The domestic yak (Bos grunniens) from the Qinghai-Tibet Plateau is an important animal model in high-altitude adaptation studies. Here, we performed the genome-wide selective sweep analysis to identify the candidate copy number variation (CNV) for the high-altitude adaptation of yaks. A total of 531 autosomal CNVs were determined from 29 yak genome-wide resequencing data (15 high- and 14 low-altitude distributions) by using a CNV caller with a CNV identification interval > 5 kb, CNV silhouette score > 0.7, and minimum allele frequency > 0.05. Most high-frequency CNVs were located at the exonic (44.63%) and intergenic (46.52%) regions. In accordance with the results of the selective sweep analysis, 7 candidate CNVs were identified from the interaction of the top 20 CNVs with highest divergence from the F ST and V ST between the low (LA) and high (HA) altitudes. Five genes (i.e., GRIK4, IFNLR1, LOC102275985, GRHL3, and LOC102275713) were also annotated from the seven candidate CNVs and their upstream and downstream ranges at 300 kb. GRIK4, IFNLR1, and LOC102275985 were enriched in five known signal pathways, namely, glutamatergic synapse, JAK-STAT signaling pathway, cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and olfactory transduction. These pathways are involved in the environmental adaptability and various physiological functions of animals, especially the physiological regulation under a hypoxic environment. The results of this study advanced the understanding of CNV as an important genomic structure variant type that contributes to HA adaptation and helped further explain the molecular mechanisms underlying the altitude adaptability of yaks.

中文翻译：

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通过使用拷贝数变异对牛的高海拔适应性进行全基因组选择性扫描分析。

来自青藏高原的家养牛（Bos grunniens）是高海拔适应性研究中的重要动物模型。在这里，我们进行了全基因组选择性扫描分析，以识别the牛的高海拔适应性的候选拷贝数变异（CNV）。通过使用CNV识别间隔> 5 kb，CNV轮廓评分> 0.7和最小等位基因的CNV调用者，从29个ak牛全基因组重测序数据（15个高海拔和14个低海拔分布）中确定了总共531个常染色体CNV。频率> 0.05。大多数高频CNV位于外显子（44.63％）和基因间（46.52％）区域。根据选择性扫描分析的结果，从前20个CNV的相互作用中识别出7个候选CNV，在低海拔（LA）和高海拔（HA）之间与F ST和V ST的差异最大。还从七个候选CNV中注释了五个基因（即GRIK4，IFNLR1，LOC102275985，GRHL3和LOC102275713），它们的上游和下游范围为300 kb。GRIK4，IFNLR1和LOC102275985富含五个已知的信号途径，即谷氨酸能突触，JAK-STAT信号通路，细胞因子-细胞因子受体相互作用，神经活性配体-受体相互作用和嗅觉转导。这些途径涉及动物的环境适应性和各种生理功能，特别是在低氧环境下的生理调节。