Development of polymorphic microsatellite markers in bocaccio rockfish

The bocaccio rockfish, Sebastes paucispinis, is a species of concern on the west coast of the United States. In order to further resolve the species’ population structure, thirty microsattellite loci were developed and scored for polymorphism and optimized for multiplex amplification. A total of 1400 congeneric expressed sequence tags (EST) containing microsatellites were obtained by GenBank. Translated ESTs were Blasted against several protein databases, and those that consistently matched metabolic proteins were used to design PCR primers. In order to predict intron positions and lengths, the EST sequences were matched against the Spinachia or Tetradon genome sequence available on the UCSC genome browser. Of 41 EST-SSR loci, 73% amplified and 27% were polymorphic.  A total of 38 extant anonymous microsatellite loci were also scored for amplification and polymorphisms. Of these 95% amplified and 63% were polymorphic. These loci will be useful for analyses of population structure and demographic parameter estimation.