Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.

中文翻译：

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利用基因组SNP数据对高山本地牛品种的遗传遗产进行研究。

对遗传多样性和种群结构的评估提供了重要的控制指标，可避免遗传侵蚀，近亲衰退和外来和本地适应的牛种之间的杂交，因为这些事件可能造成有害后果并最终导致灭绝。从历史上看，高山弧线代表着牛群生物多样性的重要组成部分，拥有大量的本地品种，为整个区域经济提供了基本的收入来源。通过使用来自中等密度单核苷酸多态性（SNP）阵列的基因型数据，我们对来自高寒弧地区和三个世界性品种的23个牛群进行了全基因组比较研究。过滤后，我们获得了由711个个体的30,176个SNP组成的最终基因分型数据集。与高度选择的世界性品种相比，本地品种显示出较高或中等的遗传多样性值。遗传分化，多维尺度化，混合分析和构建的系统树的模式显示出趋同性，这表明根据地理起源和历史背景，各品种之间存在基因流。在最具差异性的品种中，我们鉴定了现代棕牛。尽管发生混合事件，但一些地方品种仍保留了鲜明的特征，这可能是由于遗传起源和地理位置的差异。这项研究代表了迄今为止对高山牛品种最全面的全基因组分析之一。使用如此庞大的数据集，其中包括该地区发现的大多数本地品种，使我们能够扩展有关高山牛生物多样性评估和状况的知识。我们的结果表明，尽管许多分析过的本地品种都被列为濒危物种，但即使与某些国际性品种相比，它们仍具有大量的遗传多样性。这一发现，再加上系统发育的重建以及这些高山弧形牛品种之间的关系，不仅为改善遗传资源，而且为实施未来的保护战略提供了重要的见识。