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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-12

AUTHORS

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, Zhanjiang Liu, Luiz Lehmann Coutinho

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. More... »

PAGES

46112

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/srep46112

    DOI

    http://dx.doi.org/10.1038/srep46112

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1084538177

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28387238


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