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Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig

文献类型： 外文期刊

作者： Zong, Wencheng 1 ; Zhao, Runze 1 ; Wang, Xiaoyan 2 ; Zhou, Chenyu 2 ; Wang, Jinbu 1 ; Chen, Cai 2 ; Niu, Naiqi 1 ; Zheng, Yao 2 ; Chen, Li 1 ; Liu, Xin 1 ; Hou, Xinhua 1 ; Zhao, Fuping 1 ; Wang, Ligang 1 ; Wang, Lixian 1 ; Song, Chengyi 2 ; Zhang, Longchao 1 ;

作者机构： 1.Chinese Acad Agr Sci CAAS, Inst Anim Sci, State Key Lab Anim Biotech Breeding, Beijing, Peoples R China

2.Yangzhou Univ, Coll Anim Sci & Technol, Yangzhou, Peoples R China

3.Shanxi Agr Univ, Coll Anim Sci, Jinzhong, Peoples R China

4.Chongqing Acad Anim Sci, Chongqing, Peoples R China

关键词： pig; transposable elements; structural variations; population genetic; transduction

期刊名称：DNA RESEARCH （ 影响因子：4.1； 五年影响因子：4.4 ）

ISSN： 1340-2838

年卷期： 2024 年 31 卷 2 期

页码：

收录情况： SCI

摘要： 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.

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