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This study tested and compared different implementation strategies for genomic selection for Norwegian White Sheep, aiming to increase genetic gain for maternal traits. These strategies were evaluated for their genetic gain ingrowth, carcass and maternal traits, total genetic gain, a weighted sum of the gain in each trait and rates of inbreeding through a full‐scale stochastic simulation. Results showed genomic selection schemes to increase genetic gain for maternal traits but reduced genetic gain for other traits. This could also be obtained by selecting rams for artificial selection at a higher age. Implementation of genomic selection in the current breeding structure increased genetic gain for maternal traits up to 57%, outcompeted by reducing the generation interval for artificial insemination rams from current 3 to 2 years. Then, total genetic gain for maternal traits increased by 65%–77% and total genetic gain by18%–20%, but at increased rates of inbreeding. [ABSTRACT FROM AUTHOR]

Abstract: A simulation study was conducted to investigate the potential advantage of two-step selection for dissemination of genetic gains in salmon production through a system with a nucleus breeding population, a multiplier tier and a grow-out tier. Results demonstrated that profit (measured in the grow-out tier in generation 8) can be substantially increased through production and dissemination of specialised stocks suited for e.g. specific production environments or markets. Truncation selection alternatives in two steps with varying selection proportions were compared to random sampling of parents in both dissemination steps: from the nucleus to the multiplier and from the multiplier to the grow-out tier. Strategies where truncation selection was used in one step and random sampling of parents in the other step were also tested. The selection alternatives with truncation selection in both steps gave on average between 31% and 26% higher profit than random selection. The selection alternative with an extremely low truncation selection proportion in two steps would on average give 2% higher profit than the selection alternative with extremely low truncation selection proportion from the nucleus to the multiplier (1st step), and a normally low truncation selection proportion from the multiplier to the grow-out (2nd step). However, the former alternative yielded five times fewer eggs. The study also showed that one step of truncation selection and one of random sampling of parents, irrespective of the order, would give on average about 19% higher profit compared to random selection in two steps. The effect of the correlation between the nucleus/multiplier breeding goal and the breeding objective of the grow-out was that profit was highest when the correlation was high. With a negative genetic correlation between the traits, profit was still high if the trait with the highest heritability (i.e. the trait measured on candidate itself) had the highest economic value. It was concluded that selection of specialised stocks for specific breeding objectives in two steps from the nucleus via the multiplier and to the grow-out could increase profit by 24%. Specific breeding objectives would also give more flexibility for a final product when the grow-out producers could ask for unique trait-combinations for their fish. [Copyright &y& Elsevier]

Abstract: A simple selection scheme is proposed that facilitates the selection for a growth trait (GROWTH) with heritability of 0.25 and one disease trait (SURVIVAL) with heritability of 0.1 or 0.4 using a two step selection procedure. First, the scheme applies phenotypic selection for SURVIVAL among all the 10,000 candidates per generation, assuming that Nsurvival=2500, 5000 or 7500 survived a disease challenge test. Survivors were measured for GROWTH, and the (Ngenotyped=1000 or 2000) highest ranked were DNA genotyped for parentage testing. Second, parents were selected for GROWTH on their BLUP breeding values using optimum contribution selection, which restricted the rates of inbreeding to 1% per generation. At this second selection step, no selection for SURVIVAL was possible, because all survivors had the same phenotype for this trait and the pedigree of the dead individuals were not known. Results show that selection for SURVIVAL was very efficient for schemes with high heritability of SURVIVAL (0.4) and positive genetic correlation between the traits (0.3), and more efficient with decreasing survival rate, because of the higher intensity of selection. However, for schemes with negative correlation between the traits (−0.3), the heritability of 0.1 of SURVIVAL was too low to get positive genetic response for SURVIVAL. Genetic gain for GROWTH and SURVIVAL was not significantly improved by increasing Ngenotyped=1000 to 2000 for the schemes used here, i.e. genotyping 1000 individuals allowed the best possible parents to be selected for breeding when using optimum contribution selection. In conclusion, this is an efficient and very simple selection scheme for aquaculture species which can be used for specific cases where a whole production system is limited by a disease that is not transmitted from parent to offspring. The scheme may be worth considering also for vertically transmitted diseases for which the breeding candidates or their gametes can be reliably disinfected and screened before being transferred to the nucleus and the industry. [Copyright &y& Elsevier]

