Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

中文翻译：

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瑞典本地牛品种的基因组相关性和多样性

鉴于本地牛品种适应其饲养的当地环境，因此它们是重要的遗传资源。然而，商业化牛品种的广泛使用已导致全球几种本地牛品种的种群规模显着减少。因此，原生牛品种的保护管理需要紧急注意，以免其灭绝。为此，我们对九个瑞典本地牛品种进行了基因分型，这些品种具有全基因组150 K单核苷酸多态性（SNP），以研究这些品种之间的遗传多样性水平和相关性。我们在此数据集上使用了各种基于SNP的方法，以将人口历史与这些瑞典牛品种的遗传多样性和种群结构联系起来。我们的结果表明，源自瑞典南部的Väne和Ringamåla品种经历了种群隔离并且遗传多样性低，而Fjäll品种拥有较大的创始种群和相对较高的遗传多样性。基于共同的血统和构建的系统发育树，我们确定了瑞典本地牛的两个主要集群。在第一个集群中，其中包括瑞典山区的牛品种，在Fjäll，Fjällnära，Swedish Polled和Bohus Polled品种之间几乎没有区别。第二类包括来自瑞典南部的品种：韦恩，林加拉和瑞典红。有趣的是，我们还确定了Fjällnära品种的子结构，这表明在维持该品种的农场上存在不同的育种方法。这项研究代表了瑞典原生牛品种的遗传相关性和多样性的第一个全面的全基因组分析。我们的结果表明，不同的人口统计学模式，例如遗传隔离和杂交育种，已经塑造了瑞典本土牛品种的基因组多样性，并且瑞典山区品种保留了其真正的独特基因库，而没有其他任何欧洲牛品种做出重大贡献包括在这项研究中。