Abstract
AbstractNile 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.
Funder
Consejo Nacional de Innovación, Ciencia y Tecnología
Publisher
Springer Science and Business Media LLC
Reference88 articles.
1. Eknath, A. E. & Hulata, G. Use and exchange of genetic resources of Nile tilapia (Oreochromis niloticus). Rev. Aquac. 1, 197–213 (2009).
2. Harache, Y. Development and diversification issues in aquaculture. A historical and dynamic view of fish culture diversification. Cah. Options Méditerranéennes 59, 15–23 (2002).
3. Dias, M. A., Freitas, R. T., Arranz, S., Villanova, G. & Hilsdorf, A. Evaluation of the genetic diversity of microsatellite markers among four strains of Oreochromis niloticus. Anim. Genet. 47, 345–353 (2016).
4. FAO. The state of world fisheries and aquaculture. Food and Agriculture Organization (2014). doi:978-92-5-308275-9 ISSN1020–5500.
5. Taniguchi, N., Macaranas, J. & Pullin, S. Introgressive hybridization in cultured tilapia stocks in the Philippines. Bull. Jpn. Soc. Sci. Fish. 51, 1219–1224 (1985).