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

Author(s)

Paulo Henrique Jorge

• Document type: Master's Dissertation
• Press: Botucatu. 2016-09-22.
• Institution: Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu
• Defense date: 2016-02-25
• Advisor: Diogo Teruo Hashimoto

Abstract

The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish that occurrs in the Amazon basin and it is considered as one of the main native species used for production in aquaculture in South America. The main objectives of this study were: 1) to perform the transcriptome sequencing of P. brachypomus through Next Generation Sequencing (NGS) and then characterize a set of microsatellite markers for this species; 2) to apply microsatellite polymorphic markers for analysis of genetic variability in cultured stocks of pirapitinga. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant (nr) contigs. Of these total, 2,568 genes had similarity in the protein database nr (Genbank) and were characterized in the categories of Gene Ontology (GO), with 2,075 sequences (80.8%) annotated in GO terms. After the validation process of 30 microsatellite loci, 8 microsatellite markers showed polymorphism. The analysis of these polymorphic markers in cultured stocks revealed that the Northern fish farms had a higher genetic diversity (allele richness and heterozygosity) than the Southeastern fish farms. In addition, the AMOVA results demonstrated the highest variation present within the populations (62.5%). However, when comparing the groups according to the geographic distribution (Wild, North Fish farms and fish farms in the Southeast), it was observed a considerable variation (31.76%) among the groups. The Fst values showed there is a genetic structure among the broodstocks analyzed. Microsatellites generated by transcriptome sequencing in this study are important tools to be used in the genetic management of cultivated breeding stocks, as well to identify different gene banks, which might provide a basis for a genetic pre-breeding program in pirapitinga. (AU)

• FAPESP's process: 14/05732-2 - Transcriptome sequencing and microsatellites characterization in pirapitinga Piaractus brachypomus for analysis of genetic variability
• Grantee: Paulo Henrique Jorge
• Support Opportunities: Scholarships in Brazil - Master