The Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and colour, and severe population bottlenecks that are connected with its initial foundation and subsequent changes in agricultural and forestry practices. Here, we used sequences of the mitochondrial control region and genomic single nucleotide polymorphisms (SNPs) to estimate the genetic diversity and differentiation of the four Finnhorse breeding sections: trotters, pony-sized horses, draught horses and riding horses. Furthermore, we estimated inbreeding and effective population sizes over time to infer the history of this breed. We found a high level of mitochondrial genetic variation and identified 16 of the 18 haplogroups described in present-day horses. Interestingly, one of these detected haplogroups was previously reported only in the Przewalski’s horse. Female effective population sizes were in the thousands, but declines were evident at the times when the breed and its breeding sections were founded. By contrast, nuclear variation and effective population sizes were small (approximately 50). Nevertheless, inbreeding in Finnhorses was lower than in many other horse breeds. Based on nuclear SNP data, genetic differentiation among the four breeding sections was strongest between the draught horses and the three other sections (FST = 0.007–0.018), whereas based on mitochondrial DNA data, it was strongest between the trotters and the pony-sized and riding horses (ΦST = 0.054–0.068). The existence of a Przewalski’s horse haplogroup in the Finnhorse provides new insights into the domestication of the horse, and this finding supports previous suggestions of a close relationship between the Finnhorse and eastern primitive breeds. The high level of mitochondrial DNA variation in the Finnhorse supports its domestication from a large number of mares but also reflects that its founding depended on many local landraces. Although inbreeding in Finnhorses was lower than in many other horse breeds, the small nuclear effective population sizes of each of its breeding sections can be considered as a warning sign, which warrants changes in breeding practices.

中文翻译：

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芬兰本土马种的遗传变异性和历史

Finnhorse于110年前通过结合芬兰当地的地方品种而被确立为一个品种。自建立以来，该品种既经历了强烈的方向选择，特别是在大小和颜色方面，也经历了严重的种群瓶颈，这与其最初的建立以及随后的农业和林业实践的变化有关。在这里，我们使用线粒体控制区的序列和基因组单核苷酸多态性（SNP）来评估四个Finnhorse繁殖区的遗传多样性和分化：猪蹄，矮马，起草和骑乘马。此外，我们估算了随着时间推移的近亲繁殖和有效种群数量，以推断出该品种的历史。我们发现了高水平的线粒体遗传变异，并鉴定了当今马中描述的18个单倍体中的16个。有趣的是，这些检测到的单倍群之一以前仅在普氏原羚的马中报告过。女性有效种群数量为数千，但在建立该品种及其繁殖区的时期明显减少了。相比之下，核变异和有效种群规模较小（约50）。尽管如此，芬霍斯的近交比其他许多马种都少。根据核SNP数据，四个繁殖区之间的遗传分化在吃草的马和其他三个区之间最强（FST = 0.007–0.018），而基于线粒体DNA数据，在猪蹄和小马大小的骑马者之间最强（ΦST= 0.054–0.068）。Finnhorse中Przewalski的马单倍群的存在为马的驯化提供了新见解，这一发现支持了先前有关Finnhorse与东部原始品种之间存在密切关系的建议。Finnhorse中高水平的线粒体DNA变异支持其从大量母马中驯化，但也反映出其建立依赖于许多当地地方品种。尽管Finnhorses的近交比其他许多马种都少，但可以将其每个繁殖区的核有效种群数量视为一个警告信号，以保证改变繁殖作法。Finnhorse中Przewalski的马单倍群的存在为马的驯化提供了新见解，这一发现支持了先前有关Finnhorse与东部原始品种之间存在密切关系的建议。Finnhorse中高水平的线粒体DNA变异支持其从大量母马中驯化，但也反映出其建立依赖于许多当地地方品种。尽管Finnhorses的近交比其他许多马种都少，但可以将其每个繁殖区的核有效种群数量视为一个警告信号，以保证改变繁殖作法。Finnhorse中Przewalski的马单倍群的存在为马的驯化提供了新见解，这一发现支持了先前有关Finnhorse与东部原始品种之间存在密切关系的建议。Finnhorse中高水平的线粒体DNA变异支持其从大量母马中驯化，但也反映出其建立依赖于许多当地地方品种。尽管Finnhorses的近交比其他许多马种都少，但可以将其每个繁殖区的核有效种群数量视为一个警告信号，以确保改变繁殖作法。Finnhorse中高水平的线粒体DNA变异支持其从大量母马中驯化，但也反映出其建立依赖于许多当地地方品种。尽管Finnhorses的近交比其他许多马种都少，但可以将其每个繁殖区的核有效种群数量视为一个警告信号，以确保改变繁殖作法。Finnhorse中线粒体DNA的高水平变异支持其从大量母马中驯化，但也反映出其建立依赖于许多当地地方品种。尽管Finnhorses的近交比其他许多马种都少，但可以将其每个繁殖区的核有效种群数量视为一个警告信号，以保证改变繁殖作法。