ArticleBMC genomics2025
High-quality, haplotype-resolved reference genomes of the Dutch warmblood horse and Friesian horse using trio binning.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- Comparative genomic analysis of oxytocin and oxytocin receptor genes in the family Equidae.Molecular biology reports · 2026Article
- Targeted allele frequency tuning in breeding populations via alternative optimum contribution selection.Genetics · 2026Article
- Integrative Advances in Equine Genomics From Reference Assemblies to Evolutionary History and Key Traits.Evolutionary applications · 2026Review
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Authors and funding
8 authors.
Funding
Abstract
backgroundIn horses, genetic diversity is predominantly observed between breeds, with little variation within breeds. The studbooks of the two largest horse populations in the Netherlands, the Dutch Warmblood horse and Friesian horse population, have ongoing conservation projects including collecting large-scale genotype and sequence data. The current reference genome, derived from a Thoroughbred horse can lead to bias in genetic analyses of other horse breeds. Therefore, the aim of this study was to create high-quality breed-specific reference genomes of Dutch Warmblood and Friesian horses.
resultsWe performed nanopore long-read sequencing (R10.4, Q20+) of an F1 cross between a Dutch Warmblood horse and a Friesian horse to create two breed-specific reference genomes by trio binning. This resulted in high-quality, haplotype-resolved reference genomes with contig N50 of 37 and 35 Mb and single copy gene completeness of 99.2 and 99.3% for the Friesian and Warmblood, respectively. The majority of the chromosomes contained telomeric and /or centromeric sequences. The Ensembl gene annotation resulted in 19,750 and 19,872 protein coding genes for the Friesian and Warmblood, respectively. No large chromosomal rearrangements were observed between the Friesian and Warmblood genomes. However, a total of 722 large structural variations (> 10 kb) were identified, of which 14 affect the coding sequence of protein-coding genes.
conclusionThe novel breed-specific reference genomes provide a valuable resource for future genetic analysis and breed conservation efforts and will contribute to ongoing equine pangenome efforts.
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