Abstract: We studied a typical breeding nucleus with dissemination of genetic material directly from the nucleus to the grow-out level by stochastic simulation. Profits could be increased through production and dissemination of specialised stocks suited for specific production environments or markets. Truncation selection of 50 sires and 200 dams (trunc ♂2.5% ♀10%) and of 5 sires and 25 dams (trunc ♂0.25% ♀1.25%) were compared to random selection of 50 sires and 200 dams (rand ♂2.5% ♀10%). Higher profit was obtained for all truncation selection schemes as compared to random selection, and increasing with decreasing proportion selected. By optimising the selection of parents, which are used for dissemination from the nucleus to the grow-out, instead of using randomly selected nucleus parents, an additional response corresponding of approximately 1.5 generations of selection in the nucleus was achieved. The effect of the correlation between the nucleus breeding goal and the breeding objective of the grow-out was that profit was highest when the correlation was high. With a negative genetic correlation between the traits, profit was still high if the trait with the highest heritability (i.e. the trait measured on candidate itself) had the highest economic value. The range of ΔF in the 7th generation in the nucleus was [−0.0075–0.0269] with SD equal to 0.0056. The average over all the replicates was 0.0095. This study showed that selection of specialised stocks for specific breeding objectives from the nucleus to the grow-out level will give the grow-out producers a direct and extra genetic improvement and that selecting breeders in the nucleus for dissemination gives also more flexibility for a final product, by adapting economic weights for each grow-out producer. [Copyright &y& Elsevier]

Abstract: This study compared the accuracy for genome-wide breeding values (GWEBV) with traditional BLUP breeding values estimated from phenotypic performance of sibs (BLUPEBV) in a typical sib based aquaculture breeding scheme. The breeding schemes were closed nuclei with 1000 selection candidates from 100 families in each generation G1 to G5. Phenotypes were recorded on sibs of the selection candidates. Both selection candidates and their recorded sibs were genotyped using dense SNP genotyping technology and marker effects estimated from the sibs were used to predict GWEBV of the selection candidates. With 40 sibs, accuracy in G3 was 0.54 for BLUPEBV compared to 0.78 for GWEBV (marker density 0.5N e /M), i.e. a relative increase of 44%. When the number of sibs for the GWEBV scheme decreased from 40 to 20 sibs, accuracy decreased by 7% in G3. Both for BLUPEBV and GWEBV breeding schemes, the effect of heritability on accuracy was small and accuracy increased around 4% when increasing heritability from 0.2 to 0.4. Contrary to expectations differences in accuracy between BLUPEBV and GWEBV were the same for the low (0.2) and high (0.4) heritability, which may be due to the large number of phenotypic records used. When records were only available in generation G1, accuracy of GWEBV decreased over generations and was 0.66 in G1, 0.57 in G2 and 0.51 in G3 with 40 sibs and marker density 0.5N e /M. Accuracy increased with increased marker density for GWEBV, but the increase was small when marker density increased from 0.5 to 1.0N e /M except when the test group size was increased from 20 to 40, indicating that with a higher marker density a higher number of phenotypes is needed. Increasing the size of the genome (1000 cM vs. 2000 cM) decreased the accuracy for the GWEBV breeding values but increased the accuracy for the BLUPEBV breeding values. Overall, accuracy was up to 33% higher for GWEBV than for BLUPEBV for the studied scenarios because both between and within family genetic variances are utilized when estimating genome-wide breeding values. The results indicate that aquaculture breeding companies can increase the accuracy of selection when using genomic selection in a typical sib based aquaculture breeding scheme. [Copyright &y& Elsevier]

Abstract: Fish-breeding programs may be based on fish from wild or from domesticated populations. The knowledge of the genetic properties of these populations is often poor. One alternative is to assume that all fish are unrelated, having the same genetic variance within subpopulations, but different genetic means. The effects of increasing the number of subpopulations in the base (1–8) and the mating design in the base (mating within subpopulations, or at random, within and across subpopulations) on genetic variance, genetic gain and the contributions of the different subpopulations in the following generations were studied for a base population with a realistic number of families (160 or 240) and a somewhat low number of offspring per family (20 or 30). Stochastic simulation was used, assuming an infinitesimal additive genetic model. Selection was carried out for 10 generations, applying optimal contribution selection on phenotype, which maximizes genetic gain at a fixed rate of inbreeding. The largest genetic gain was obtained when sampling fish from at least four subpopulations, and mating within subpopulation(s) in the base. Given a genetic variance within and between subpopulations of 0.2, increasing the number of subpopulations from one to four and from four to eight led to an improvement of the genetic level in generation 11 by 7.0% and 0.3%, respectively. Standard deviations of genetic level, i.e., risk, were also lower from sampling from a larger number of subpopulations. However, sampling from a larger number of subpopulations may introduce larger costs connected with sampling of fish from more locations. [Copyright &y& Elsevier]

