Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
Commun Biol. 2023 Aug 31;6(1):894. doi: 10.1038/s42003-023-05234-x.
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
转座元件 (TEs) 是遗传多态性的主要来源，在染色质结构、基因调控网络和基因组进化中发挥作用。然而，它们在猪中的功能作用及其对复杂性状的贡献在很大程度上尚不清楚。我们在猪中创建了一个 TEs 目录 (n = 3087929)，发现年轻的 SINEs 主要通过组蛋白修饰、DNA 甲基化和降低可及性来沉默。然而，一些来自活跃的年轻 SINEs 的转录本表现出高度的组织特异性，这一点通过分析 3570 个 RNA-seq 样本得到了证实。我们还在 374 个人中检测到 211067 个二态 SINEs，其中包括 340 个与局部适应相关的种群特异性 SINEs。将这些二态 SINEs映射到猪 97 个复杂性状的全基因组关联分析中，我们发现了 54 个候选基因（例如，ANK2 和 VRTN），这些基因可能由 TEs 介导。我们的研究结果强调了年轻 SINEs 的重要作用，并为基因型与表型关联和猪的现代育种提供了补充。
