Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844).

BACKGROUND: The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of the population genetic structure of this species is limited by the low number of molecular markers currently described. METHODS AND RESULTS: In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16 (average = 7.89). The results showed that, the polymorphism information content (PIC) of these simple sequence repeat (SSR) loci varied from 0.254 to 0.888. The observed heterozygosity (HO) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (HE) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05). CONCLUSIONS: These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate and other closely related species.

Robust DNase activity of the ooplasm can act as a gametic transfection barrier in rainbow trout.

In this study, we evaluated DNase activity of rainbow trout oocyte using an in vitro and in vivo study. First, synthetic single strand and natural double strand DNA from Eukaryotic and prokaryotic sources as well as naked DNA were in vitro incubated with the oocyte cytoplasm. Results showed that the DNase activity of rainbow trout oocyte is strong enough to degrade any type of DNA at the onset of the incubation. Then, we evaluated if similar to the mammalian species, dead spermatozoa from rainbow trout can protect exogenous DNA from oocyte DNases. A series of dead spermatozoa was incubated with pDB2, carrying EGFP transgene, for 30 min followed by the ooplasm treatment for an additional 30 min. Not only did oocyte DNases completely degrade the exogenous DNA, but also it degraded the compact genome of spermatozoa. In conclusion, in vitro results clearly showed that strong DNase activity of ooplasm could degrade any types of foreign DNAs including oligonucleotides and intensively compact sperm genome. The strong DNase activity of rainbow trout ooplasm could be a stumbling block for genetic modification using plasmids in salmonids.