Abstract: Traceability schemes for aquaculture species are essential for tracing market product to farm of origin in the event of detection of disease or toxins in the market fish. DNA markers have been proposed as a tool for traceability. These markers can be used to genotype fish by taking a sample from live fish or fish product at any stage along the production chain. In this paper, we consider three alternate traceability schemes using DNA markers. The example of the Norwegian farmed Atlantic salmon industry was used. This industry, like many aquaculture industries, has three tiers, the nucleus, multiplier and commercial tiers. The nucleus individuals are grandparents of the commercial fish, and the multiplier individuals are the parents of the commercial fish. The traceability strategies we considered were: (1) FS, assignment of market place fish to full sib families based on the marker information (this strategy assumes all individuals from a full sib family are allocated to a single farm and a limited number of fish, representing all full sib families on that farm, are genotyped); (2) PAR, assignment of market place fish to parents (multiplier individuals) and (3) GRAND, assignment of market place fish to grandparents (nucleus individuals). Using simulation, we determined the number of DNA markers required to achieve 95% of correct assignment decisions for each strategy. The simulation included a wild population which contributed to market place fish. The wild fish were correctly assigned if they were excluded from belonging to the farmed population in each strategy, otherwise they were incorrectly assigned. Both microsatellite markers or single nucleotide polymorphism markers were considered. Seventy five, 15, and 50 microsatellites were required to achieve 95% correct assignment decisions for FS, PAR and GRAND, respectively. Four hundred, 75 and 200 SNPs were required to achieve 95% correct assignment decisions for FS, PAR and GRAND, respectively. If the cost of genotyping microsatellites is assumed to be five times as high as genotyping a SNP, GRAND using SNP markers is the cheapest strategy. The logistics of implementing each strategy are discussed. GRAND in particular and PAR in some industries requires complicated logistics. The most suitable and cost effective traceability strategy for a particular industry will depend heavily on the organisation of that industry, for example the degree of recording transfer of fish, eggs and larvae between tiers. Even if complicated logistics prevent the adoption of marker based schemes by some industries, traceability with DNA markers may still be important for verification of labelling-based schemes. [Copyright &y& Elsevier]

Abstract: We have compared rate of inbreeding (ΔF) and genetic gain (ΔG) in truncation selection schemes for fish on best linear unbiased prediction (BLUP) estimated breeding values (EBVs; BTS) or phenotypic values (PTS) with one constraint on the number of tanks (100 or 200) to rear the families, e.g., until tagging size, and one constraint on the total number of selection candidates (3200 or 6400). Single trait selection was practiced for a trait with heritability of 0.1, 0.4 or 0.7 and 5, 10, 20, 50, 100 or 200 selected sires and dams were selected. When going from PTS to BTS, we found an overall increase of ΔG and ΔF of a factor of 0.07 and 1.45, respectively; that is, the increase of ΔG was moderate and accompanied by a dramatic increase of ΔF. In general, ΔF was reduced by increasing the number of tanks at a given number of selection candidates and by decreasing the number of selection candidates at a given number of tanks. ΔF was also reduced for schemes with high heritability because BLUP breeding value estimation then increases the weight on the individual''s phenotype, which leads to a reduced correlation between BLUP estimated breeding values within a family, and fish from more families become selected. In practical fish breeding schemes, PTS seems preferable over BTS because BTS generally give unacceptable high ΔF (≫0.01) for these schemes with few but large families. PTS can, however, only be used for traits measured on the selection candidate, which makes PTS less valuable for schemes with comprehensible breeding goals, including, for example, growth, disease resistance, maturity and fillet quality traits. Several traits are measured today on sibs only. [Copyright &y& Elsevier]

