Abstract

BackgroundGenetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population. Genotyping-by-sequencing approaches such as Restriction-site Associated DNA sequencing (RAD-Seq) now enable the rapid discovery and genotyping of genome-wide SNP markers suitable for the development of dense SNP linkage maps, including in non-model organisms such as Atlantic salmon (Salmo salar). This paper describes the development and characterisation of a high density SNP linkage map based on SbfI RAD-Seq SNP markers from two Atlantic salmon reference families.ResultsApproximately 6,000 SNPs were assigned to 29 linkage groups, utilising markers from known genomic locations as anchors. Linkage maps were then constructed for the four mapping parents separately. Overall map lengths were comparable between male and female parents, but the distribution of the SNPs showed sex-specific patterns with a greater degree of clustering of sire-segregating SNPs to single chromosome regions. The maps were integrated with the Atlantic salmon draft reference genome contigs, allowing the unique assignment of ~4,000 contigs to a linkage group. 112 genome contigs mapped to two or more linkage groups, highlighting regions of putative homeology within the salmon genome. A comparative genomics analysis with the stickleback reference genome identified putative genes closely linked to approximately half of the ordered SNPs and demonstrated blocks of orthology between the Atlantic salmon and stickleback genomes. A subset of 47 RAD-Seq SNPs were successfully validated using a high-throughput genotyping assay, with a correspondence of 97% between the two assays.ConclusionsThis Atlantic salmon RAD-Seq linkage map is a resource for salmonid genomics research as genotyping-by-sequencing becomes increasingly common. This is aided by the integration of the SbfI RAD-Seq SNPs with existing reference maps and the draft reference genome, as well as the identification of putative genes proximal to the SNPs. Differences in the distribution of recombination events between the sexes is evident, and regions of homeology have been identified which are reflective of the recent salmonid whole genome duplication.

Highlights

  • Genetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population

  • The main aim of this study was to construct a high density single nucleotide polymorphisms (SNPs) linkage map of the Atlantic salmon genome using SNP markers derived from a Restriction-site Associated DNA sequencing (RAD-Seq) analysis using the SbfI restriction enzyme

  • As RAD-Seq becomes increasingly utilised as a cost- and time-efficient method of SNP discovery and genotyping in salmonid genomic studies, this map will provide a framework for orientation of the marker genotypes with the Atlantic salmon reference genome and putative candidate genes

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Summary

Introduction

Genetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population. This paper describes the development and characterisation of a high density SNP linkage map based on SbfI RAD-Seq SNP markers from two Atlantic salmon reference families. Homeologous pairing is thought to occur only at the telomeres since it takes place after homologous chromosome pairing, and has been postulated to be responsible for the distinct lack of recombination observed in male salmon [2,6]. Existing linkage maps for Atlantic salmon highlight a marked difference between the sexes in the distribution of putative crossover events; equal dispersion is observed along chromosomes in females, in contrast to telomere-specific recombination in males with little or no recombination at centromeric regions [9,10,11]. Marker order and positions are more reliably estimated in female-specific recombination maps

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