454 Sequencing of Part of the Atlantic Cod Gadus morhua Genome: a Source of Large Numbers of Microsatellite and SNP Loci

Microsatellite DNA loci are currently the markers of choice for most molecular genetic applications. However there is increasing interest in the deployment of single nucleotide polymorphisms (SNPs) for such studies. Traditional microsatellite locus isolation and characterisation has relied on the sequencing of standard or enriched libraries whereas SNP discovery has primarily been based on the mining of existing sequences. Unfortunately, extensive sequence information is often only available for model organisms, and acquisition of such information in other species can be time consuming, expensive and redundant (due to ascertainment bias). By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, we demonstrate the rapid and economical isolation of over 25 000 potential SNPs and more than 6000 putative microsatellite loci from approximately 2% of the genome of the non-model teleost, Atlantic cod (Gadus morhua) from the Celtic Sea, south of Ireland. A small scale validation of markers indicated that 80% (11/14) of SNP loci and 40% (6/15) of the microsatellite loci could be amplified and showed variability. Our results clearly show that small scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and/or study questions.