Fusarium head blight (FHB) is the predominant disease in oat in Norway caused by the fungus Fusarium graminearum. It causes yield loss, reduced seed quality, reduced germination ability and accumulation of deoxynivalenol (DON). The FHB resistance is quantitative, and most genes have small effect. Markers with verified effect in the breeding program could further enhance the resistance breeding. This study aims to use a large and diverse population of 541 lines to identify quantitative trait loci (QTL) associated to FHB resistance in a genome‐wide association study (GWAS) and verify their effect in independent breeding material. The material has been tested in six environments over three years and two locations in spawn inoculated and mist irrigated disease trials. The traits tested were germination ability and DON accumulation. A total of 15 significant QTL‐regions were detected across 12 different linkage groups. Haplotypes for each region was constructed and the effect of the alleles in each environment was calculated, which identified the most likely resistant and susceptible alleles. Five QTL‐regions were validated showing consistent effect in the GWAS population and the breeding material. Stacking of the resistant alleles of these regions from zero to five showed significant decrease in DON values and increased germination ability. The haplotype information of a set of historical and modern Nordic varieties were analysed, and the results could be used to select parents for future crossings. The validated haplotypes from this study can be used either to do marker assisted selection (MAS) or improve genomic prediction models in breeding programs. [ABSTRACT FROM AUTHOR]

Genomic selection is a promising breeding methodology that could increase selection accuracy and intensity and reduce generation interval. As the cost of genotyping decreases, it will be important to optimize training populations for costly phenotypic experiments for many complex traits. The aim of this research was to evaluate different optimization strategies, by using historical data from the Norwegian oat breeding programme at Graminor. In this paper, we focus on the optimization criteria: genetic diversity, phenotypic variance and genetic similarity between the training and testing populations. The four training population strategies—prediction core, diversity core, phenotypic selection and random selection—were applied to an oat candidate population of 1124 lines. An independent testing population was used to calculate the mean prediction abilities for the traits days to heading and plant height. Moreover, the strategies were tested in three independent wheat populations. The results showed that prediction core was the most promising strategy to select training populations with high genetic similarity to the testing set, high genetic diversity, and high phenotypic variance, which resulted in higher prediction ability across population sizes and traits. [ABSTRACT FROM AUTHOR]

Background: Infectious pancreatic necrosis (IPN) is one of the most prevalent and economically devastating diseases in Atlantic salmon (Salmo salar) farming worldwide. The disease causes large mortalities at both the fry- and post-smolt stages. Family selection for increased IPN resistance is performed through the use of controlled challenge tests, where survival rates of sib-groups are recorded. However, since challenge-tested animals cannot be used as breeding candidates, within-family selection is not performed and only half of the genetic variation for IPN resistance is being exploited. DNA markers linked to quantitative trait loci (QTL) affecting IPN resistance would therefore be a powerful selection tool. The aim of this study was to identify and fine-map QTL for IPN-resistance in Atlantic salmon, for use in marker-assisted selection to increase the rate of genetic improvement for this trait. Results: A genome scan was carried out using 10 large full-sib families of challenge-tested Atlantic salmon post-smolts and microsatellite markers distributed across the genome. One major QTL for IPN-resistance was detected, explaining 29% and 83% of the phenotypic and genetic variances, respectively. This QTL mapped to the same location as a QTL recently detected in a Scottish Atlantic salmon population. The QTL was found to be segregating in 10 out of 20 mapping parents, and subsequent fine-mapping with additional markers narrowed the QTL peak to a 4 cM region on linkage group 21. Challenge-tested fry were used to show that the QTL had the same effect on fry as on post-smolt, with the confidence interval for QTL position in fry overlapping the confidence interval found in post-smolts. A total of 178 parents were tested for segregation of the QTL, identifying 72 QTL-heterozygous parents. Genotypes at QTL-heterozygous parents were used to determine linkage phases between alleles at the underlying DNA polymorphism and alleles at single markers or multi-marker haplotypes. One four-marker haplotype was found to be the best predictor of QTL alleles, and was successfully used to deduce genotypes of the underlying polymorphism in 72% of the parents of the next generation within a breeding nucleus. A highly significant population-level correlation was found between deduced alleles at the underlying polymorphism and survival of offspring groups in the fry challenge test, parents with the three deduced genotypes (QQ, Qq, qq) having mean offspring mortality rates of 0.13, 0.32, and 0.49, respectively. The frequency of the high-resistance allele (Q) in the population was estimated to be 0.30. Apart from this major QTL, one other experiment-wise significant QTL for IPN-resistance was detected, located on linkage group 4. Conclusion: The QTL confirmed in this study represents a case of a major gene explaining the bulk of genetic variation for a presumed complex trait. QTL genotypes were deduced within most parents of the 2005 generation of a major breeding company, providing a solid framework for linkage-based MAS within the whole population in subsequent generations. Since haplotype-trait associations valid at the population level were found, there is also a potential for MAS based on linkage disequilibrium (LD). However, in order to use MAS across many generations without reassessment of linkage phases between markers and the underlying polymorphism, the QTL needs to be positioned with even greater accuracy. This will require higher marker densities than are currently available. [ABSTRACT FROM AUTHOR]

