Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations
Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilap...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Wiley Open Access
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/131025 |
| _version_ | 1855532100562714624 |
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| author | Barria, Agustin Penaloza, Carolina Papadopoulou, Athina Mahmuddin, Mahirah Benzie, John Houston, Ross Wiener, Pamela |
| author_browse | Barria, Agustin Benzie, John Houston, Ross Mahmuddin, Mahirah Papadopoulou, Athina Penaloza, Carolina Wiener, Pamela |
| author_facet | Barria, Agustin Penaloza, Carolina Papadopoulou, Athina Mahmuddin, Mahirah Benzie, John Houston, Ross Wiener, Pamela |
| author_sort | Barria, Agustin |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (FST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement. |
| format | Journal Article |
| id | CGSpace131025 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Wiley Open Access |
| publisherStr | Wiley Open Access |
| record_format | dspace |
| spelling | CGSpace1310252025-12-18T02:11:31Z Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations Barria, Agustin Penaloza, Carolina Papadopoulou, Athina Mahmuddin, Mahirah Benzie, John Houston, Ross Wiener, Pamela aquaculture nile tilapia fish gift population genomics snp array poolseq Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (FST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement. 2023-06-22 2023-07-06T16:07:33Z 2023-07-06T16:07:33Z Journal Article https://hdl.handle.net/10568/131025 en Open Access application/pdf Wiley Open Access Agustin Barria, Carolina Penaloza, Athina Papadopoulou, Mahirah Mahmuddin, John Benzie, Ross Houston, Pamela Wiener. (22/6/2023). Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations. Evolutionary Applications, 16 (6), pp. 1220-1235. |
| spellingShingle | aquaculture nile tilapia fish gift population genomics snp array poolseq Barria, Agustin Penaloza, Carolina Papadopoulou, Athina Mahmuddin, Mahirah Benzie, John Houston, Ross Wiener, Pamela Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations |
| title | Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations |
| title_full | Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations |
| title_fullStr | Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations |
| title_full_unstemmed | Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations |
| title_short | Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Oreochromis niloticus) populations |
| title_sort | genetic differentiation following recent domestication events a study of farmed nile tilapia oreochromis niloticus populations |
| topic | aquaculture nile tilapia fish gift population genomics snp array poolseq |
| url | https://hdl.handle.net/10568/131025 |
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