The breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid-nineteenth century, it was decided to use European Warmblood stallions for cross-breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high-density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches-Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine-scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed-specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed-specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions.

中文翻译：

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艾因西德勒马的种群结构和基因组多样性

艾因西德马的饲养历史与本笃会修道院艾因西德伦密切相关。十九世纪中叶，决定使用欧洲温血种公马进行杂交，并放弃种公马的选育。从那时起，只能利用母系血统信息来追溯艾因西德勒马的起源。在这里，我们收集了欧洲温血马（法国塞勒马、瑞士温血马和艾因西德勒马）和最后一个瑞士本土马品种弗朗什-山地马的高密度基因型数据，以揭示艾因西德勒马当前的种群结构。使用常用的方法来确定精细的种群结构，不可能将艾因西德勒马与其他欧洲温血马清楚地区分开来。然而，通过纯合性 (ROH) 运行，我们能够检测到艾因西德勒马的品种特异性 ROH 岛，包括参与驯化和适应高海拔的基因。因此，未来的育种活动应包括筛选这些品种特定的ROH片段、冷冻精子的复活以及艾因西德勒种马的选择。