Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis)
Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to sh...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/110363 |
| _version_ | 1855538908836659200 |
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| author | Liang, D. Zhao, P. Si, J. Fang, L. Pairo-Castineira, E. Hu, X. Xu, Q. Hou, Y. Gong, Y. Liang, Z. Tian, B. Mao, H. Yindee, M. Faruque, M.O. Kongvongxay, S. Khamphoumee, S. Liu, G.E. Wu, D.-D. Barker, J.S.F. Han Jianlin Zhang, Y. |
| author_browse | Barker, J.S.F. Fang, L. Faruque, M.O. Gong, Y. Han Jianlin Hou, Y. Hu, X. Khamphoumee, S. Kongvongxay, S. Liang, D. Liang, Z. Liu, G.E. Mao, H. Pairo-Castineira, E. Si, J. Tian, B. Wu, D.-D. Xu, Q. Yindee, M. Zhang, Y. Zhao, P. |
| author_facet | Liang, D. Zhao, P. Si, J. Fang, L. Pairo-Castineira, E. Hu, X. Xu, Q. Hou, Y. Gong, Y. Liang, Z. Tian, B. Mao, H. Yindee, M. Faruque, M.O. Kongvongxay, S. Khamphoumee, S. Liu, G.E. Wu, D.-D. Barker, J.S.F. Han Jianlin Zhang, Y. |
| author_sort | Liang, D. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3′ truncated and containing only 5′ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5′ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe. |
| format | Journal Article |
| id | CGSpace110363 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1103632024-08-27T10:37:05Z Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis) Liang, D. Zhao, P. Si, J. Fang, L. Pairo-Castineira, E. Hu, X. Xu, Q. Hou, Y. Gong, Y. Liang, Z. Tian, B. Mao, H. Yindee, M. Faruque, M.O. Kongvongxay, S. Khamphoumee, S. Liu, G.E. Wu, D.-D. Barker, J.S.F. Han Jianlin Zhang, Y. water buffaloes genetics animal breeding Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3′ truncated and containing only 5′ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5′ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe. 2021-03-09 2020-12-01T08:11:19Z 2020-12-01T08:11:19Z Journal Article https://hdl.handle.net/10568/110363 en Open Access Oxford University Press Liang, D., Zhao, P., Si, J., Fang, L, Pairo-Castineira, E., Hu, X., Xu, Q., Hou, Y., Gong, Y., Liang, Z., Tian, B., Mao, H., Yindee, M., Faruque, M.O., Kongvongxay, S., Khamphoumee, S., Liu, G.E., Wu, D.-D., Barker, J.S.F., Han, J. and Zhang, Y. 2020. Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis). Molecular Biology and Evolution |
| spellingShingle | water buffaloes genetics animal breeding Liang, D. Zhao, P. Si, J. Fang, L. Pairo-Castineira, E. Hu, X. Xu, Q. Hou, Y. Gong, Y. Liang, Z. Tian, B. Mao, H. Yindee, M. Faruque, M.O. Kongvongxay, S. Khamphoumee, S. Liu, G.E. Wu, D.-D. Barker, J.S.F. Han Jianlin Zhang, Y. Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis) |
| title | Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis) |
| title_full | Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis) |
| title_fullStr | Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis) |
| title_full_unstemmed | Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis) |
| title_short | Genomic analysis revealed a convergent evolution of LINE-1 in coat color: A case study in water buffaloes (Bubalus bubalis) |
| title_sort | genomic analysis revealed a convergent evolution of line 1 in coat color a case study in water buffaloes bubalus bubalis |
| topic | water buffaloes genetics animal breeding |
| url | https://hdl.handle.net/10568/110363 |
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