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Front. Genet. | doi: 10.3389/fgene.2018.00046

Genetic characterization of the fish Piaractus brachypomus by microsatellites derived from transcriptome sequencing

  • 1Aquaculture Center of Unesp, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Brazil
  • 2Universidade de Santiago de Compostela, Spain
  • 3School of Sciences, São Paulo State University (Unesp), Brazil

The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: 1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and 2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, 8 markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The FST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme.

Keywords: Aquaculture, NGS, Pirapitinga, Serrasalmidae, Genetic structure

Received: 01 Sep 2017; Accepted: 31 Jan 2018.

Edited by:

Rodrigo A. Torres, Universidade Federal de Pernambuco, Brazil

Reviewed by:

Pedro M. Galetti Jr, Federal University of São Carlos, Brazil
Maria Raquel M. Coimbra, Federal Rural University of Pernambuco, Brazil  

Copyright: © 2018 Jorge, Mastrochirico-Filho, Hata, Mendes, Ariede, Freitas, Vera, Porto-Foresti and Hashimoto. 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 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: MD, PhD. Diogo T. Hashimoto, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Aquaculture Center of Unesp, São Paulo, SP, Brazil, diogo@caunesp.unesp.br