title: Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing.
abstract: Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs.
authors.affiliation: Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.|The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America.|Nature and Culture Institute, Federal University of Amazon (UFAM), Benjamin Constant, Amazonas, Brazil.
authors.forename: José de Ribamar da Silva
authors.initials: JR
authors.lastname: Nunes
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America.
authors.forename: Shikai
authors.initials: S
authors.lastname: Liu
authors.affiliation: Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Fábio
authors.initials: F
authors.lastname: Pértille
authors.affiliation: Unit of Biotechnology, University of Mogi das Cruzes, P.O. Box 411, 08701-970, Mogi das Cruzes, SP, Brazil.
authors.forename: Caio Augusto
authors.initials: CA
authors.lastname: Perazza
authors.affiliation: Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Priscilla Marqui Schmidt
authors.initials: PM
authors.lastname: Villela
authors.affiliation: Brazilian National Institute for Research of the Amazon, Laboratory of Ecophysiology and Molecular Evolution, Manaus, Amazonas, Brazil.|University Nilton Lins, Aquaculture Graduate Program, Manaus, Amazonas, Brazil.
authors.forename: Vera Maria Fonseca
authors.initials: VM
authors.lastname: de Almeida-Val
authors.affiliation: Unit of Biotechnology, University of Mogi das Cruzes, P.O. Box 411, 08701-970, Mogi das Cruzes, SP, Brazil.
authors.forename: Alexandre Wagner Silva
authors.initials: AW
authors.lastname: Hilsdorf
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Luiz Lehmann
authors.initials: LL
authors.lastname: Coutinho
mesh_terms: D000818:Animals; D060125:Characiformes / Q000235:genetics*; D002874:Chromosome Mapping; D005787:Gene Frequency / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D023281:Genomics; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics
chemical_list: D005819:Genetic Markers