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Open Access Highly Accessed Research article

Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing

Meredith V Everett1*, Michael R Miller2 and James E Seeb1*

Author affiliations

1 School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195-5020, USA

2 Institute of Molecular Biology and Institute of Neuroscience, 1229 University of Oregon, Eugene, OR 97403-1229, USA

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Citation and License

BMC Genomics 2012, 13:521  doi:10.1186/1471-2164-13-521

Published: 3 October 2012

Abstract

Background

Meiotic maps are a key tool for comparative genomics and association mapping studies. Next-generation sequencing and genotyping by sequencing are speeding the processes of SNP discovery and the development of new genetic tools, including meiotic maps for numerous species. Currently there are limited genetic resources for sockeye salmon, Oncorhynchus nerka. We develop the first dense meiotic map for sockeye salmon using a combination of novel SNPs found in restriction site associated DNA (RAD tags) and SNPs available from existing expressed sequence tag (EST) based assays.

Results

We discovered and genotyped putative SNPs in 3,430 RAD tags. We removed paralogous sequence variants leaving 1,672 SNPs; these were combined with 53 EST-based SNP genotypes for linkage mapping. The map contained 29 male and female linkage groups, consistent with the haploid chromosome number expected for sockeye salmon. The female map contains 1,057 loci spanning 4,896 cM, and the male map contains 1,118 loci spanning 4,220 cM. Regions of conservation with rainbow trout and synteny between the RAD based rainbow trout map and the sockeye salmon map were established.

Conclusions

Using RAD sequencing and EST-based SNP assays we successfully generated the first high density linkage map for sockeye salmon.

Keywords:
RAD sequencing; Meiotic map; Linkage map; SNP