Abstract: The simulation study examined the effect in optimal contribution selection of specifying an additive genetic relationship matrix (A-matrix) deviating from the true A-matrix of the base population. A base population of 160 males and 160 females was sampled evenly from 4 or 8 randomly chosen, drift-differentiated, wild subpopulations. Wild fish had true inbreeding coefficient of F wild, either 0.05 or 0.20, giving additive genetic relationships of 2F wild within, and 0 between subpopulations. Selection based upon phenotypes was simulated on one continuous trait of heritability, h wild 2, either 0.1 or 0.3. Base animals were mated either within subpopulations, or at random, so that the first round of selection occurred either on purebred or crossbred fish respectively. Optimum contributions was implemented from generation 1 for a desired rate of inbreeding of 0.5% per generation, using an assumed F wild ⁎ which varied between 0.0 and 0.3. Assuming F wild ⁎ =0.0 compared to 0.3, resulted in steeper regressions of the fractional contributions of subpopulations on average breeding value, higher true inbreeding and consequently reduced additive genetic variance, albeit with larger genetic gain from the first round of selection. When the first round of selection followed random mating the regression of the fractional contributions of the subpopulations was also less steep. These effects persisted, but originated from the misspecification of F wild ⁎ and so will not accumulate further in the medium-to long-term. Consequently, assuming F wild ⁎ was less than the true value led to sub-optimal use of subpopulations with an increased risk of loss of alleles of direct and strategic relevance to the breeding program. In conclusion, assuming F wild ⁎ ≈0.0 should be avoided and F wild ⁎ should be estimated with procedures such as marker estimated kinships, Q ST estimates or empirical observations of clines. [Copyright &y& Elsevier]

Abstract: Guidelines for constructing base populations in fish were examined using a drift model. A large number of drift differentiated, wild subpopulations, with inbreeding F wild (F wild ∈[0.05–0.20]), and a trait with heritability h tot 2 (h tot 2 ∈[0.10–0.30]), were assumed. A base population was generated by sampling 2N fish from each of nsub subpopulations (nsub ∈[1–8]), and then mated to produce 160 or 240 families per generation. The matings were either at random, in a structured diallel-cross, or within subpopulations to produce generation 1. Optimal contribution selection on phenotype was applied from generation 1 to11, with a rate of inbreeding of 0.5% per generation. Genetic gain (Δg) improved with nsub, the improvement being largest when going from one to two subpopulations, with diminishing returns. Most of the potential improvement was obtained with nsub =4, and was well predicted by . Initial matings across subpopulations improved Δg from the second round of selection compared to within. Consequently the effect of the mating strategy were first observed 3 generation after decisions were made and persisted over subsequent generations, but with minimal effect on the accumulated additive genetic gain in generation 11. It was concluded that sampling from at least four subpopulations was beneficial and that mating across subpopulations should start as early as possible. [Copyright &y& Elsevier]

