Signatures of selection in tilapia revealed by whole genome resequencing
Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection s...
| Main Authors: | , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2015
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| Online Access: | https://hdl.handle.net/10356/79251 http://hdl.handle.net/10220/38801 |
| _version_ | 1826128396081430528 |
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| author | Bai, Zhiyi Meng, Zining Zhang, Yong Wang, Le Liu, Feng Jing, Wu Li, Jiale Lin, Haoran Xia, Jun Hong Wan, Zi Yi Yue, Gen Hua |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Bai, Zhiyi Meng, Zining Zhang, Yong Wang, Le Liu, Feng Jing, Wu Li, Jiale Lin, Haoran Xia, Jun Hong Wan, Zi Yi Yue, Gen Hua |
| author_sort | Bai, Zhiyi |
| collection | NTU |
| description | Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10–100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia. |
| first_indexed | 2024-10-01T07:24:17Z |
| format | Journal Article |
| id | ntu-10356/79251 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T07:24:17Z |
| publishDate | 2015 |
| record_format | dspace |
| spelling | ntu-10356/792512023-02-28T16:58:13Z Signatures of selection in tilapia revealed by whole genome resequencing Bai, Zhiyi Meng, Zining Zhang, Yong Wang, Le Liu, Feng Jing, Wu Li, Jiale Lin, Haoran Xia, Jun Hong Wan, Zi Yi Yue, Gen Hua School of Biological Sciences Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10–100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia. Published version 2015-10-13T08:42:23Z 2019-12-06T13:20:50Z 2015-10-13T08:42:23Z 2019-12-06T13:20:50Z 2015 2015 Journal Article Hong Xia, J., Bai, Z., Meng, Z., Zhang, Y., Wang, L., Liu, F., et al. (2015). Signatures of selection in tilapia revealed by whole genome resequencing. Scientific Reports, 5, 14168-. 2045-2322 https://hdl.handle.net/10356/79251 http://hdl.handle.net/10220/38801 10.1038/srep14168 26373374 en Scientific Reports This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ application/pdf |
| spellingShingle | Bai, Zhiyi Meng, Zining Zhang, Yong Wang, Le Liu, Feng Jing, Wu Li, Jiale Lin, Haoran Xia, Jun Hong Wan, Zi Yi Yue, Gen Hua Signatures of selection in tilapia revealed by whole genome resequencing |
| title | Signatures of selection in tilapia revealed by whole genome resequencing |
| title_full | Signatures of selection in tilapia revealed by whole genome resequencing |
| title_fullStr | Signatures of selection in tilapia revealed by whole genome resequencing |
| title_full_unstemmed | Signatures of selection in tilapia revealed by whole genome resequencing |
| title_short | Signatures of selection in tilapia revealed by whole genome resequencing |
| title_sort | signatures of selection in tilapia revealed by whole genome resequencing |
| url | https://hdl.handle.net/10356/79251 http://hdl.handle.net/10220/38801 |
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