High-Throughput Single Nucleotide Polymorphism (SNP) Discovery and Validation Through Whole-Genome Resequencing in Nile Tilapia (Oreochromis niloticus)
Nile tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world. Currently, the estimation of genetic merit of breeders is typically based on genealogical and phenotypic information. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to measure into the breeding goal. Thus, single nucleotide polymorphisms (SNPs) are required to investigate phenotype–genotype associations and determine the genomic basis of economically important traits. We performed de novo SNP discovery in three different populations of farmed Nile tilapia. A total of 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After applying several filtering steps, including removing SNP based on genotype and site quality, presence of Mendelian errors, and non-unique position in the genome, a total of 50,000 high-quality SNPs were selected for the development of a custom Illumina BeadChip SNP panel. These SNPs were highly informative in the three populations analyzed showing between 43,869 (94%) and 46,139 (99%) SNPs in Hardy-Weinberg Equilibrium; 37,843 (76%) and 45,171(90%) SNPs with a minor allele frequency (MAF) higher than 0.05; and 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The 50K SNP panel developed in the current work will be useful for the dissection of economically relevant traits, enhancing breeding programs through genomic selection, as well as supporting genetic studies in farmed populations of Nile tilapia using dense genome-wide information.
KeywordsSNP Oreochromis niloticus Next-generation sequencing Illumina Genomic selection
We would like to acknowledge the Aqua America and Aquacorporación Internacional for kindly providing the samples used in this work, and Gabriel Rizzato and Natalí Kunita from Aqua America and Diego Salas and José Soto from Aquacorporación International for their contribution of the samples from Brazil and Costa Rica, respectively.
J.M.Y. conceived of and designed the study, contributed to the analysis, and drafted the manuscript. G.Y. contributed to the analysis and writing. A.B. drafted the first version of the manuscript. G.C., M.E.L., and A.J. participated in the data collection, purification, and management of the samples for sequencing and genotyping. R.P., D.D., D.T., and A.M. assisted with the bioinformatics analysi and contributed to writing. J.P.L. participated in the design of the study and writing. JS and DS contributed to the collection of the samples and managmenent of populations from Costa Rica. All authors have reviewed and approved the manuscript.
This study was partially funded from CORFO grant number 14EIAT-28667 from the Government of Chile. This work was supported by the Basal grant of the Center for Mathematical Modeling AFB170001 (UMI2807 UCHILE-CNRS) and the Center for Genome Regulation Fondap Grant 15090007 Powered@NLHPC. This research was partially supported by the supercomputing infrastructure of the NLHPC (ECM-02).
Compliance with Ethical Standards
Conflict of Interest
Two commercial organizations (Aquainnovo and Illumina) were involved in the SNP identification and preparation of the manuscript. GMY and JPL were employed by Benchmark Genetics Chile during the course of the study.
- Berthelot C, Brunet F, Chalopin D et al (2014) The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun 5Google Scholar
- Cáceres G, López ME, Cádiz MI et al (2019) Fine mapping using whole-genome sequencing confirms anti-Müllerian hormone as a major gene for sex determination in farmed Nile tilapia (Oreochromis niloticus L.). G3 (Bethesda). https://doi.org/10.1534/g3.119.400297 PubMedPubMedCentralCrossRefGoogle Scholar
- Gonzalez-Pena D, Gao G, Baranski M, Moen T, Cleveland BM, Kenney PB, Vallejo RL, Palti Y, Leeds TD (2016) Genome-wide association study for identifying loci that affect fillet yield, carcass, and body weight traits in rainbow trout (Oncorhynchus mykiss). Front Genet 7:203PubMedPubMedCentralCrossRefGoogle Scholar
- Houston RD, Haley CS, Hamilton A et al (2008) Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar). 1115:1109–1115Google Scholar
- Liu Z, Liu S, Yao J et al (2016) The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun 7Google Scholar
- López ME, Benestan L, Moore J, Perrier C, Gilbey J, di Genova A, Maass A, Diaz D, Lhorente JP, Correa K, Neira R, Bernatchez L, Yáñez JM (2019a) Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins. Evol Appl 12:137–156PubMedCrossRefPubMedCentralGoogle Scholar
- Neira R (2010) Breeding in aquaculture species: genetic improvement programs in developing countries. In: Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, vol 8. Leipzig, GermanyGoogle Scholar
- Ødegård J, Moen T, Santi N et al (2014) Genomic prediction in an admixed population of Atlantic salmon (Salmo salar). Front Genet 5:1–8Google Scholar
- Palaiokostas C, Ferarreso S, Franch R, et al (2016) Genomic prediction of resistance to pasteurellosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing. G3 (Bethesda) X:1–8Google Scholar
- Rodríguez FH, Flores-Mara R, Yoshida GM et al (2019) Genome-wide association analysis for resistance to infectious pancreatic necrosis virus identifies candidate genes involved in viral replication and immune response in rainbow trout (Oncorhynchus mykiss). G3 (Bethesda). https://doi.org/10.1534/g3.119.400463 PubMedPubMedCentralCrossRefGoogle Scholar
- Webster C, Lim C (2006) Tilapia: biology, culture, and nutritionGoogle Scholar
- Yáñez JM, Houston RD, Newman S (2014) Genetics and genomics of disease resistance in salmonid species. Front Genet 5:1–13Google Scholar
- Yáñez JM, Newman S, Houston RD (2015) Genomics in aquaculture to better understand species biology and accelerate genetic progress. Front Genet 6:1–3Google Scholar
- Yáñez JM, Yoshida GM, Parra Á, Correa K, Barría A, Bassini LN, Christensen KA, López ME, Carvalheiro R, Lhorente JP, Pulgar R (2019) Comparative genomic analysis of three salmonid species identifies functional candidate genes involved in resistance to the intracellular bacterium Piscirickettsia salmonis. Front Genet 10:665PubMedPubMedCentralCrossRefGoogle Scholar
- Yoshida GM, Lhorente JP, Correa K et al (2019b) Genome-wide association study and cost-efficient genomic predictions for growth and fillet yield in Nile tilapia (Oreochromis niloticus). G3 (Bethesda) 9Google Scholar