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Abstract：
Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome.
摘要：
转座因子（TE）的移动性能够产生大量的结构变体（SV），作为家畜遗传分析和分子育种的分子标记具有相当大的潜力。我们的结果表明，猪基因组主要包含由短散布核元素（SINE）产生的TE-SV（51,873/76.49％），其次是长散布核元素(LINEs)(11,131/16.41%)，和超过84%的常见TE-SV(次要等位基因频率，MAF>0.10)被验证为多态。随后，我们利用确定的TE-SV来深入了解种群结构，导致三个猪群之间的明显差异，并有助于识别中国当地猪种之间的关系。此外,我们调查了不同猪群基因编码区的TEs频率，并注释了相应的TE类型，相关基因和功能通路。通过利用北京黑猪对大型白猪和中国本地猪进行全基因组比较，我们确定了TE介导的SVs与数量性状位点（QTLs）相关，并观察到它们主要涉及car体性状和肉质性状。最后,我们提出了猪基因组中TE转导的第一个证据。
