The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (FROH) by means of Runs of Homozygosity. To assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and FROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders. The FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.

中文翻译：

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利用高密度 SNP 数据解开弗朗什-山地马品种的起源


弗朗什-山地马 (FM) 是瑞士最后一个本土马种，于 19 世纪末通过当地母马与盎格鲁-诺曼种马杂交培育而成。我们从 522 匹 FM 马中收集了高密度 SNP 基因型数据（Axiom™ 670 K 马基因分型阵列），其中包括 44 匹旧型马 (OF)、来自瑞典和瑞士的 514 匹欧洲温血马 (WB)（包括用于杂交的种马） -1990 年繁育），136 匹纯种阿拉伯马 (AR)、32 匹 Shagya 阿拉伯马 (SA) 和 64 匹纯种马 (TB)，因为基因渗入的 WB 种马在其血统中显示出 TB 起源。该研究的目的是确定 FM 品种的精细种群结构，包括通过纯合性运行估计个体混合水平和基因组近交 (FROH)。为了评估 FM 品种内的精细种群结构，我们采用了三步方法，将个体的混合、遗传贡献和 FROH 结合到高分辨率网络可视化中。基于这种方法，我们能够证明，通过基于模型的聚类检测到的群体子结构可以与不同的遗传起源相关，也可以与最有影响力的父亲的后代相关。在FM品种中，混血马解释了当前育种群体的大部分遗传变异，而OF马只占变异的一小部分。此外，我们还发现 FM 马表现出较高的 TB 混合水平，并且我们发现 FM 马的起源不一致，是阿拉伯种马 Doktryner 的后代。除 WB 外，与其他品种相比，FM 马的近亲繁殖较少。然而，相对较少但较长的 ROH 片段表明两个 FM 亚群都存在多样性损失。 位于 FM 和 OF 特异性 ROH 岛的基因具有涉及构象和行为的已知功能，这两个特征受到育种者的高度重视。 FM仍然是最后一个瑞士本土品种，与其他历史上渗入的品种有明显区别，但由于对种马的密集选择、基于纯种繁殖的任意定义的限制性交配选择以及对稀有毛色的选择，它遇到了瓶颈。为了保护 FM 马的遗传多样性，未来的保护管理策略应涉及对种马的均衡选择（例如，通过将 OF 种马纳入 FM 育种群体中）并避免选择稀有的毛色。