The genome‐wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome‐wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole‐genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi‐allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3–1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR‐corrected p‐value < 0.05), respectively, among which cGMP‐PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

中文翻译：

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使用全基因组测序数据表征美国水貂的纯合岛群

对纯合性（ROH）岛进行全基因组分析可以成为识别群体内共享变异并发现与复杂性状相关的重要基因组区域的有效策略。当前的研究使用 100 只美国水貂的全基因组测序数据进行 ROH 分析，以表征全基因组纯合性模式，识别这些候选区域内的 ROH 岛和注释基因（尼盖尔愿景）。序列处理后，使用 GATK 和 Samtools 管道调用变体。经过质量控制后，两条管道鉴定出的 8,373,854 个双等位基因变体仍有待进一步分析。在所有个体中总共鉴定出 34,652 个 ROH 片段，其中较短的片段（0.3-1 Mb）在整个基因组中丰富，约占所有 ROH 的 84.39%。在这些片段中，我们确定了 63 个 ROH 岛，其中包含 156 个带注释的基因。位于 ROH 岛的基因与毛皮质量相关（EDNRA、FGF2、FOXA2和SLC24A4）、体型/体重（MYLK4、PRIM2、FABP2、EYS和PHF3）、免疫能力（IL2、IL21、PTP4A1、SEMA4C、JAK2、CCNA2和TNIP3）和繁殖（ADAD1、KHDRBS2、INSL6、PGRMC2和HSPA4L）。此外，基因本体论和 KEGG 通路富集分析揭示了 56 个和 9 个显着术语（FDR 校正p‐值 < 0.05），其中 cGMP-PKG 信号通路、肌动蛋白细胞骨架的调节和钙信号通路因其在生长和毛皮特性中的功能作用而受到关注。这是第一项展示美洲水貂 ROH 岛的研究。ROH 岛的候选基因和功能富集分析表明，可能存在针对水貂育种目标的选择特征，例如增加体长、繁殖性能和毛皮质量。这些发现有助于我们了解遗传特征，并提供补充信息，以协助实施美国水貂遗传改良的育种策略。