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

José Gregorio Martínez; Valéria Nogueira Machado; Susana J. Caballero-Gaitán; Maria da C.Freitas Santos; Rodrigo Maciel Alencar; Maria Doris Escobar L; Tomas Hrbek; Izeni Pires Farias

doi:10.1007/s12686-016-0610-3

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

José Gregorio Martínez
, Valéria Nogueira Machado
, Susana J. Caballero-Gaitán
, Maria da C.Freitas Santos
, Rodrigo Maciel Alencar
, Maria Doris Escobar L
, Tomas Hrbek
, Izeni Pires Farias

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Pages (from-to)	29-33
Number of pages	5
Journal	Conservation Genetics Resources
Volume	9
Issue number	1
DOIs	https://doi.org/10.1007/s12686-016-0610-3
State	Published - Mar 1 2017
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2016, Springer Science+Business Media Dordrecht.

ASJC Scopus Subject Areas

Ecology, Evolution, Behavior and Systematics
Genetics

Keywords

Conservation/population genomics
De novo SNPs development
IonTorrent PGM
Orinoco/Amazon basins

Access to Document

10.1007/s12686-016-0610-3

Cite this

Martínez, J. G., Machado, V. N., Caballero-Gaitán, S. J., Santos, M. D. C. F., Alencar, R. M., Escobar L, M. D., Hrbek, T., & Farias, I. P. (2017). SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping. Conservation Genetics Resources, 9(1), 29-33. https://doi.org/10.1007/s12686-016-0610-3

SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping. / Martínez, José Gregorio; Machado, Valéria Nogueira; Caballero-Gaitán, Susana J. et al.
In: Conservation Genetics Resources, Vol. 9, No. 1, 01.03.2017, p. 29-33.

Research output: Contribution to journal › Article › peer-review

Martínez, JG, Machado, VN, Caballero-Gaitán, SJ, Santos, MDCF, Alencar, RM, Escobar L, MD, Hrbek, T & Farias, IP 2017, 'SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping', Conservation Genetics Resources, vol. 9, no. 1, pp. 29-33. https://doi.org/10.1007/s12686-016-0610-3

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abstract = "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. ",

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

Abstract

Bibliographical note

ASJC Scopus Subject Areas

Keywords

Access to Document

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