Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations
Abstract Sus scrofa is a globally distributed livestock species that still maintains two different ways of life: wild and domesticated. Herein, we detected copy number variation (CNV) of 328 animals using short read alignment on Sscrofa11.1. We compared CNV among five groups of porcine populations:...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-22373-z |
| _version_ | 1797945925824413696 |
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| author | Jisung Jang Bongsang Kim So Yun Jhang Byeongyong Ahn Mingue Kang Chankyu Park Eun Seok Cho Young-Sin Kim Woncheoul Park Heebal Kim |
| author_facet | Jisung Jang Bongsang Kim So Yun Jhang Byeongyong Ahn Mingue Kang Chankyu Park Eun Seok Cho Young-Sin Kim Woncheoul Park Heebal Kim |
| author_sort | Jisung Jang |
| collection | DOAJ |
| description | Abstract Sus scrofa is a globally distributed livestock species that still maintains two different ways of life: wild and domesticated. Herein, we detected copy number variation (CNV) of 328 animals using short read alignment on Sscrofa11.1. We compared CNV among five groups of porcine populations: Asian domesticated (AD), European domesticated (ED), Asian wild (AW), European wild (EW), and Near Eastern wild (NEW). In total, 21,673 genes were identified on 154,872 copy number variation region (CNVR). Differences in gene copy numbers between populations were measured by considering the variance-based value $${V}_{ST}$$ V ST and the one-way ANOVA test followed by Scheffe test. As a result, 111 genes were suggested as copy number variable genes. Abnormally gained copy number on EEA1 in all populations was suggested the presence of minor CNV in the reference genome assembly, Sscrofa11.1. Copy number variable genes were related to meat quality, immune response, and reproduction traits. Hierarchical clustering of all individuals and mean pairwise $${V}_{ST}$$ V ST in breed level were visualized genetic relationship of 328 individuals and 56 populations separately. Our findings have shown how the complex history of pig evolution appears in genome-wide CNV of various populations with different regions and lifestyles. |
| first_indexed | 2024-04-10T21:02:46Z |
| format | Article |
| id | doaj.art-076432c89188444e860a751729e51b35 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-10T21:02:46Z |
| publishDate | 2023-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-076432c89188444e860a751729e51b352023-01-22T12:11:00ZengNature PortfolioScientific Reports2045-23222023-01-0113111010.1038/s41598-022-22373-zPopulation differentiated copy number variation between Eurasian wild boar and domesticated pig populationsJisung Jang0Bongsang Kim1So Yun Jhang2Byeongyong Ahn3Mingue Kang4Chankyu Park5Eun Seok Cho6Young-Sin Kim7Woncheoul Park8Heebal Kim9Interdisciplinary Program in Bioinformatics, Seoul National UniversityeGnome, IncInterdisciplinary Program in Bioinformatics, Seoul National UniversityDepartment of Stem Cell and Regenerative Biotechnology, Konkuk UniversityDepartment of Stem Cell and Regenerative Biotechnology, Konkuk UniversityDepartment of Stem Cell and Regenerative Biotechnology, Konkuk UniversitySwine Science Division, Rural Development Administration, National Institute of Animal ScienceSwine Science Division, Rural Development Administration, National Institute of Animal ScienceAnimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDAInterdisciplinary Program in Bioinformatics, Seoul National UniversityAbstract Sus scrofa is a globally distributed livestock species that still maintains two different ways of life: wild and domesticated. Herein, we detected copy number variation (CNV) of 328 animals using short read alignment on Sscrofa11.1. We compared CNV among five groups of porcine populations: Asian domesticated (AD), European domesticated (ED), Asian wild (AW), European wild (EW), and Near Eastern wild (NEW). In total, 21,673 genes were identified on 154,872 copy number variation region (CNVR). Differences in gene copy numbers between populations were measured by considering the variance-based value $${V}_{ST}$$ V ST and the one-way ANOVA test followed by Scheffe test. As a result, 111 genes were suggested as copy number variable genes. Abnormally gained copy number on EEA1 in all populations was suggested the presence of minor CNV in the reference genome assembly, Sscrofa11.1. Copy number variable genes were related to meat quality, immune response, and reproduction traits. Hierarchical clustering of all individuals and mean pairwise $${V}_{ST}$$ V ST in breed level were visualized genetic relationship of 328 individuals and 56 populations separately. Our findings have shown how the complex history of pig evolution appears in genome-wide CNV of various populations with different regions and lifestyles.https://doi.org/10.1038/s41598-022-22373-z |
| spellingShingle | Jisung Jang Bongsang Kim So Yun Jhang Byeongyong Ahn Mingue Kang Chankyu Park Eun Seok Cho Young-Sin Kim Woncheoul Park Heebal Kim Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations Scientific Reports |
| title | Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations |
| title_full | Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations |
| title_fullStr | Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations |
| title_full_unstemmed | Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations |
| title_short | Population differentiated copy number variation between Eurasian wild boar and domesticated pig populations |
| title_sort | population differentiated copy number variation between eurasian wild boar and domesticated pig populations |
| url | https://doi.org/10.1038/s41598-022-22373-z |
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