Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification
Laura Taillebois,
Christine Dudgeon,
Safia Maher,
David A. Crook,
Thor M. Saunders,
Diane P. Barton,
Jonathan A. Taylor,
David J. Welch,
Stephen J. Newman,
Michael J. Travers,
Richard J. Saunders,
Jennifer Ovenden
Affiliations
Laura Taillebois
Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
Christine Dudgeon
Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
Safia Maher
Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
David A. Crook
Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
Thor M. Saunders
Fisheries Research, Northern Territory Department of Primary Industries and Fisheries, Berrimah, Northern Territory, Australia
Diane P. Barton
Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
Jonathan A. Taylor
Fisheries Research, Northern Territory Department of Primary Industries and Fisheries, Berrimah, Northern Territory, Australia
David J. Welch
C2O Fisheries, Cairns, Queensland, Australia
Stephen J. Newman
Western Australian Fisheries and Marine Research Laboratories, Department of Fisheries, Government of Western Australia, North Beach, Western Australia, Australia
Michael J. Travers
Western Australian Fisheries and Marine Research Laboratories, Department of Fisheries, Government of Western Australia, North Beach, Western Australia, Australia
Richard J. Saunders
Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Douglas, Queensland, Australia
Jennifer Ovenden
Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.
