A Meta-Assembly of Selection Signatures in Cattle

Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.

自牛被驯化以来，诸多具有经济重要性的性状已在牛类身上实现显著遗传改良，涵盖适应性、外观表现与生产性能等维度。为应对此类高强度选择压力，牛基因组在功能性遗传变异的核心区域发生了序列改变，这类区域被称为“选择信号（selection signatures）”。本文综述了2009至2015年间的64项最新研究，这些研究针对全球牛种群的基因组多样性偏离中性进化的情形展开检验。其中，我们基于涵盖90个纯种与杂交牛品种、共70743头个体的56项全基因组扫描数据，构建了涵盖16158个选择信号的元组装数据集，这些信号对应单个牛品种及其类群（欧洲牛、非洲牛、瘤牛及合成品种牛类群）。元选择得分（meta-selection-scores, MSS）通过在指定滑动窗口区间内，对每个位点的已发表研究结果进行整合计算得到；该得分针对跨研究共享的样本进行了校正，并依据研究间与研究内的显著性阈值完成加权处理。已发表的选择信号在牛基因组中分布广泛，但本次元组装得到了263个基因组区域的共识图谱：其中141个为独有区域（含113个品种特异性区域），剩余122个为不同牛类群共享的区域。元选择得分最显著的峰值区段代表了多个种群共同受到选择的基因组区域，其中既包含已知具有主要效应的基因（如被毛颜色、无角性状与肌肉肥大相关基因），也涵盖已知影响多基因性状的基因，包括体型、适应性、饲料利用率、免疫力、行为、繁殖性能、肉牛及奶牛生产性状相关基因。作为首个针对选择信号的元组装研究，本工作为牛基因组选择性清除热点区域提供了全新的研究视角，且该分析方法同样可推广应用至其他物种。