De novo SNP markers development for the Neotropical gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing-based genotyping
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We generated for the first time nuclear SNP loci for the commercially exploited gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing. We implemented double-digest-Restriction-Associated-DNA-based de novo SNP genotyping for 30 individuals (Orinoco and Amazon basins) using the IonTorrent PGM. It was analyzed the sequence reads using the Stacks pipeline. We detected 18,772 tags with 6170 polymorphic sites and 91 SNPs recovered for both basins. A significant divergence in the allele frequencies was observed between basins for some of those SNPs. Information about diversity and other statistics index are presented for these SNPs. Some of them (23) could be useful for population and conservation genetics of this species using traditional PCR-based genotyping methods.
KeywordsSNPs Gilded catfish IonTorrent PGM Population/conservation genomics
This study was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) of Brazil, and the Departamento Administrativo de Ciencia, Tecnolgía e Innovación (COLCIENCIAS) of Colombia (code: 490682/2010-3). In Brazil, permission to collect tissue samples was Granted by SISBIO/IBAMA, and in Colombia by ANLA (to Universidad de los Andes). This study is part of JGM’s doctoral thesis in the Biotechnology program of UFAM. JGM was supported by a Beca de Formación doctoral scholarship Francisco José de Caldas from COLCIENCIAS, and IPF and TH were supported by a Bolsa de Pesquisa scholarship from CNPq during this study.
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Conflict of interest
The authors declare that they have no conflict of interest.
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