNA Analysis Kit. 2022.
- Colli L, Milanesi M, Talenti A, Bertolini F, Chen M, Crisa A. Genome‐wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post‐domestication migration routes. Genetics, Selection, Evolution 50, 58.
- Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O. The horse Y chromosome as an informative marker for tracing sire lines. Scientific Reports 9, 1–12.
- Groenen MAM, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393–398.
- Harrison RG. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends in Ecology & Evolution 4(1), 6–11.
- Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C. Mitochondrial DNA and the origins of the domestic horse. Proceedings of the National Academy of Sciences of the United States of America 99, 10905–10910.
- Kijas JW, Lenstra JA, Hayes B, Boitard S, Neto LR, Cristobal MS. Genome‐wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology 10, 1001258.
- Kranis A, Gheyas AA, Boschiero C, Turner F, Yu L, Smith S. Development of a high density 600K SNP genotyping array for chicken. BMC Genomics 14, 1–13.
- Leroy G, Boettcher P, Besbes B, Danchin‐Burge C, Baumung R, Hiemstra SJ. Cryoconservation of animal genetic resources in Europe and two African countries: a gap analysis. Diversity 11(12), 240.
- Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4(4), e5350.
- McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM. A high density SNP Array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genetics 8, e1002451.
- Melo ATO, Hale I. Apparent’: a simple and flexible R package for accurate SNP‐based parentage analysis in the absence of guiding information. BMC Bioinformatics 20, 1–10.
- Paradis E, Schliep K. Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35(3), 526–528.
- Pariset L, Cappuccio I, Joost S, D'Andrea M, Marletta D, Ajmone Marsan P. Characterization of single nucleotide polymorphisms in sheep and their variation as evidence of selection. Animal Genetics 37, 290–292.
- Pariset L, Mariotti M, Gargani M, Joost S, Negrini R, Perez T. Genetic diversity of sheep breeds from Albania, Greece, and Italy assessed by mitochondrial DNA and nuclear polymorphisms (SNPs). ScientificWorldJournal 11, 1641–1659.
- Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E. Genetic diversity in the modern horse illustrated from genome‐wide SNP data. PLoS One 8, e54997.
- Poklukar K, Mestre C, Škrlep M, Čandek‐Potokar M, Ovilo C, Fontanesi L. A meta‐analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits. Genetics, Selection, Evolution 55, 88.
- Purcell S, Neale B, Todd‐Brown K, Thomas L, Ferreira M.A.R, Bender D. PLINK: a tool set for whole‐genome association and population‐based linkage analyses. American Journal of Human Genetics 81, 559–575.
- Ramos AM, Crooijmans RPMA, Affara NA, Amaral AJ, Archibald AL, Beever JE. Design of a High Density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4, e6524.
- Roorkiwal M, Jain A, Kale SM, Doddamani D, Chitikineni A, Thudi M. Development and evaluation of high‐density axiom® CicerSNP Array for high‐resolution genetic mapping and breeding applications in chickpea. Plant Biotechnology Journal 16(4), 890–901.
- Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar‐Gal GK. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 18, 1–18.
- Sharmaa A, Lee JS, Dang CG, Sudrajad P, Kim HC, Yeon SH. Stories and challenges of genome wide association studies in livestock – a review. Asian‐Australasian Journal of Animal Sciences 28, 1371–1379.
- Tosser‐Klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, Dong Y. Design and characterization of a 52K SNP chip for goats. PLoS One 9(1), e86227.
- Upadhyay MR, Chen W, Lenstra JA, Goderie CRJ, Machugh DE, Park SDE. Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle. Heredity 118, 169–176.
- Várquez‐Miranda H, Barker FK. Autosomal, sex‐linked and mitochondrial loci resolve evolutionary relationships among wrens in the genus Campylorhynchus. Molecular Phylogenetics and Evolution 163, 107242.
- Wolc A, Czwarno WD, Fulton J, Settar P, Arango J, Lubritz D. Detection of CNVs in layer chickens using 42K, 50K and 600K SNP chips. .
- Wong GKS, Liu B, Wang J, Zhang Y, Yang X, Zhang Z. A genetic variation map for chicken with 2.8 million single‐nucleotide polymorphisms. Nature 432, 717–722.
- Yang B, Cui L, Perez‐Enciso M, Traspov A, Crooijmans RPMA, Zinovieva N. Genome‐wide SNP data unveils the globalization of domesticated pigs. Genetics, Selection, Evolution 49, 71.
- Yu G. Using ggtree to visualize data on tree‐like structures. Current Protocols in Bioinformatics 69(1), e96.
Citations
This article has been cited 0 times.Use Nutrition Calculator
Check if your horse's diet meets their nutrition requirements with our easy-to-use tool Check your horse's diet with our easy-to-use tool
Talk to a Nutritionist
Discuss your horse's feeding plan with our experts over a free phone consultation Discuss your horse's diet over a phone consultation
Submit Diet Evaluation
Get a customized feeding plan for your horse formulated by our equine nutritionists Get a custom feeding plan formulated by our nutritionists
