Isolation and characterization of 17 polymorphic microsatellite loci with tri- and tetra-nucleotide repeat motifs for Ayu (Plecoglossus altivelis) using next-generation sequencing.

BACKGROUND: Ayu or sweetfish, Plecoglossus altivelis, an amphidromous fish ranging in the northwestern Pacific, is economically important inland fisheries and aquaculture resources. Genetic characterization of wild Ayu and derived culture seeds with competent molecular genetic markers is still insufficient for their sustainable use. Microsatellite DNA markers with larger repeat motifs (e.g. tri- and tetra-nucleotide motifs) are convenient and accurate compared with those having mono- and di-nucleotide motifs, but the latter motifs characterized most Ayu microsatellite markers developed previously. METHODS AND RESULTS: Here, we isolated and characterized 17 polymorphic microsatellite DNA markers with tri- and tetra-nucleotide repeat motif using next-generation sequencing. Alleles per locus varied from 6 to 23. The observed and expected heterozygosities ranged from 0.542 to 1.000 and 0.709 to 0.951, respectively. Polymorphic information content (PIC) of 15 out of the 17 loci were high (≧ 0.700), suggesting them to be highly informative. Twelve of the 17 loci were used for preliminary assignment test among three collections, and successfully allocated the examined fish to the original populations. CONCLUSION: The novel polymorphic microsatellite markers developed herein will be useful to examine the genetic diversity and population structure of wild Ayu and the effect of seed transplantation on native populations, providing a tool for conservation and sustainable adaptive management of this species.

Mitochondrial DNA analysis reveals a unique population structure of the amphidromous sculpin Cottus pollux middle-egg type (Teleostei: Cottidae).

In this study, we examined nucleotide sequences from the first half of the mitochondrial control region gene to test for genetic differentiation in an amphidromous sculpin, Cottus pollux middle-egg type (ME) (Cottidae), obtained from 19 localities across its distribution range. Spatial analysis of molecular variance revealed five divergent groups of related haplotypes among this populations. Analysis with Migrate software revealed that gene flow was quite restricted among the groups, although it occurred practically between neighboring groups. It has previously been reported that the population structure among the amphidromous fishes of the various islands is low or non-existent, and is characterized mainly by the duration of the pelagic larval life. However, the present study demonstrated that the various C. pollux ME populations were different both among the islands, and within the island of the Japanese Archipelago. Our finding indicate that the unique population structure of C. pollux ME may be influenced not only by the extent of the pelagic larval phase of the species but also by the seasonal differentiation of its dispersal phase.