eCite Digital Repository

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

Citation

Villacorta-Rath, C and Ilyushkina, I and Strugnell, JM and Green, BS and Murphy, NP and Doyle, SR and Hall, NE and Robinson, AJ and Bell, JJ, Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii, Marine Biology, 163 Article 223. ISSN 0025-3162 (2016) [Refereed Article]

Copyright Statement

Copyright 2016 Springer-Verlag Berlin Heidelberg

DOI: doi:10.1007/s00227-016-3000-1

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 FST values (FST outlier SNP panel = 0.134, P < 0.0001; FST 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.

Item Details

Item Type:Refereed Article
Keywords:outlier SNPs, food traceability, southern rock lobster, Jasus edwardsii
Research Division:Agricultural and Veterinary Sciences
Research Group:Fisheries Sciences
Research Field:Aquatic Ecosystem Studies and Stock Assessment
Objective Division:Environment
Objective Group:Flora, Fauna and Biodiversity
Objective Field:Marine Flora, Fauna and Biodiversity
Author:Villacorta-Rath, C (Ms Cecilia Villacorta Rath)
Author:Green, BS (Associate Professor Bridget Green)
ID Code:111957
Year Published:2016
Funding Support:Australian Research Council (LP120200164)
Web of Science® Times Cited:1
Deposited By:Sustainable Marine Research Collaboration
Deposited On:2016-10-18
Last Modified:2017-11-06
Downloads:0

Repository Staff Only: item control page