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Research article - Peer-reviewed, 2020

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

Cadiz, Maria, I; Lopez, Maria E.; Diaz-Dominguez, Diego; Caceres, Giovanna; Yoshida, Grazyella M.; Gomez-Uchida, Daniel; Yanez, Jose M.

Abstract

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, similar to 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.

Published in

Scientific Reports
2020, volume: 10, number: 1, article number: 11514
Publisher: NATURE PUBLISHING GROUP

Authors' information

Cadiz, Maria
Univ Chile
López, Maria-Eugenia (López, María-Eugenia)
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
López, Maria-Eugenia (López, María-Eugenia)
University of Chile
Diaz-Dominguez, Diego
Univ Chile
Caceres, Giovanna
Univ Chile
Yoshida, Grazyella M.
Univ Chile
Gomez-Uchida, Daniel
Univ Concepcion
Yanez, Jose M.
Univ Chile

UKÄ Subject classification

Fish and Aquacultural Science

Publication Identifiers

DOI: https://doi.org/10.1038/s41598-020-68064-5

URI (permanent link to this page)

https://res.slu.se/id/publ/107126