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Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)
Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be d...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359307/ https://www.ncbi.nlm.nih.gov/pubmed/32661317 http://dx.doi.org/10.1038/s41598-020-68064-5 |
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author | Cádiz, María I. López, María E. Díaz-Domínguez, Diego Cáceres, Giovanna Yoshida, Grazyella M. Gomez-Uchida, Daniel Yáñez, José M. |
author_facet | Cádiz, María I. López, María E. Díaz-Domínguez, Diego Cáceres, Giovanna Yoshida, Grazyella M. Gomez-Uchida, Daniel Yáñez, José M. |
author_sort | Cádiz, María I. |
collection | PubMed |
description | Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, by two haplotype-based (iHS and Rsb) and one F(ST) based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and F(ST) based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed Nile tilapia. |
format | Online Article Text |
id | pubmed-7359307 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-73593072020-07-14 Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus) Cádiz, María I. López, María E. Díaz-Domínguez, Diego Cáceres, Giovanna Yoshida, Grazyella M. Gomez-Uchida, Daniel Yáñez, José M. Sci Rep Article Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, by two haplotype-based (iHS and Rsb) and one F(ST) based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and F(ST) based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed Nile tilapia. Nature Publishing Group UK 2020-07-13 /pmc/articles/PMC7359307/ /pubmed/32661317 http://dx.doi.org/10.1038/s41598-020-68064-5 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Cádiz, María I. López, María E. Díaz-Domínguez, Diego Cáceres, Giovanna Yoshida, Grazyella M. Gomez-Uchida, Daniel Yáñez, José M. Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus) |
title | Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus) |
title_full | Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus) |
title_fullStr | Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus) |
title_full_unstemmed | Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus) |
title_short | Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus) |
title_sort | whole genome re-sequencing reveals recent signatures of selection in three strains of farmed nile tilapia (oreochromis niloticus) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359307/ https://www.ncbi.nlm.nih.gov/pubmed/32661317 http://dx.doi.org/10.1038/s41598-020-68064-5 |
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