Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

José De Ribamar Da Silva Nunes, Shikai Liu, Fábio Pértille, Caio Augusto Perazza, Priscilla Marqui Schmidt Villela, Vera Maria Fonseca De Almeida-Val, Alexandre Wagner Silva Hilsdorf, Zhanjian "John" Liu, Luiz Lehmann Coutinho

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish (US)
Article number46112
JournalScientific Reports
Volume7
DOIs
StatePublished - Apr 7 2017
Externally publishedYes

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Colossoma macropomum
genotyping
single nucleotide polymorphism
chromosome mapping
linkage groups
Orinoco River
genomics
Amazon River
Danio rerio
genetic resources
genetic improvement
gene frequency
linkage (genetics)
indigenous species
breeding

ASJC Scopus subject areas

  • General

Cite this

Da Silva Nunes, J. D. R., Liu, S., Pértille, F., Perazza, C. A., Villela, P. M. S., De Almeida-Val, V. M. F., ... Coutinho, L. L. (2017). Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing. Scientific Reports, 7, [46112]. https://doi.org/10.1038/srep46112

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing. / Da Silva Nunes, José De Ribamar; Liu, Shikai; Pértille, Fábio; Perazza, Caio Augusto; Villela, Priscilla Marqui Schmidt; De Almeida-Val, Vera Maria Fonseca; Hilsdorf, Alexandre Wagner Silva; Liu, Zhanjian "John"; Coutinho, Luiz Lehmann.

In: Scientific Reports, Vol. 7, 46112, 07.04.2017.

Research output: Contribution to journalArticle

Da Silva Nunes, JDR, Liu, S, Pértille, F, Perazza, CA, Villela, PMS, De Almeida-Val, VMF, Hilsdorf, AWS, Liu, ZJ & Coutinho, LL 2017, 'Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing', Scientific Reports, vol. 7, 46112. https://doi.org/10.1038/srep46112
Da Silva Nunes, José De Ribamar ; Liu, Shikai ; Pértille, Fábio ; Perazza, Caio Augusto ; Villela, Priscilla Marqui Schmidt ; De Almeida-Val, Vera Maria Fonseca ; Hilsdorf, Alexandre Wagner Silva ; Liu, Zhanjian "John" ; Coutinho, Luiz Lehmann. / Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing. In: Scientific Reports. 2017 ; Vol. 7.
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