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Front. Genet. | doi: 10.3389/fgene.2019.00745

Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

 Grazyella M. Yoshida1, 2,  Agustin Barria1, Giovanna Cáceres1, Katharina Correa2,  Ana Jedlicki1, María I. Cadiz1, Jean P. Lhorente2 and  José M. Yáñez1, 2, 3*
  • 1University of Chile, Chile
  • 2Benchmark Genetics Chile, Chile
  • 3Nucleus Millennium Salmonids Invaders, Invasal, Chile

Nile tilapia (Oreochromis niloticus) is one of the most produced farmed fish in the world and represents an important source of protein for human consumption. Farmed Nile tilapia populations are increasingly based on genetically improved stocks, which have been established from admixed populations. To date, there is scarce information about the population genomics of farmed Nile tilapia, assessed by dense single nucleotide polymorphism (SNP) panels. The patterns of linkage disequilibrium (LD) may affect the success of genome-wide association studies (GWAS) and genomic selection and can also provide key information about demographic history of farmed Nile tilapia populations. The objectives of this study were to provide further knowledge about the population structure and LD patterns, as well as, estimate the effective population size (Ne) for three farmed Nile tilapia populations, one from Brazil (POP A) and two from Costa Rica (POP B and POP C). A total of 55, 56 and 57 individuals from POP A, POP B and POP C, respectively, were genotyped using a 50K SNP panel selected from a whole-genome sequencing (WGS) experiment. Two principal components explained about 20% of the total variation and clearly discriminated between the three populations. Population genetic structure analysis showed evidence of admixture, especially for POP C. The contemporary Ne values calculated based to LD values, ranged from 71 to 141. No differences were observed in the LD decay among populations, with a rapid decrease of r2 when increasing inter-marker distance. Average r2 between adjacent SNP pairs ranged from 0.03 to 0.18, 0.03 to 0.17 and 0.03 to 0.16 for POP A, POP B and POP C, respectively. Based on the number of independent chromosome segments in the Nile tilapia genome, at least 4.2 K SNP are required for the implementation of GWAS and genomic selection in farmed Nile tilapia populations.
Keywords

Keywords: effective population size (Ne), Genomic prediction, GWAS, Oreochromis niloticus, population structure

Received: 13 Jan 2019; Accepted: 16 Jul 2019.

Copyright: © 2019 Yoshida, Barria, Cáceres, Correa, Jedlicki, Cadiz, Lhorente and Yáñez. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. José M. Yáñez, University of Chile, Santiago, 3580000, Santiago Metropolitan Region (RM), Chile, jmayanez@uchile.cl