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

Cadiz, Maria and López, Maria-Eugenia and Diaz-Dominguez, Diego and Caceres, Giovanna and Yoshida, Grazyella M. and Gomez-Uchida, Daniel and Yanez, Jose M. (2020). Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus). Scientific Reports. 10 , 11514 , 1-14
[Journal article]

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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.

Authors/Creators:Cadiz, Maria and López, Maria-Eugenia and Diaz-Dominguez, Diego and Caceres, Giovanna and Yoshida, Grazyella M. and Gomez-Uchida, Daniel and Yanez, Jose M.
Title:Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)
Year of publishing :2020
Volume:10
Article number:11514
Number of Pages:14
Publisher:NATURE PUBLISHING GROUP
ISSN:2045-2322
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Fish and Aquacultural Science
URN:NBN:urn:nbn:se:slu:epsilon-p-107126
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-107126
Additional ID:
Type of IDID
DOI10.1038/s41598-020-68064-5
Web of Science (WoS)000550582400002
ID Code:17428
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:07 Sep 2020 12:46
Metadata Last Modified:07 Sep 2020 12:46

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