Development of SSR markers from the muscle transcriptome of the Amur
sleeper, Perccottus glenii
Abstract
The Amur sleeper (Perccottus glenii), which inhabits the Far East of
Eurasia, can adapt to cold waters, including frozen water bodies.
Therefore, this fish is a vertebrate model for research on the mechanism
of cryopreservation in whole bodies. Moreover,the fish is one of the
most invasive fish species. However, about the evolution mechanism of
the fish resistance to cold and genetic variation in native and
non-native is not clear. Currently, only few genetic markers have been
developed and no detailed genetic information is available for P.
glenii. Here, we characterized a large set of genome-wide
gene-associated microsatellite markers for P. glenii from muscle
transcriptome. A total of 134,865,569 clean reads of 39.98 Gb
nucleotides were generated. From these, 11,117 microsatellites were
screened based on RNA-seq > 1 kb unigenes and 7802
sequences with enough flanking regions were used for designing SSR
primers. We randomly chose 150 microsatellites for further
characterization. Of these, 94 were successfully amplified and 91 were
found to be polymorphic in at least one of the two populations assessed,
which indicated the high quality of the generated transcripts. Moderate
differentiation was observed between the populations, indicating the
need for protecting the fish before loss of genetic diversity. Based on
the microsatellites that were successfully validated, 4733 SSR markers
could be developed; this large set of markers would provide a powerful
genome-wide tool for future population or ecological studies.