Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig
© The Author(s) 2024. Published by Oxford University Press on behalf of Kazusa DNA Research Institute..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:31 |
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| Enthalten in: |
DNA research : an international journal for rapid publication of reports on genes and genomes - 31(2024), 2 vom: 01. März |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Zong, Wencheng [VerfasserIn] |
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| Links: |
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| Themen: |
DNA Transposable Elements |
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| Anmerkungen: |
Date Completed 26.03.2024 Date Revised 26.03.2024 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/dnares/dsae008 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 245 | 1 | 0 | |a Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig |
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| 520 | |a © The Author(s) 2024. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a structural variations | |
| 650 | 4 | |a transduction | |
| 650 | 4 | |a transposable elements | |
| 650 | 7 | |a DNA Transposable Elements |2 NLM | |
| 700 | 1 | |a Zhao, Runze |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Xiaoyan |e verfasserin |4 aut | |
| 700 | 1 | |a Zhou, Chenyu |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Jinbu |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Cai |e verfasserin |4 aut | |
| 700 | 1 | |a Niu, Naiqi |e verfasserin |4 aut | |
| 700 | 1 | |a Zheng, Yao |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Li |e verfasserin |4 aut | |
| 700 | 1 | |a Liu, Xin |e verfasserin |4 aut | |
| 700 | 1 | |a Hou, Xinhua |e verfasserin |4 aut | |
| 700 | 1 | |a Zhao, Fuping |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Ligang |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Lixian |e verfasserin |4 aut | |
| 700 | 1 | |a Song, Chengyi |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Longchao |e verfasserin |4 aut | |
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