The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.

中文翻译：

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克罗地亚、塞尔维亚和斯洛文尼亚六个本土猪种的遗传多样性和种群结构

地方品种作为有价值遗传变异的遗传储存库的重要性已得到充分证实。中欧和东南欧的养猪有着悠久的传统，导致形成了几个当地的猪品种。在本研究中，分析了来自斯洛文尼亚、克罗地亚和塞尔维亚的六个本土猪品种（Banija 斑猪、Black Slavonian、Turopolje 猪、Swallow-belied Mangalitsa、Moravka 和 Krskopolje 猪）的遗传多样性参数。使用微卫星和单核苷酸多态性 (SNP) 对来自这些品种的动物进行基因分型。比较了使用这两种标记系统获得的结果和基于谱系数据的结果。此外，我们根据纯合性 (ROH) 运行的分布估计近交水平，并使用 ROH 岛和综合单倍型评分 (iHS) 在选择压力下确定基因组区域。在 Turopolje 猪中观察到根据微卫星和 SNP 数据计算的最低杂合度值。观察到的杂合度高于黑斯拉沃尼亚猪、摩拉夫卡猪和图罗波利猪的预期杂合度。两种类型的标记都使我们能够区分属于每个品种的个体集群。对品种间混合物的分析揭示了 Mangalitsa 和 Moravka 之间以及 Mangalitsa 和 Black Slavonian 之间的潜在基因流动，但在 Banija 斑点猪和 Turopolje 猪中没有检测到基因渗入事件。ROH 在整个基因组中的分布并不均匀。对 ROH 岛的分析确定了燕腹 Mangalitsa 中具有极高频率共享 ROH 的基因组区域，其中包含与胆固醇生物合成、脂肪酸代谢和每日体重增加相关的基因。用于检测选择特征的 iHS 方法揭示了包含在繁殖性状和抗病性中具有潜在作用的基因的候选区域。基于从三个数据集中获得的种群参数估计，我们展示了这里分析的六个猪品种之间存在关系。对 ROH 分布的分析使我们能够估计这些品种的近交水平和纯合区域的范围。