SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping

• Published in: Conservation genetics resources Vol. 9; no. 1; pp. 29 - 33
• Main Authors: Martínez, José Gregorio, Machado, Valéria Nogueira, Caballero-Gaitán, Susana J., Santos, Maria da C. Freitas, Alencar, Rodrigo Maciel, Escobar L., Maria Doris, Hrbek, Tomas, Farias, Izeni Pires
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.03.2017; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Basins; Biodiversity; Biomedical and Life Sciences; Colossoma macropomum; Conservation Biology/Ecology; Ecology; Evolutionary Biology; Genotyping; Life Sciences; Next-generation sequencing; Plant Genetics and Genomics; Population genetics; Single-nucleotide polymorphism; Technical Note; Conservation/population genomics; De novo SNPs development; IonTorrent PGM; Orinoco/Amazon basins
• ISSN: 1877-7252; 1877-7260
• DOI: 10.1007/s12686-016-0610-3

We developed nuclear SNPs for the heavily overfished tambaqui/cachama negra Colossoma macropomum using next-generation sequencing-based genotyping. We created a reduced-representation library for 30 individuals from Orinoco and Amazon basins following the ddRAD methodology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the software Stacks. We detected 22,476 tags characterized by 7,181 polymorphic sites, recovering 177 loci (268 SNPs) shared between both basins. A significant difference in the allelic frequencies was observed between basins for a subset of these SNPs. Thirty-nine SNPs could be useful for conservation/population genetics using traditional PCR-based genotyping methods.