De novo SNP markers development for the Neotropical gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing-based genotyping

• Published in: Conservation genetics resources Vol. 8; no. 4; pp. 415 - 418
• Main Authors: Martínez, José Gregorio, Caballero-Gaitán, Susana Josefina, Sánchez-Bernal, Diana, de Assunção, Enedina Nogueira, Astolfi-Filho, Spartaco, Hrbek, Tomas, Farias, Izeni Pires
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.12.2016; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Basins; Biodiversity; Biomedical and Life Sciences; Brachyplatystoma rousseauxii; Conservation Biology/Ecology; Conservation genetics; Divergence; DNA sequencing; Ecology; Evolutionary Biology; Gene frequency; Genotyping; Life Sciences; Next-generation sequencing; Plant Genetics and Genomics; Population genetics; Single-nucleotide polymorphism; Technical Note; SNPs; Population/conservation genomics; Gilded catfish; IonTorrent PGM
• ISSN: 1877-7252; 1877-7260
• DOI: 10.1007/s12686-016-0584-1

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.