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Background: Fully isogenic lines in fish can be developed using "mitotic" gynogenesis (suppression of first zygotic mitosis following inactivation of the sperm genome). However, genome-wide verification of the steps in this process has seldom been applied. We used ddRADseq to generate SNP markers in a meiotic gynogenetic family of European seabass (Dicentrarchus labrax): (i) to verify the lack of paternal contribution in a meiotic gynogenetic family; (ii) to generate a gene-centromere map from this family; (iii) to identify telomeric markers that could distinguish mitotic gynogenetics from meiotic gynogenetics, which sometimes arise spontaneously in mitotic gynogenetic families. Results: From a single meiotic gynogenetic family consisting of 79 progeny, 42 million sequencing reads (Illumina, trimmed to 148 bases) resolved 6866 unique RAD-tags. The 340 male-informative SNP markers that were identified confirmed the lack of paternal contribution. A gene-centromere map was constructed based on 804 female-informative SNPs in 24 linkage groups (2n = 48) with a total length of 1251.02 cM (initial LG assignment was based on the seabass genome assembly, dicLab v1). Chromosome arm structure could be clearly discerned from the pattern of heterozygosity in each linkage group in 18 out of 24 LGs: the other six showed anomalies that appeared to be related to issues in the genome assembly. Conclusion: Genome-wide screening enabled substantive verification of the production of the gynogenetic family used in this study. The large number of telomeric and subtelomeric markers with high heterozygosity values in the meiotic gynogenetic family indicate that such markers could be used to clearly distinguish between meiotic and mitotic gynogenetics. [ABSTRACT FROM AUTHOR]

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, 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. Results: DNA 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). Conclusion: P. 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. [ABSTRACT FROM AUTHOR]

Background: European sea bass (Dicentrarchus labrax) is one of the most important farmed species in Mediterranean aquaculture. The observed sexual growth and maturity dimorphism in favour of females adds value towards deciphering the sex determination system of this species. Current knowledge indicates the existence of a polygenic sex determining determination system that interacts with temperature. This was explored by restriction-site associated DNA (RAD) marker analysis in a test panel of 175 offspring that originated from a factorial cross between two dams and four sires from a single full-sib family. Results: The first high-density single nucleotide polymorphism (SNP) based linkage map for sea bass was constructed, consisting of 6706 SNPs on 24 linkage groups. Indications for putative sex-determining QTL (quantitative trait loci) that were significant at the genome-wide threshold were detected on linkage groups 6, 11 and 18 to 21, although a genome-wide association study (GWAS) did not identify individual significant SNPs at a genome-wide threshold. A preliminary genomic prediction approach that tested the efficiency of SNP-based selection for female sea bass showed a slight advantage compared to traditional pedigree-based selection. However, when the same models were tested on the same animals for selection for greater length, a clear advantage of the SNP-based selection was observed. Conclusions: Overall, the results of this study provide additional support to the polygenic sex determination hypothesis in sea bass. In addition, identification of sex-ratio QTL may provide new opportunities for sex-ratio control in sea bass. [ABSTRACT FROM AUTHOR]

Background: Fish species often exhibit significant sexual dimorphism for commercially important traits. Accordingly, the control of phenotypic sex, and in particular the production of monosex cultures, is of particular interest to the aquaculture industry. Sex determination in the widely farmed Nile tilapia (Oreochromis niloticus) is complex, involving genomic regions on at least three chromosomes (chromosomes 1, 3 and 23) and interacting in certain cases with elevated early rearing temperature as well. Thus, sex ratios may vary substantially from 50%. Results: This study focused on mapping sex-determining quantitative trait loci (QTL) in families with skewed sex ratios. These included four families that showed an excess of males (male ratio varied between 64% and 93%) when reared at standard temperature (28°C) and a fifth family in which an excess of males (96%) was observed when fry were reared at 36°C for ten days from first feeding. All the samples used in the current study were genotyped for two single-nucleotide polymorphisms (rs397507167 and rs397507165) located in the expected major sex-determining region in linkage group 1 (LG 1). The only misassigned individuals were phenotypic males with the expected female genotype, suggesting that those offspring had undergone sex-reversal with respect to the major sex-determining locus. We mapped SNPs identified from double digest Restriction-site Associated DNA (ddRAD) sequencing in these five families. Three genetic maps were constructed consisting of 641, 175 and 1,155 SNPs from the three largest families. QTL analyses provided evidence for a novel genome-wide significant QTL in LG 20. Evidence was also found for another sex-determining QTL in the fifth family, in the proximal region of LG 1. Conclusions: Overall, the results from this study suggest that these previously undetected QTLs are involved in sex determination in the Nile tilapia, causing sex reversal (masculinisation) with respect to the XX genotype at the major sex-determining locus in LG 1. [ABSTRACT FROM AUTHOR]

