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Marine Biology

, 163:223 | Cite as

Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii

  • Cecilia Villacorta-RathEmail author
  • Irina Ilyushkina
  • Jan M. Strugnell
  • Bridget S. Green
  • Nicholas P. Murphy
  • Stephen R. Doyle
  • Nathan E. Hall
  • Andrew J. Robinson
  • James J. Bell
Original paper

Abstract

Recent advances in next-generation sequencing have enhanced the resolution of population genetic studies of non-model organisms through increased marker generation and sample throughput. Using double digest restriction site-associated DNA sequencing (ddRADseq), we investigated the population structure of the commercially important southern rock lobster, Jasus edwardsii, in Australia and New Zealand with the aim of identifying a panel of SNP markers that could be used to trace country of origin. Four ddRADseq libraries comprising a total of 88 individuals were sequenced on the Illumina MiSeq platform, and demultiplexed reads were used to create a reference catalog of loci. Individual reads were then mapped to the reference catalog, and variant calling was performed. We have characterized two single-nucleotide polymorphism (SNP) panels comprised in total of 656 SNPs. The first panel contained 535 neutral SNPs and the second, 121 outlier SNPs that were characteristic of being putatively under selection. Both neutral and outlier SNP panels showed significant differentiation between the two countries, with the outlier loci demonstrating much larger F ST values (F ST outlier SNP panel = 0.134, P < 0.0001; F ST neutral SNP panel = 0.022, P < 0.0001). Assignment tests performed with the outlier SNP panel allocated 100 % of the individuals to country of origin, demonstrating the usefulness of these markers for food traceability of J. edwardsii.

Keywords

Effective Population Size Lamp Assay Outlier Locus Pelagic Larval Duration Heterozygote Excess 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

We would like to thank Gary Carlos (University of Tasmania), Colin Fry (University of Tasmania), Daniel Ierodiaconou (Deakin University), Andrew Kent and Kent Way for field assistance and sample collection in Australia. Thanks to Daryl Sykes (New Zealand Rock Lobster Industry Council) for organizing all sample collections in New Zealand and Don Nelson (New Zealand Rock Lobster Industry Council) and Dr. Debbie Freeman (Department of Conservation, New Zealand) for collecting samples in New Zealand. Thanks for laboratory assistance to Mel Best, Adam Smolenski and Cecilia Carrea (University of Tasmania). We also thank Michael Amor and Laura Woodings (La Trobe University) who helped developing the ddRADseq protocol and the rad-loci pipeline, respectively. Special thanks to Karen J Miller who contributed to the original project idea. We would like to thank the editor, Cristian E. Hernández and one anonymous reviewer for their constructive suggestions.

Funding

Funding for this research was provided by an Australian Research Council Linkage Project grant (Project No. LP120200164) from BSG, an Australian Research Council Discovery Project grant (Project No. DP150101491) awarded to JMS NPM, BSG and JJB, a Fisheries Research and Development Corporation grant 2015-025 as well as the Tasmanian Rock Lobster Fisherman’s Association, the Department of Primary Industries, Park Water and Environment (Tasmania, Australia), Seafood Innovations Limited (Wellington, New Zealand) and the New Zealand Rock Lobster Industry Council.

Data accessibility

Reference loci sequences available through Dryad, doi: 10.5061/dryad.5c960.

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

All applicable international, national and/or institutional guidelines for the care and use of animals were followed.

Supplementary material

227_2016_3000_MOESM1_ESM.docx (4.2 mb)
Supplementary material 1 (DOCX 4283 kb)
227_2016_3000_MOESM2_ESM.docx (65 kb)
Supplementary material 2 (DOCX 65 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Cecilia Villacorta-Rath
    • 1
    Email author
  • Irina Ilyushkina
    • 2
  • Jan M. Strugnell
    • 3
  • Bridget S. Green
    • 1
  • Nicholas P. Murphy
    • 3
  • Stephen R. Doyle
    • 4
  • Nathan E. Hall
    • 5
    • 6
  • Andrew J. Robinson
    • 5
    • 6
  • James J. Bell
    • 2
  1. 1.Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartAustralia
  2. 2.School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
  3. 3.Department of Ecology, Environment and Evolution, School of Life SciencesLa Trobe UniversityMelbourneAustralia
  4. 4.Department of Animal, Plant and Soil Sciences, School of Life SciencesLa Trobe UniversityMelbourneAustralia
  5. 5.Genomics Research PlatformLa Trobe UniversityMelbourneAustralia
  6. 6.Life Sciences Computation CentreVictorian Life Sciences Computation InitiativeMelbourneAustralia

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