ArticleBMC genomics2017
Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-Wide Association Analyses of Equine Metabolic Syndrome Phenotypes in Welsh Ponies and Morgan Horses.Genes · 2019Pooled it
- Phased T2T horse and donkey assemblies from a mule reveal peculiar equid centromere evolution.Cell genomics · 2026Article
- Approaches to Thoroughbred Horse Identification in Diverse Sample Types Using Multiplexed SNP-PCR Sequencing Panels.Animal genetics · 2026Article
- A Comprehensive Analysis of the Agreement and Performance of Variant Annotation Programs in Equine Genomes.Genes · 2026Article
- An increased number of heterozygous calls in the AxiomTM Equine Genotyping Array.G3 (Bethesda, Md.) · 2026Article
- Development and validation of high-density SNP array for genomic studies in Indian yak populations.BMC genomic data · 2026Article
- Detection of homozygosity and heterozygosity regions in mediterranean sheep breeds revealed by high-density SNP array.Journal of animal science · 2026Article
- Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds.BMC genomics · 2025Article
- Fine-scale assessment of ROH patterns and genomic inbreeding in diverse horse breeds using two SNP array densities.BMC veterinary research · 2025Article
- IMAGE001: A new livestock multispecies SNP array to characterize genomic variation in European livestock gene bank collections.Animal genetics · 2025Article
- High-quality, haplotype-resolved reference genomes of the Dutch warmblood horse and Friesian horse using trio binning.BMC genomics · 2025Article
- Rewilded horses in European nature conservation - a genetics, ethics, and welfare perspective.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies.Functional & integrative genomics · 2024Article
- Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations.Scientific reports · 2024Article
- Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.BMC genomics · 2024Article
- Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed.Genetics, selection, evolution : GSE · 2024Article
- Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses.PloS one · 2024Article
- Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach.Genetics, selection, evolution : GSE · 2023Article
- Article
- Detecting SNP markers discriminating horse breeds by deep learning.Scientific reports · 2023Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
35 authors.
Funding
Abstract
backgroundTo 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.
resultsUsing 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.
conclusionsHere, 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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