Background: Atlantic halibut (Hippoglossus hippoglossus) is a high-value, niche market species for cold-water marine aquaculture. Production of monosex female stocks is desirable in commercial production since females grow faster and mature later than males. Understanding the sex determination mechanism and developing sex-associated markers will shorten the time for the development of monosex female production, thus decreasing the costs of farming. Results: Halibut juveniles were masculinised with 17 α-methyldihydrotestosterone (MDHT) and grown to maturity. Progeny groups from four treated males were reared and sexed. Two of these groups (n = 26 and 70) consisted of only females, while the other two (n = 30 and 71) contained balanced sex ratios (50% and 48% females respectively). DNA from parents and offspring from the two mixed-sex families were used as a template for Restriction-site Associated DNA (RAD) sequencing. The 648 million raw reads produced 90,105 unique RAD-tags. A linkage map was constructed based on 5703 Single Nucleotide Polymorphism (SNP) markers and 7 microsatellites consisting of 24 linkage groups, which corresponds to the number of chromosome pairs in this species. A major sex determining locus was mapped to linkage group 13 in both families. Assays for 10 SNPs with significant association with phenotypic sex were tested in both population data and in 3 additional families. Using a variety of machine-learning algorithms 97% correct classification could be obtained with the 3% of errors being phenotypic males predicted to be females. Conclusion: Altogether our findings support the hypothesis that the Atlantic halibut has an XX/XY sex determination system. Assays are described for sex-associated DNA markers developed from the RAD sequencing analysis to fast track progeny testing and implement monosex female halibut production for an immediate improvement in productivity. These should also help to speed up the inclusion of neomales derived from many families to maintain a larger effective population size and ensure long-term improvement through selective breeding. [ABSTRACT FROM AUTHOR]

Background: European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding. A population of 1538 sea bass juveniles from a factorial cross between 48 sires and 17 dams was challenged with RGNNV with mortalities and survivors being recorded and sampled for genotyping by the RAD sequencing approach. Results: We used genome-wide genotype data from 9195 single nucleotide polymorphisms (SNPs) for downstream analysis. Estimates of heritability of survival on the underlying scale for the pedigree and genomic relationship matrices were 0.27 (HPD interval 95%: 0.14-0.40) and 0.43 (0.29–0.57), respectively. Classical genome-wide association analysis detected genome-wide significant quantitative trait loci (QTL) for resistance to VNN on chromosomes (unassigned scaffolds in the case of 'chromosome' 25) 3, 20 and 25 (P < 1e06). Weighted genomic best linear unbiased predictor provided additional support for the QTL on chromosome 3 and suggested that it explained 4% of the additive genetic variation. Genomic prediction approaches were tested to investigate the potential of using genome-wide SNP data to estimate breeding values for resistance to VNN and showed that genomic prediction resulted in a 13% increase in successful classification of resistant and susceptible animals compared to pedigree-based methods, with Bayes A and Bayes B giving the highest predictive ability. Conclusions: Genome-wide significant QTL were identified but each with relatively small effects on the trait. Tests of genomic prediction suggested that incorporating genome-wide SNP data is likely to result in higher accuracy of estimated breeding values for resistance to VNN. RAD sequencing is an effective method for generating such genome-wide SNPs, and our findings highlight the potential of genomic selection to breed farmed European sea bass with improved resistance to VNN. [ABSTRACT FROM AUTHOR]