Background Allele-specific expression (ASE) refers to the preferential expression of one allele over the other and contributes to adaptive phenotypic plasticity. Here, we used a reciprocal cross-model between phenotypically divergent European Berkshire and Asian Tibetan pigs to characterize 2 ASE classes: imprinting (i.e., the unequal expression between parental alleles) and sequence dependent (i.e., unequal expression between breed-specific alleles). We examined 3 transcript types, including protein-coding genes (PCGs), long noncoding RNAs, and transcripts of unknown coding potential, across 7 representative somatic tissues from hybrid pigs generated by reciprocal crosses. Results We identified a total of 92 putative imprinted transcripts, 69 (75.00%) of which are described here for the first time. By combining the transcriptome from purebred Berkshire and Tibetan pigs, we found ∼6.59% of PCGs are differentially expressed between breeds that are regulated by trans-elements (e.g., transcriptional factors), while only ∼1.35% are attributable to cis (e.g., promoters). The higher prevalence of trans-PCGs indicates the dominated effects of trans-regulation in driving expression differences and shaping adaptive phenotypic plasticity between breeds, which were supported by functional enrichment analysis. We also found strong evidence that expression changes mediated by cis-effects were associated with accumulated variants in promoters. Conclusions Our study provides a comprehensive map of expression regulation that constitutes a valuable resource for the agricultural improvement of pig breeds.

中文翻译：

---

对猪转录组的等位基因特异性调节作用

背景等位基因特异性表达（ASE）是指一个等位基因相对于另一个等位基因的优先表达，并有助于适应性表型可塑性。在这里，我们使用表型差异的欧洲伯克夏猪和亚洲藏猪之间的相互交叉模型来表征 2 个 ASE 类别：印记（即亲本等位基因之间的不等表达）和序列依赖性（即品种特异性等位基因之间的不等表达）。我们通过互交产生的杂交猪的 7 个代表性体细胞组织检查了 3 种转录物类型，包括蛋白质编码基因 (PCG)、长非编码 RNA 和未知编码潜力的转录物。结果我们总共鉴定了 92 个假定的印记转录本，其中 69 个 (75.00%) 是首次在此描述。通过结合纯种伯克夏猪和藏猪的转录组，我们发现〜6.59％的PCG在受反式元件（例如转录因子）调节的品种之间差异表达，而只有〜1.35％归因于顺式元件（例如启动子） ）。反式 PCG 的较高患病率表明反式调节在驱动表达差异和塑造品种间适应性表型可塑性方面的主导作用，这一点得到了功能富集分析的支持。我们还发现强有力的证据表明顺式效应介导的表达变化与启动子中累积的变异有关。结论我们的研究提供了表达调控的综合图谱，为猪品种的农业改良提供了宝贵的资源。