Onzima Robert B, Upadhyay Maulik R, Doekes Harmen P, Brito Luiz F, Bosse Mirte, Kanis Egbert, Groenen Martien A M, Crooijmans Richard P M A
Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands.
National Agricultural Research Organization (NARO), Entebbe, Uganda.
Front Genet. 2018 Aug 14;9:318. doi: 10.3389/fgene.2018.00318. eCollection 2018.
Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, , based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer ( = 13), and the indigenous breeds Karamojong ( = 15), Kigezi ( = 29), Mubende ( = 29), Small East African ( = 29), and Sebei ( = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., and ), growth and fatty acid composition (e.g., and ), and thermo-tolerance (e.g., and ). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., and ) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
自然选择和人工选择都是影响家畜物种全基因组遗传变异的主要驱动力。选择通常会在基因组中留下印记，其特征往往是不同品种间存在高度遗传分化，和/或在受到强烈选择压力的性状相关区域遗传多样性大幅降低。在本研究中，我们基于纯合子片段（ROH）评估了六个乌干达山羊品种的选择印记和基因组近亲繁殖系数，这六个品种分别是波尔山羊（n = 13）以及本地品种卡拉莫琼山羊（n = 15）、基盖齐山羊（n = 29）、穆本德山羊（n = 29）、东非小山羊（n = 29）和塞贝山羊（n = 29）。经过基因分型质量控制后，剩余45,294个常染色体单核苷酸多态性（SNP）用于进一步分析。基于标记特异性固定指数（F - 值）和单倍型分化（hapFLK），在所有品种中分别总共鉴定出394个和6个特定品种的假定选择印记区域。这些区域富含直接或间接参与环境适应相关信号通路的基因，如免疫反应（如IL1B和TLR4）、生长和脂肪酸组成（如GHR和FASN）以及耐热性（如HSP90AA1和HSP90AB1）。该研究表明，选择中的基因组区域在品种间几乎没有重叠，并且由于性状的复杂性，通常未显示出预期的典型经典选择印记。在波尔山羊品种中，还鉴定出了与生产性状相关的候选基因，如体型和生长（如GHR和IGF1）。此外，对本地山羊品种ROH的分析表明，与波尔山羊较高的近亲繁殖水平（平均F = 13.8%）相比，其基因组近亲繁殖水平非常低（每个品种的平均F范围为0.8%至2.4%）。除卡拉莫琼山羊外，短ROH比长ROH更常见，这为这些山羊品种的发展历史提供了见解。本研究深入了解了长期选择对波尔山羊和乌干达本地山羊品种的影响，这对于育种计划的实施、遗传资源的保护以及它们的可持续利用和管理具有重要意义。
