Gutiérrez-Gil Beatriz, Arranz Juan J, Wiener Pamela
Departamento de Producción Animal, Universidad de León León, Spain.
Division of Genetics and Genomics, Roslin Institute and R(D)SVS, University of Edinburgh Midlothian, UK.
Front Genet. 2015 May 13;6:167. doi: 10.3389/fgene.2015.00167. eCollection 2015.
This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as "divergence signals," which may be useful in characterizing and protecting livestock genetic diversity.
本综述汇总了21项针对欧洲牛品种的基因组研究结果，从而呈现了通过全基因组选择图谱扫描鉴定出的黄牛选择印记的总体情况。通过对文献报道结果进行全面总结，我们编制了一份清单，其中包含在37个牛品种（17个肉牛品种、14个奶牛品种和6个兼用品种）中描述的1049个选择清除区域，以及四项不同的肉牛与奶牛比较研究，随后我们将这些区域归类为核心选择清除（CSS）区域，定义为彼此距离在1兆碱基内的连续信号。我们在29条牛常染色体上共定义了409个CSS区域，其中232个（57%）与单一品种相关（单一品种CSS区域），134个CSS区域（33%）与少数几个品种相关（两到四个品种CSS区域），39个CSS区域（9%）与五个或更多品种相关（多品种CSS区域）。对于每个CSS区域，我们进行了候选基因调查，在CSS区间内（从通过BioMart提取的5183个基因的总列表中）鉴定出291个与奶牛和肉类生产、体型以及毛色性状相关的基因。对CSS位置候选基因进行的补充功能富集分析突出了与行为、免疫反应和繁殖性状潜在途径相关的其他基因。单一品种CSS区域显示出与奶牛和肉牛生产相关基因的过度富集，基于功能富集分析，这些区域中与生产相关的途径术语的过度富集进一步支持了这一点。总体而言，本综述提供了欧洲牛品种中报道的选择清除区域的比较图谱，并首次对各个品种中发现的选择清除区域进行了特征描述。基于其独特性，这些品种特异性信号可被视为“分化信号”，这可能有助于表征和保护家畜遗传多样性。
