Identification of species-specific microsatellite markers in three Siniperca species by RNA-Seq

Siniperca chuatsi, Siniperca kneri, and Siniperca scherzeri are three most important perciform aquaculture fish species in China. Due to their morphological similarities, it is difficult to distinguish them, especially at juvenile stage. Furthermore, interspecies hybridization between them has been performed for economic benefit, while makes species identification more difficultly. Therefore, species-specific genetic markers are needed for species identification among them. In this study, a total of 991 SSR primer pairs were identified in 8923 SSR-containing sequences (transcripts >1 kb) by RNA-Seq. Then, 566 loci were randomly selected for primer synthesis and 394 of which were successfully amplified in S. chuatsi. All the non-polymorphic loci (308) were evaluated among three Siniperca species, and 18 species-specific microsatellite markers were finally validated among three Siniperca species. These species-specific microsatellite markers would not only easily discriminate these three Siniperca species at juvenile stage, but also effectively monitor the statuses of hybridization and introgression for germplasm resources protection.