Mobile element variants (MEVs) have a significant and complex impact on genomic diversity and phenotypic traits. However, the quantity, distribution, and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood. We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing (WGS) data from 747 pigs across 59 breeds worldwide. This database identified a total of 147,993 polymorphic MEVs, including 121,099 short interspersed nuclear elements (SINEs), 26,053 long interspersed nuclear elements (LINEs), 802 long terminal repeats (LTRs), and 39 other transposons, among which 54% are newly discovered. We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selection effects. Importantly, we identified 514, 530, and 584 candidate MEVs associated with population differentiation, domestication, and breed formation, respectively. For example, a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs, whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue. In addition, we identified 4,169 expressed MEVs (eMEVs) significantly associated with gene expression and 6,914 splicing MEVs (sMEVs) associated with gene splicing based on RNA-seq data from 266 porcine liver tissues. These eMEVs and sMEVs explain 6.24% and 9.47%, respectively, of the observed cis-heritability and highlight the important role of MEVs in the regulation of gene expression. Finally, we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs. Notably, we identified a candidate MEV significantly associated with total teat number, demonstrating the functionality of this reference panel. The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity, gene expression and phenotypic traits, which may provide useful resources and theoretical support for pig genetics and breeding.

中文翻译：

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猪基因组移动元件变异的构建及其在种群多样性和基因表达中的作用研究


移动元件变体 （MEV） 对基因组多样性和表型性状具有显著而复杂的影响。然而，猪基因组中 MEV 的数量、分布以及与基因表达和复杂性状的关系仍然知之甚少。我们基于来自全球 59 个品种的 747 头猪的高深度全基因组测序 （WGS） 数据构建了最全面的猪 MEV 文库。该数据库共鉴定出 147,993 个多态性 MEV，包括 121,099 个短散布核元件 （SINE）、26,053 个长散布核元件 （LINEs）、802 个长末端重复序列 （LTR） 和 39 个其他转座子，其中 54% 是新发现的。我们发现 MEVs 在基因组中分布不均匀，并且受负选择效应的强烈影响。重要的是，我们分别确定了 514 、 530 和 584 个与种群分化、驯化和品种形成相关的候选 MEV。例如，亚洲猪和欧洲猪之间的 ATRX 内含子中具有显著差异的 MEV，而亚洲猪和欧洲猪之间的 ATRX 在肌肉组织中也存在差异表达。此外，我们根据 266 个猪肝组织的 RNA-seq 数据，鉴定了 4,169 个与基因表达显著相关的表达 MEV （eMEV） 和 6,914 个与基因剪接相关的剪接 MEV （sMEV）。这些 eMEV 和 sMEV 分别解释了观察到的 6.24% 和 9.47% 的顺式遗传性，并强调了 MEV 在基因表达调节中的重要作用。最后，我们提供了一个高质量的 SNP-MEV 参考单倍型面板，以从全基因组 SNP 中估算 MEV 基因型。 值得注意的是，我们确定了一个与总数量显著相关的候选 MEV，证明了该参考面板的功能。本研究证明了 MEVs 在猪种群多样性、基因表达和表型性状方面的重要性，这可能为猪遗传学和育种提供有用的资源和理论支持。