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

doi:10.7717/peerj.2418

Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

PeerJ. 2016 Aug 31:4:e2418. doi: 10.7717/peerj.2418. eCollection 2016.

Authors

Affiliations

¹ Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia; North Australia Marine Research Alliance, Arafura Timor Research Facility, Darwin, Northern Territory, Australia.
² Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland , Brisbane , Queensland , Australia.
³ Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin , Northern Territory , Australia.
⁴ Fisheries Research, Northern Territory Department of Primary Industries and Fisheries , Berrimah , Northern Territory , Australia.
⁵ Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia; Fisheries Research, Northern Territory Department of Primary Industries and Fisheries, Berrimah, Northern Territory, Australia.
⁶ C2O Fisheries , Cairns , Queensland , Australia.
⁷ Western Australian Fisheries and Marine Research Laboratories, Department of Fisheries, Government of Western Australia , North Beach , Western Australia , Australia.
⁸ Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Douglas, Queensland, Australia; Animal Science, Queensland Department of Agriculture and Fisheries, Brisbane, Queensland, Australia.

Abstract

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.

Keywords: Lethrinus laticaudis; Lutjanus johnii; Microsatellite markers; Multiplex panels; Next-generation sequencing; Protonibea diacanthus.

Grants and funding

This research was supported by the Fisheries Research and Development Corporation (Project 2013/017); LT received additional funding support from the North Australia Marine Research Alliance (NAMRA—AIMS/ANU/CDU/NT Government) Postdoctoral Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.