Abstract
BackgroundMeiotic 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.ResultsWe 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.ConclusionsUsing RAD sequencing and EST-based SNP assays we successfully generated the first high density linkage map for sockeye salmon.
Highlights
Meiotic maps are a key tool for comparative genomics and association mapping studies
Over 3.5 million restriction site associated DNA sequencing (RAD) tag sequences were generated in both the male and female parents (Table 2). These RAD tag sequences as well as the RAD tag sequences from the offspring were deposited in the NCBI short read archive (Accession: SRA051991.1)
Here we present a first-pass meiotic map for sockeye salmon that contains 29 linkage groups, the number expected based upon the sockeye salmon karyotype (2n = 58) [42]
Summary
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. 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. Meiotic maps have been used to unravel the interactions among linkage, pseudolinkage, homeologous pairing, and interference in duplicated teleosts for more than three decades [7,8,9]. Meiotic maps have become important for comparative genomics [10] and association mapping studies [11]
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