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,Luiz Lehmann Coutinho,Vera Maria Fonseca De Almeida-Val,Priscilla Marqui Schmidt Villela,Zhanjiang Liu,Alexandre Wagner Silva Hilsdorf,Caio Augusto Perazza,Fábio Pértille,Shikai Liu

doi:10.1038/srep46112

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.

Highlights

IntroductionHigh-density genetic mapping can provide a genome-scan of segregation distortion within the genome[12] and can investigate genomic incompatibilities between species at the genome level[13]
Groups to build chromosomal assembly[11]
This study provides large-scale SNP markers and high-density linkage maps in tambaqui, which can be a useful resource for facilitating the tambaqui physical map construction, genome assembly, and QTL mapping to enhance genetic studies and breeding programs

Summary

Introduction

High-density genetic mapping can provide a genome-scan of segregation distortion within the genome[12] and can investigate genomic incompatibilities between species at the genome level[13] Genetic studies such as genetic linkage mapping[14], QTL mapping[15], populational genetic analysis[16], and genome-wide association studies[17] require a large number of reliable molecular markers across the genome. We applied GBS to identify large-scale SNPs and construct a high-density genetic linkage map for tambaqui, using the Illumina HiSeq 2500 platform. This study provides large-scale SNP markers and high-density linkage maps in tambaqui, which can be a useful resource for facilitating the tambaqui physical map construction, genome assembly, and QTL mapping to enhance genetic studies and breeding programs

Methods

Results

Discussion

Conclusion