Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright’s fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

中文翻译：

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美国朗布依埃羊、卡塔丁羊和杜泊羊的遗传多样性


管理遗传多样性对于维持物种适应性至关重要。遗传多样性丧失导致的过度纯合性会对品种的繁殖和生产性能产生不利影响。遗传多样性分析可以促进选择特征的识别，这可能有助于品种或种群的健康、生产和外观的具体特征。在这项研究中，对具有细羊毛产量（Rambouillet，N = 745）、寄生虫抗性（Katahdin，N = 581）和环境耐受性（Dorper，N = 265）等良好特征的品种进行了近交、有效种群规模的评估。 (Ne)，运行纯合性 (ROH) 和 Wright 固定指数 (FST) 异常值方法来识别 36,113 个常染色体单核苷酸多态性 (SNP) 的选择差异特征。通过 GONe 和 NeEstimator 软件估计，卡塔丁羊在最近一代中具有最大的电流 Ne。最高度保守的 ROH 岛在朗布依埃 (Rambouillet) 被发现，其 6 号染色体上的选择特征包含 202 个 SNP，在 50% 至 94% 的个体中称为 ROH。该区域包含 DCAF16、LCORL 和 NCAPG 基因，此前已报道这些基因处于选择状态，并且具有与产奶和生长性状相关的生物学作用。通过 Katahdin 与 Rambouillet 和 Dorper 的 FST 比较确定的离群区域包含在产奶和乳腺炎抗性或易感性方面具有已知作用的基因，并且 Rambouillet 与 Katahdin 和 Dorper 的 FST 比较确定了与羊毛生长相关的基因，表明这些性状已被这些群体受到自然或人工选择的压力。 在所有 FST 品种比较中都鉴定出了参与细胞因子-细胞因子受体相互作用途径的基因，这表明这些品种之间在控制细胞因子信号传导机制的基因组区域中存在等位基因多样性。在本文中，我们描述了多种且具有重要经济意义的美国绵羊品种的选择特征。建议对这些特征中包含的基因进行进一步研究，以了解它们与生物性状的相关性并增进对品种多样性的理解。