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Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Mapping the sex determination locus in the hāpuku (Polyprion oxygeneios) using ddRAD sequencing
Authors: Brown, Jeremy
Taggart, John
Bekaert, Michaël
Wehner, Stefanie
Palaiokostas, Christos
Setiawan, Alvin N
Symonds, Jane E
Penman, David
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Keywords: Hapuku
Sex chromosome
New Zealand groper
Issue Date: 10-Jun-2016
Publisher: BioMed Central
Citation: Brown J, Taggart J, Bekaert M, Wehner S, Palaiokostas C, Setiawan AN, Symonds JE & Penman D (2016) Mapping the sex determination locus in the hāpuku (Polyprion oxygeneios) using ddRAD sequencing, BMC Genomics, 17 (1), Art. No.: 448.
Abstract: Background  Hāpuku (Polyprion oxygeneios) is a member of the wreckfish family (Polyprionidae) and is highly regarded as a food fish. Although adults grow relatively slowly, juveniles exhibit low feed conversion ratios and can reach market size in 1–2 years, makingP. oxygeneiosa strong candidate for aquaculture. However, they can take over 5years to reach sexual maturity in captivity and are not externally sexually dimorphic, complicating many aspects of broodstock management. Understanding the sex determination system ofP. oxygeneiosand developing accurate assays to assign genetic sex will contribute significantly towards its full-scale commercialisation.  Results  DNA from parents and sexed offspring (n = 57) from a single family of captive bredP. oxygeneioswas used as a template for double digestion Restriction-site Associated DNA (ddRAD) sequencing. Two libraries were constructed usingSbfI–SphI andSbfI –NcoI restriction enzyme combinations, respectively. Two runs on an Illumina MiSeq platform generated 70,266,464 raw reads, identifying 19,669 RAD loci. A combined sex linkage map (1367cM) was constructed based on 1575 Single Nucleotide Polymorphism (SNP) markers that resolved into 35 linkage groups. Sex-specific linkage maps were of similar size (1132 and 1168cM for male and female maps respectively). A single major sex-determining locus, found to be heterogametic in males, was mapped to linkage group 14. Several markers were found to be in strong linkage disequilibrium with the sex-determining locus. Allele-specific PCR assays were developed for two of these markers, SphI6331 and SphI8298, and demonstrated to accurately differentiate sex in progeny within the same pedigree. Comparative genomic analyses indicated that many of the linkage groups within theP. oxygeneiosmap share a relatively high degree of homology with those published for the European seabass (Dicentrarchus labrax).  Conclusion  P. oxygeneioshas an XX/XY sex determination system. Evaluation of allele-specific PCR assays, based on the two SNP markers most closely associated with phenotypic sex, indicates that a simple molecular assay for sexingP. oxygeneiosshould be readily attainable. The high degree of synteny observed withD. labraxshould aid further molecular genetic study and exploitation of hāpuku as a food fish.
Type: Journal Article
DOI Link:
Rights: © The Author(s). 2016 This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
Affiliation: Aquaculture
University of Edinburgh
New Zealand National Institute of Water and Atmospheric Research
New Zealand National Institute of Water and Atmospheric Research

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