Polyploids can be defined as organisms with one or more additional chromosome sets with respect to the number most frequently found in nature for a given species. Triploids, organisms with three sets of homologous chromosomes, are found spontaneously in both wild and cultured populations and can be easily induced in many commercially relevant species of fish and shellfish. The major consequence of triploidy is gonadal sterility, which is of advantage in the aquaculture of molluscs since it can result in superior growth. In fish, the induction of triploidy is mainly used to avoid problems associated with sexual maturation such as lower growth rates, increased incidence of diseases and deterioration of the organoleptic properties. Triploidy can also be used to increase the viability of some hybrids, and is regarded as a potential method for the genetic containment of farmed shellfish and fish. This review focuses on some current issues related to the application of induced polyploidy in aquaculture, namely: 1) the artificial induction of polyploidy and the effectiveness of current triploidisation techniques, including the applicability of tetraploidy to generate auto-and allotriploids; 2) the performance capacity of triploids with respect to diploids; 3) the degree and permanence of gonadal sterility in triploids; and 4) the prospects for the potential future generalised use of triploids to avoid the genetic impact of escapees of farmed fish and shellfish on wild populations. Finally, directions for future research on triploids and their implementation are discussed.

253 full-sib families from 33 males and 23 females of European seabass were produced in a partly factorial mating design. All fish were reared in the same tank during 14 months, then 7000 of them were dispatched in four farms to different locations (France, Israel, Italy, Portugal) representing a wide variety of environmental conditions. Around 400 g mean weight, 1177 to 1667 fish in each site were weighed and length was measured. Condition factor (K) was calculated. Pedigrees were redrawn a posteriori using microsatellites markers: parental origin could be retraced for 99.2% of fish. Due to a high incidence of deformities, the useful sample size was reduced to 491-670 fish per site.Maternal effects were small. Using a simple animal model, heritability of weight ranged from 0.38 ± 0.14 to 0.44 ± 0.14 in the different sites. Length was highly correlated to weight, with similar heritabilities. GxE interaction, estimated through genetic correlations of weight across the different environments ranged from 0.70 ± 0.10 to 0.99 ± 0.05. Genetic correlations between weight or length and K were not similar in the different sites.

Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long‐reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi‐C, we generated a high‐continuity chromosome‐scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome‐size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male‐specific duplicate of the anti‐Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex‐specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (amhr2by+) from XX genetic females (amhr2by−). Our high‐quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex‐determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

The effect of temperature on sex-ratios in 27 families of sea bass reared in the same tank from the fertilization stage onward was investigated. An excess of males (68%) was found in the groups that were reared at high temperature (mean +/- standard deviation: 20+/-1 degrees C) until they reached the mean size of 8.1 cm (Standard Length, 149 days post-fertilization [p.f.]). Masculinization was higher (89% of males) in the groups maintained at low temperature (13 degrees C), from fertilization to a mean length of 6.5 cm (346 days p.f.). Shifts from high to low temperature at 8.1cm and from low to high temperature at 6.5 cm had no consequence on the sex-ratio. The percentage of males showing intratesticular oocytes was higher at low temperature (63%) than at high temperature (36%), suggesting that these males may be sensitive fish that have been masculinized by environmental factors. Fish sampled in the groups reared at high (2,200 fish) and low (500 fish) temperature were genotyped on three microsatellite loci. This allowed them to be assigned to the breeders used in the crossing design, thus permitting an analysis of parental influence on sex-ratios. In groups reared at high temperature, both parents had a significant additive effect on the percentage of females, and the interaction between sire and dam was not significant. Genotype temperature interactions were also detected and their existence suggests the interesting possibility of selecting nonsensitive genotypes in breeding programs.

Eight turbot (Scophthalmus maximus) and eight rainbow trout (Oncorhynchus mykiss) microsatellites were selected for parentage assignment in fish-farmed populations. The number of alleles, gene diversity, polymorphic information content, and the probabilities of exclusion of these loci were 8, 0.76, 0.73, and 0.55 in turbot and 4, 0.65, 0.59 and 0.39 in rainbow trout, respectively. The power of the markers for parentage assignment was assessed by computing the frequency of good and unique decisions (fgu) in a population of genitors defined by its allele frequencies and assuming three different types of mating schemes. The eight turbot microsatellites gave larger maximal mating schemes (the largest mating structure with a fgu >= 0.95) than the eight rainbow trout loci: 1 female (F) mated to 520 males (M) (paternity retrieval scheme), more than 140F x 140M (factorial scheme), and more than 15 000 independent pairs (natural population scheme) for turbot, and 1F x 88M, 34F x 34M, and 7000 independent pairs for rainbow trout. The variation of the fgu values with the number of loci confirmed that the turbot set of microsatellites was more efficient for parentage assignment than the rainbow trout markers.

BackgroundEuropean 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.ResultsWe 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.ConclusionsGenome-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.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0401-2) contains supplementary material, which is available to authorized users.

Background Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout ( Oncorhynchus mykiss ) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index ( F ST ), linkage disequilibrium (LD), effective population size ( N e ) and inbreeding coefficient derived from runs of homozygosity (ROH). Results Our results showed a moderate level of genetic differentiation between selected lines ( F ST ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of N e in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. Conclusions This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome. Electronic supplementary material The online version of this article (10.1186/s12711-019-0468-4) contains supplementary material, which is available to authorized users.

The use of selective breeding is still relatively limited in aquaculture species. Information on such activities is sparse, hindering an overall evaluation of their success. Here, we report on the results of an online survey of the major aquaculture breeding companies operating in Europe. Six main reared fish species were targeted. A total of 31 respondents contributed to the survey, representing 75 % of European breeding organizations. Family-based breeding schemes were predominant, but individual selection was more frequently applied in marine species. Artificial fertilization is the preferred means of reproduction; however, mass spawning is often used as a fallback method. The most frequently selected trait is growth performance, but the number of selected traits has been increasing over the years through the addition of traits such as disease resistance or product quality. The use of molecular tools is now common in all programs, mainly for pedigree traceability. An increasing number of programs use either genomic or marker-assisted selection. Results related to the seed production market confirmed that for Atlantic salmon there are a few dominant players at the European level, with 30-50 % market share. Only part of the European fish aquaculture industry today fully exploits selective breeding to the best advantage. A larger impact assessment still needs to be made by the remainder, particularly on the market share of fish seed (eggs, larvae or juveniles) and its consequences for hatchery stability