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

被引：2
|
作者：
Martinez, Jose Gregorio [1 ,2 ,3 ]
Machado, Valeria Nogueira [1 ]
Caballero-Gaitan, Susana J. [2 ]
Freitas Santos, Maria da C. [1 ,3 ]
Alencar, Rodrigo Maciel [3 ]
Escobar L, Maria Doris [4 ]
Hrbek, Tomas [1 ]
Farias, Izeni Pires [1 ]
机构：
[1] Univ Fed Amazonas, Inst Ciencias Biol, Dept Genet, Lab Evolucao & Genet Anim,Programa Posgrad Biodiv, Ave Rodrigo Octavio Jordao Ramos 3000, BR-69077000 Manaus, Amazonas, Brazil
[2] Univ Los Andes, Dept Ciencias Biol, Fac Ciencias, Lab Ecol Mol Vertebrados Acuat, Cra 1 18A-12,Codigo Postal 4-72, Bogota, Colombia
[3] Univ Estado Amazonas, Grp Pesquisa Genet Mol & Citogenet, Programa Posgrad Mestrado Biotecnol & Recursos Na, Lab Proteom & Genom, BR-69065001 Manaus, Amazonas, Brazil
[4] Univ Fed Amazonas, Programa Posgrad Recursos Pesqueiros, BR-69065001 Manaus, Amazonas, Brazil
来源：
CONSERVATION GENETICS RESOURCES | 2017年 / 9卷 / 01期
关键词：
De novo SNPs development; Conservation/population genomics; IonTorrent PGM; Orinoco/Amazon basins; AMAZON RIVER; CHARACIFORMES; FLOODPLAIN;
D O I：
10.1007/s12686-016-0610-3
中图分类号：
X176 [生物多样性保护];
学科分类号：
090705 ;
摘要：
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.
引用
收藏
页码：29 / 33
页数：5
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