Runs of homozygosity (ROH) are continuous segments of the genome that arose as a result of inbreeding, resulting in the inheritance of identical haplotypes from both parents who shared a common ancestor. In the present study, we performed a detailed characterization and comparison of ROH in four pig breeds, including intensively selected Polish Landrace as well as native unselected animals of Puławska and two Złotnicka breeds (White and Spotted). We used a medium-density PorcineSNP60 BeadChip assay (Illumina) and cgaTOH software to detect ROH covering a minimum of 30 adjacent SNPs and maintaining a size over 1 Mb. By analysing ROH distribution and frequency across the genome, we also identified genomic regions with high ROH frequency (so-called "ROH hotspots"). The obtained results showed that the analysed conserved breeds were characterized by a higher ROH span and higher ROH-based inbreeding coefficients (FROH ), which likely result from past population bottlenecks, increasing the overall inbreeding level within these populations. The analysis of ROH distribution across the genomes revealed the presence of both shared and breed-specific ROH hotspots. These hotspots, presumably representing genome regions under selection, overlapped with a variety of genes associated with processes connected with immune system functioning, reproduction, glucose homeostasis and metabolism. The genome regions with ROH hotspots overlapping in all analysed populations, located on SSC4 (51.9-55.9 Mb) and 13 (92.6-97.8 Mb), covered thirty-one different genes, including MMP16, SLC7A13, ATP6V0D2, CNGB3, WWiP1, RiMDN1 and CPNE3. These genes are primarily associated with biological regulation and metabolism, processes that could be responsible for the variety of the selected production and functional features.

中文翻译：

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检测波兰保守和商业猪品种的纯合子运行

纯合子序列 (ROH) 是由于近亲繁殖而产生的基因组的连续片段，导致从拥有共同祖先的父母双方遗传相同的单倍型。在本研究中，我们对四种猪品种的 ROH 进行了详细的表征和比较，包括精挑细选的波兰长白猪以及 Puławska 的本地未选择动物和两个 Złotnicka 品种（白猪和斑点猪）。我们使用中密度 PorcineSNP60 BeadChip 检测 (Illumina) 和 cgaTOH 软件来检测覆盖至少 30 个相邻 SNP 并保持大小超过 1 Mb 的 ROH。通过分析整个基因组的 ROH 分布和频率，我们还确定了具有高 ROH 频率的基因组区域（所谓的“ROH 热点”）。获得的结果表明，分析的保守品种具有更高的 ROH 跨度和更高的基于 ROH 的近交系数 (FROH)，这可能是由于过去的种群瓶颈造成的，增加了这些种群内的整体近交水平。对整个基因组中 ROH 分布的分析揭示了共享和特定品种 ROH 热点的存在。这些热点可能代表选择的基因组区域，与与免疫系统功能、繁殖、葡萄糖稳态和代谢相关过程相关的各种基因重叠。在所有分析的群体中具有 ROH 热点重叠的基因组区域位于 SSC4 (51.9-55.9 Mb) 和 13 (92.6-97.8 Mb)，涵盖了 31 个不同的基因，包括 MMP16、SLC7A13、ATP6V0D2、CNGB3、WWiP1、RiMDN1 和CPNE3。