Development of 61 new transcriptome-derived microsatellites for the Atlantic herring (Clupea harengus)

Next generation sequencing has made it possible to develop large numbers of molecular markers for non-model organisms quickly and at relatively low cost. We identified and tested 155 potential new transcriptome-derived microsatellite markers for the Atlantic herring (Clupea harengus) using 454-sequencing. By testing the markers in five individuals from each of eight populations, we found that 61 of these markers are potentially useful. Further tests in 25 individuals from each of three populations indicate that 50 of these markers are polymorphic, highly reliable for scoring and show no indication of consistent heterozygote deficiency or linkage disequilibrium. Transcriptome-based microsatellite markers may prove particularly useful for studies of adaptation and population differentiation in species such as herring which live in highly variable habitats.