BackgroundAtlantic 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.ResultsHalibut 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.ConclusionAltogether 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.

Funding informationM. Oral was supported by a visiting grant from the MUSE "Explore" programme, publicly funded through the ANR (French National Research Agency) under the "Investissements d'avenir" program (ANR-16-IDEX-0006) and the Erasmus+ program of the European Union."… such abundant literature and insightful studies may be little more than a mirage".

BackgroundFully 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.ResultsFrom 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.ConclusionGenome-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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3826-z) contains supplementary material, which is available to authorized users.

In an effort to reveal the Euphrates trout taxonomy, the Karasu River, which is one of the eastern drainages of the river, was investigated and three independent populations were identified. Result revealed that two populations belonged to Salmo munzuricus, which was known only in Munzur River, while the other population belonged to an unnamed species. Salmo baliki, a new species, is described from the Murat River, a drainage of Euphrates River. It differs from Salmo species in adjacent water by the combination of the following characters: a grayish body; commonly one, rarely two pale black spots behind eye and on cheek; two to seven black spots on opercle; a few black spots on back and upper part of flank, missing on predorsal area; few to numerous large irregular-shaped red spots in median, upper and lower part of flank, surrounded by a large irregular-shaped white ring; the number of black and red spots not increasing in parallel with size; maxilla short and narrow; adipose-fin medium size, no or rarely one or two red spot its posterior edge; 107–118 lateral line scales; 24–28 scales rows between dorsal-in origin and lateral line; 18–22 scale rows between lateral line and anal–fin origin; maxilla length 7.7–9.1% SL in males, 8.2–9.6 in females. Finally, the genetic study of the Cyt b mitochondrial gene confirmed the morphological data, suggesting the separation of S. baliki from other Salmo species.

Next generation sequencing (NGS) technologies constitute the most powerful scientific advance of 21st century with a promise of fast and cost effective data generation in biology. Yet, up to date NGS studies remain often limited to laboratories with established resources. In the present study, we employed construction of ddRADseq library by using routine lab consumables (agarose gel electrophoresis: AGE thereafter) compared to high-tech NGS consumables (paramagnetic beads) during size selection. The ddRADseq library was constructed for sequencing size selected based on universally used paramagnetic beads, while remaining aliquot was used as a template to assess the feasibility of ddRADseq library construction using AGE for labs with limited resources. Both libraries were optimised for 15 PCR cycles indicating similarity in template intensity. Post-PCR quantification of the libraries was comparable (~10 ng.µL-1). Size distribution assessment revealed a cleaner pick at the ddRADseq library size selected manually based on AGE. Similarly, intercalating agent of Qubit confirmed the quantity of libraries was similar (>3 ng.µL-1). Although being more time consuming due to pre-electrophoresis preparations, serial wash and staining steps, ddRADseq library construction is achievable using routine lab consumables provided to supply the adaptors and PCR primers for the initial wet-lab work. These results manifest the feasibility of ddRADseq library generation for labs with limited resources.