Steensma Marije J, Ducro Bart J, Dibbits Bert, Doekes Harmen P, van Schipstal Job G C, Kalblfleisch Ted, Groenen Martien A M, Derks Martijn F L
Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, Wageningen, 6700 AH, the Netherlands.
Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA.
BMC Genomics. 2025 Sep 1;26(1):790. doi: 10.1186/s12864-025-11985-0.
In 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.
We 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.
The 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.
The online version contains supplementary material available at 10.1186/s12864-025-11985-0.
在马中，遗传多样性主要在品种间观察到，品种内变异很少。荷兰两个最大的马种群，荷兰温血马和弗里斯兰马种群的种马登记簿有正在进行的保护项目，包括收集大规模的基因型和序列数据。目前来自纯种马的参考基因组可能会导致对其他马品种的遗传分析产生偏差。因此，本研究的目的是创建荷兰温血马和弗里斯兰马高质量的品种特异性参考基因组。
我们对一匹荷兰温血马和一匹弗里斯兰马的F1杂交后代进行了纳米孔长读长测序（R10.4，Q20+），通过三重分箱创建了两个品种特异性参考基因组。这产生了高质量的、单倍型解析的参考基因组，弗里斯兰马和温血马的重叠群N50分别为37和35 Mb，单拷贝基因完整性分别为99.2%和99.3%。大多数染色体包含端粒和/或着丝粒序列。Ensembl基因注释分别为弗里斯兰马和温血马产生了19,750和19,872个蛋白质编码基因。在弗里斯兰马和温血马基因组之间未观察到大规模染色体重排。然而，共鉴定出722个大的结构变异（>10 kb），其中14个影响蛋白质编码基因的编码序列。
新的品种特异性参考基因组为未来的遗传分析和品种保护工作提供了宝贵资源，并将有助于正在进行的马全基因组计划。
在线版本包含可在10.1186/s12864-025-11985-0获取的补充材料。
