Development of EST-SSR PCR primers within three North Pacific rockfishes of the genus Sebastes

Abstract

Severe declines in abundance of Pacific Ocean Perch (Sebastes alutus) and other rockfishes have led to catch restrictions along the US west coast. The stock structure of many important commercial members of Sebastes spp remains a major source of uncertainty in stock assessment models. Here we report development of PCR primer pairs from 13 novel EST-SSR loci obtained from public Sebastes EST databases, and redesigned primer pairs from six published EST-SSR loci. Amplification and diversity data from these and 27 published EST-SSR loci are reported for S. polyspinis, S. alutus, and two cryptic sub-types of S. aleutianus. Loci were moderately polymorphic, with heterozygosities averaging 0.44, and allele number averaging 5.2 across all loci and species. Divergence between the two S. aleutianus sub-types was high (mean F ST = 0.33) allowing for unambiguous identification. The loci will be informative for resolving stock structure issues and possible local adaptation along the species’ ranges.