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

María I Cádiz,Daniel Gomez-Uchida,José M Yáñez,María E López,Giovanna Cáceres,Diego Díaz-Domínguez,Grazyella M Yoshida

doi:10.1038/s41598-020-68064-5

María I Cádiz, Daniel Gomez-Uchida + Show 5 more

Open Access

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

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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 FST 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 FST 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.

Highlights

Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production
Only 1.3 million variants were shared among all three populations and 280 individuals were kept after quality control, which were used for the following analysis (23 individuals with call rate below 80% and 23 with identity by descent (IBD) > 0.5 were removed)
Overall for strain A, we found a total of 647 genes, which were classified in 53 functional terms, including Biological Processes (BP, 40 terms), Cellular Components (CC, 6 terms), Molecular Function (MF, 2 terms) and the KEGG pathways (5 terms)

Summary

Introduction

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. 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. Nile tilapia can be considered to have reached the level of true domestication (level 5), according to the five categories of the domestication p rocess[11,12] This process may have shaped the genetic diversity of Nile tilapia, leaving signatures in their genomes that can be traced. Methods derived from EHH are used to detect recent positive selection withinpopulation (iHS) and between-populations (Rsb)[21], whereas methods based on FST are expected to identify older selection events[22] between-populations[23]

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