The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics. We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality. Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.

中文翻译：

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多组学数据的整合揭示了与东方猪与西方猪的表型分化相关的顺式调控变异

繁殖动物表型分化的遗传机制对进化生物学和农业具有重要意义。然而，顺式调节变体对猪表型的贡献知之甚少。因此，我们的目标是通过结合进化生物学分析和功能基因组学来阐明非编码变异导致猪表型差异的分子机制。我们获得了陆川猪品种（具有代表性的东部品种）的高分辨率分阶段染色体尺度参考基因组，contig N50 为 18.03 Mb，并通过对 234 头猪的基因组重新测序，分析了东部和西部猪的潜在选择性扫描。这些区域的多组织转录组和染色质可及性分析表明，组织特异性选择压力由启动子和远端顺式调节元件介导。与小肠中溶菌酶 (LYZ) 基因表达增加相关的启动子变体可能会增强猪的胃肠道免疫力和粗饲料耐受性。在骨骼肌中，与肌钙蛋白 C1、慢骨骼和心肌型 (TNNC1) 基因表达上调相关的增强子调节单核苷酸多态性可能会增加慢肌纤维的比例并影响肉质。