Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences

Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2–71.3 Mb), BTA5 (10.0–19.7 Mb), BTA20 (10.0–19.9 and 20.0–22.7 Mb), and BTA25 (0.5–9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., <em>CWC27</em> and <em>CLUAP1</em>), ultraviole<em>t</em> protection (e.g., <em>ERCC8</em>), and pigmentation (e.g. <em>PDE4D</em>) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.本研究旨在鉴定并表征格罗宁根白头牛（Groningen White Headed, GWH）与其他牛品种间的差异基因组区域，尤其聚焦于筛选与被毛颜色及/或眼部保护表型相关的候选基因。首先，本研究采集8个品种共170头个体的全基因组测序数据，通过主成分分析与基于模型的聚类分析，解析GWH与其他牛品种的遗传结构。其次，通过整合以下三项分析的结果筛选候选基因组区域：a）全基因组关联分析（genome-wide association study, GWAS），分析群体涵盖GWH、其他白头品种（赫里福德牛、西门塔尔牛）以及非白头表型品种（荷兰弗里生牛、深红牛、默兹-莱茵-伊塞尔牛、荷兰带纹牛与荷斯坦弗里生牛）；b）以4个荷兰地方传统品种（荷兰弗里生牛、深红牛、默兹-莱茵-伊塞尔牛、荷兰带纹牛）及商业化荷斯坦弗里生牛为对照，扫描GWH牛群中特有的选择信号；c）通过上述方法开展候选基因检测。将过滤后的测序reads比对至参考基因组（ARS-UCD1.2）后，平均测序深度达8.7倍。经变异检测后，荷斯坦弗里生牛的品种特异性变异数量最少（148213个），深红牛的品种特异性变异数量最多（558909个）。整合分析结果后，本研究在牛4号常染色体（BTA4）70.2–71.3 Mb区间、牛5号常染色体（BTA5）10.0–19.7 Mb区间、牛20号常染色体（BTA20）10.0–19.9 Mb与20.0–22.7 Mb区间，以及牛25号常染色体（BTA25）0.5–9.2 Mb区间中，共鉴定出5个受选择的基因组区域。上述区域包含与视网膜变性（如CWC27、CLUAP1）、紫外线防护（如ERCC8）以及色素沉着（如PDE4D）相关的位置候选基因与功能候选基因，这些基因可能与GWH特有的色素沉着及/或眼部保护表型相关，例如双侧围眼色素沉着（Ambilateral Circumocular Pigmentation, ACOP）。本研究结果将有助于解析GWH表型的分子基础及其适应过程的生物学意义。