Development of 21 microsatellite markers for the threatened Yarra pygmy perch (Nannoperca obscura) through 454 shot-gun pyrosequencing
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Using a next generation sequencing approach, a set of 21 new microsatellites loci was developed from the threatened freshwater fish Yarra pygmy perch (YPP) Nannoperca obscura (Percichthyidae). All markers were successfully genotyped using 28 YPP kept in captivity. These animals represent an entire population rescued from the lower Murray-Darling Basin in Australia before its habitat dried out. As expected due to the critical conservation status of the population, we observed low genetic variation across most loci (mean number of alleles per locus = 2.76; mean heterozygosity = 0.28). No deviations from Hardy–Weinberg equilibrium or linkage disequilibrium were detected and only one locus (Nob30) showed evidence for null alleles. These molecular markers represent important resources for the ongoing YPP captive breeding program, and for upcoming restoration and landscape genetic studies of this species.
KeywordsMicrosatellite development Next Generation DNA sequencing Nannoperca obscura Freshwater fish
Funding for this study was provided by the Australian Research Council (LP100200409 to Beheregaray, Harris & Adams). Additional support was received by Department of Environment and Natural Resources SA, SA Museum, SA Murray Darling NRMB, PIRSA Fisheries and NFASA. We thank Mark Adams for providing tissue samples, Mike Gardner and Minami Sasaki for data analysis and laboratory assistance. DC is grateful to CAPES, for his postdoctoral fellowship (# 4095-09-0).
- Carvalho D, Beheregaray L (2010) Rapid development of microsatellites for the endangered neotropical catfish Conorhynchus conirostris using a modest amount of 454 shot-gun pyrosequencing. Conserv Genet Resour pp 1–3. doi: 10.1007/s12686-010-9365-4
- Hall A, Higham J, Hammer M, Brice C, Zampatti B (2009) Drought action plan for south australian murray-darling basin threatened freshwater fish populations 2009–2010; rescue to recovery. AdelaideGoogle Scholar
- Hammer, M. (2008). Status review of wild and captive Yarra pygmy perch in the Murray-Darling Basin. Report to department for environment and heritage, South Australian Government. Aquasave Consultants, Adelaide, p 27Google Scholar
- Hammer M, Wedderburn S, van Weenan J (2009) Action plan for South Australian freshwater fishes. Native Fish Australia (SA) Inc., Adelaide, p 206Google Scholar
- Holleley CE, Geerts PG (2009) multiplex manager 1.0: A cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46 (7): 511–517. doi: 10.2144/000113156
- IUCN 2010. IUCN Red List of Threatened Species. Version 2010.4. < http://www.iucnredlist.org > . Downloaded on 27 Oct 2010