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BackgroundHāpuku (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, making P. oxygeneios a strong candidate for aquaculture. However, they can take over 5 years to reach sexual maturity in captivity and are not externally sexually dimorphic, complicating many aspects of broodstock management. Understanding the sex determination system of P. oxygeneios and developing accurate assays to assign genetic sex will contribute significantly towards its full-scale commercialisation.ResultsDNA from parents and sexed offspring (n = 57) from a single family of captive bred P. oxygeneios was used as a template for double digestion Restriction-site Associated DNA (ddRAD) sequencing. Two libraries were constructed using SbfI – SphI and SbfI – 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 (1367 cM) 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 1168 cM 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 the P. oxygeneios map share a relatively high degree of homology with those published for the European seabass (Dicentrarchus labrax).ConclusionP. oxygeneios has 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 sexing P. oxygeneios should be readily attainable. The high degree of synteny observed with D. labrax should aid further molecular genetic study and exploitation of hāpuku as a food fish.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2773-4) contains supplementary material, which is available to authorized users.

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Summary The prevalence and onset of radiological skeletal deformities in tagged Chinook salmon (Oncorhynchus tshawytscha) were investigated after 129 days in seawater at grading for removal of fish that failed to thrive (mean weight ± SEM, 432 ± 6.5 g) and again at harvest after 395 days (mean weight ± SEM, 3,721 ± 43 g). A scoring system identifying four categories of the radiographic deformity phenotype was established based on literature and evaluation of X‐rays of harvest‐size Chinook salmon. Deformity categories were: spinal curvature or Lordosis, Kyphosis, Scoliosis (LKS); Fusion; Compression and/or reduced inter‐vertebral (IV) space; Vertical shift. Of the 432 fish surviving to harvest and for which there were weights and diagnostic radiographs, 38.4% were affected by at least one deformity. Late onset LKS, detected at harvest, was the most prevalent deformity in 29.4% of all harvested fish. LKS was present alone with no other potentially confounding deformities in 10% of harvested fish. Cranial lordosis, a common LKS variant, in the postcranial region comprised half of LKS‐deformed fish. LKS commonly co‐existed with compression, a combination prevalent in harvest fish at 13.4%. Compression and/or reduced IV space detected in 22.0% of harvested fish was commonly associated with other deformity phenotypes (84/95 of fish with compression). Fusion and vertical shift were present in 7.6% and 4.6% of harvested fish, respectively. More than 77% of fish with any type of deformity developed the deformity within 9 months of harvest. Fusions that were visible in radiographs at grading persisted in fish that survived until harvest. In contrast, LKS, the most visible harvest deformity, was difficult to detect in radiographs from the earlier time point, suggesting that this economically important deformity develops at a relatively late stage of seawater growth. Deformed fish at harvest were smaller (mean ± SEM 3,479 ± 76 g) than normal (mean ± SEM 3,875 ± 51 g). Fish with no deformity grew at a significantly (p < .05) faster rate than fish that developed a deformity during this period or were already deformed at grading. The scoring system performed with a sensitivity of 92.4% and a specificity of 97.6% for Chinook salmon >500 g, and thus has a potential utility for other farmed salmonids.

Summary In genomic selection (GS), genome‐wide SNP markers are used to generate genomic estimated breeding values for selection candidates. The application of GS in shellfish looks promising and has the potential to help in dealing with one of the main issues currently affecting Pacific oyster production worldwide, which is the ‘summer mortality syndrome’. This causes periodic mass mortality in farms worldwide and has mainly been attributed to a specific variant of the ostreid herpesvirus (OsHV‐1). In the current study, we evaluated the potential of genomic selection for host resistance to OsHV‐1 in Pacific oysters, and compared it with pedigree‐based approaches. An OsHV‐1 disease challenge was performed using an immersion‐based virus exposure treatment for oysters for 7 days. A total of 768 samples were genotyped using the medium‐density SNP array for oysters. A GWAS was performed for the survival trait using a GBLUP approach in blupf90 software. Heritability ranged from 0.25 ± 0.05 to 0.37 ± 0.05 (mean ± SE) based on pedigree and genomic information respectively. Genomic prediction was more accurate than pedigree prediction, and SNP density reduction had little impact on prediction accuracy until marker densities dropped below approximately 500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programmes, and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate genomic estimated breeding values, thus potentially making the implementation of GS more cost effective.

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Atlantic cod is a species that has been overexploited by the capture fishery. Programs to domesticate this species are underway in several countries, including Canada, to provide an alternative route for production. Selective breeding programs have been successfully applied in the domestication of other species, with genomics-based approaches used to augment conventional methods of animal production in recent years. Genomics tools, such as gene sequences and sets of variable markers, also have the potential to enhance and accelerate selective breeding programs in aquaculture, and to provide better monitoring tools to ensure that wild cod populations are well managed. We describe the generation of significant genomics resources for Atlantic cod through an integrated genomics/selective breeding approach. These include 158,877 expressed sequence tags (ESTs), a set of annotated putative transcripts and several thousand single nucleotide polymorphism markers that were developed from, and have been shown to be highly variable in, fish enrolled in two selective breeding programs. Our EST collection was generated from various tissues and life cycle stages. In some cases, tissues from which libraries were generated were isolated from fish exposed to stressors, including elevated temperature, or antigen stimulation (bacterial and viral) to enrich for transcripts that are involved in these response pathways. The genomics resources described here support the developing aquaculture industry, enabling the application of molecular markers within selective breeding programs. Marker sets should also find widespread application in fisheries management.Electronic supplementary materialThe online version of this article (doi:10.1007/s10126-010-9285-z) contains supplementary material, which is available to authorized users.