<b>An allele-specific expression atlas across bovine breeds and multiple tissues</b>

Allele-specific expression (ASE) analysis, when integrated with eQTL mapping, selective sweep analyses, and phenotypic data, provides a powerful approach for prioritizing candidate adaptive variants underlying complex traits. This study integrates 234 genomic datasets and 623 transcriptomic datasets across seven tissues from 32 diverse Bovini breeds and populations to investigate evolutionary shifts in gene expression. We generated an ASE map across ancestries and tissues, including 10 domestic cattle breeds (nine indigenous breeds from Yunnan and one introduced breed), Zhongdian yak (Bos grunniens), and Yunnan gayal (Bos frontalis), and systematically characterized ASE variants at the individual, breed, and population levels. Furthermore, by integrating ASE variants with functional genomic data (e.g., ChIP-seq and Hi-C) and 1,028 phenotypic records (including traits such as muscle fiber diameter and relative hump weight), this dataset enables exploration of the potential roles and regulatory mechanisms of ASE in environmental adaptation in cattle. Overall, this resource expands current knowledge of cis-regulatory variation in Bovini species and provides a valuable foundation for future studies on gene regulation and adaptive evolution.等位基因特异性表达（ASE）分析若与表达数量性状位点（eQTL）定位、选择性清除分析及表型数据相结合，可成为筛选复杂性状背后适应性候选变异的有力手段。本研究整合了来自32个不同牛亚科类群与种群、覆盖7种组织的234个基因组数据集与623个转录组数据集，以探究基因表达的演化变迁。我们构建了覆盖不同祖先类群与组织的ASE图谱，涵盖10个家牛品种（其中9个为云南地方品种，1个为引进品种）、中甸牦牛（Bos grunniens）以及云南大额牛（Bos frontalis），并在个体、品种及种群层面系统表征了ASE变异。此外，通过将ASE变异与功能基因组数据（如染色质免疫共沉淀测序（ChIP-seq）与Hi-C）及1028条表型记录（涵盖肌纤维直径、相对驼峰重量等性状）相结合，本数据集可用于探究ASE在牛环境适应中的潜在作用与调控机制。总体而言，本数据集资源拓展了学界对牛亚科物种顺式调控变异的现有认知，为未来基因调控与适应性演化相关研究提供了宝贵基础。