Atlantic cod is composed of multiple migratory and stationary populations widely distributed in the North Atlantic Ocean. The Northeast Arctic cod (NEAC) population in the Barents Sea undertakes annual spawning migrations to the northern Norwegian coast. Although spawning occurs sympatrically with the stationary Norwegian coastal cod (NCC), phenotypic and genetic differences between NEAC and NCC are maintained. In this study, we resolve the enigma by revealing the mechanisms underlying these differences. Extended linkage disequilibrium (LD) and population divergence were demonstrated in a 17.4-Mb region on linkage group 1 (LG1) based on genotypes of 494 SNPs from 192 parents of farmed families of NEAC, NCC or NEACxNCC crosses. Linkage analyses revealed two adjacent inversions within this region that repress meiotic recombination in NEACxNCC crosses. We identified a NEAC-specific haplotype consisting of 186 SNPs that was fixed in NEAC sampled from the Barents Sea, but segregating under Hardy-Weinberg equilibrium in eight NCC stocks. Comparative genomic analyses determine the NEAC configuration of the inversions to be the derived state and date it to ~1.6-2.0 Mya. The haplotype block harbours 763 genes, including candidates regulating swim bladder pressure, haem synthesis and skeletal muscle organization conferring adaptation to long-distance migrations and vertical movements down to large depths. Our results suggest that the migratory ecotype experiences strong directional selection for the two adjacent inversions on LG1. Despite interbreeding between NEAC and NCC, the inversions are maintaining genetic differentiation, and we hypothesize the co-occurrence of multiple adaptive alleles forming a 'supergene' in the NEAC population. [ABSTRACT FROM AUTHOR]

The main aim of the current study was to compare the accuracy of selection for muscle content of fat and the health-promoting omega-3 fatty acids EPA and DHA in Atlantic salmon, by varying the sources of genetic information used in the estimation of breeding values. The following genetic information sources were compared: pedigree, SNP-chip markers and allele-specific expression markers. The results showed that differences between information sources were in general small, and different genetic information performed best for different traits. SNP-chip performed best for DHA, and pedigree performed best for EPA. Knowledge from gene expression analysis of a few individuals can be utilized to select a small panel of markers that perform relatively well. Genetic markers of allele-specific expression were able to capture a lot of genetic variation for DHA, but did not give significantly higher accuracies when combined with SNP-chip or pedigree information. The cross-validation accuracies for selection for DHA and EPA were moderate and offer possibilities for selection for these traits, especially if one extends the reference data set to a much bigger population, with more sibs per selection candidate. • We reveal the possibilities and accuracies of selection for the health promoting fatty acids EPA and DHA in Atlantic salmon. • The following genetic information sources were compared: pedigree, SNP-chip markers, and allele-specific expression markers. • A new discovery of this paper is that that different genetic information sources performs best for different traits. • Markers of variation in gene expression explain large fractions of the total genetic variability for DHA in Atlantic salmon. • Selection accuracies for DHA and EPA were moderate and show potential for selective breeding for these traits. [ABSTRACT FROM AUTHOR]

The objective of this study was to identify genetic variants associated with long-chain omega-3 fatty acid content in Atlantic salmon muscle, in order to identify genes underlying the genetic variation in these traits, by performing a genome-wide association study. Fatty acid composition, including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) content and the ratios DHA/DPA (docosapentaenoic acid) and DHA/ALA (α-linolenic acid) of skeletal muscle was determined in 642 Atlantic salmon individuals from the Salmobreed broodstock program. Further, a 57 K single-nucleotide polymorphism (SNP) array was used to genotype the 642 individuals to search for SNPs associated with skeletal muscle content of individual omega-3 fatty acids as well as ratios between fatty acids, using a mixed model approach. We identified markers showing a significant association with the ratio of DHA to DPA located on chromosome 19, close to the candidate gene elovl2 , which is directly involved in the conversion of DPA to DHA. The results further suggested that genetic variation affecting fillet EPA and DHA content is present on Atlantic salmon chromosome 21, as the GWAS analysis of EPA, DHA and DHA/ALA ratio all pointed to this chromosome. No known genes of direct relevance to the omega-3 bioconversion pathway were found here. We discuss the relevance of other interesting genes related to lipid metabolism and health located in this region. • 642 Atlantic salmon were genotyped (57K SNP-chip) to search for SNPs associated with muscle content of omega-3 fatty acids • Muscle omega-3 traits appeared to have a polygenic architecture • A few potential QTL were identified that explained moderate levels of the genetic variation • Significantly associated markers for DHA/DPA ratio were located near elovl2, which is involved in DPA to DHA conversion • The results suggest that genetic variation affecting fillet EPA and DHA content is present on chromosome 21 [ABSTRACT FROM AUTHOR]

Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes. Marianna Pauletto, Tereza Manousaki et al. present the genome sequence of Sparus aurata, a sequential hermaphroditic fish. Comparative analysis with gonochoristic species shows that sex-biased genes generally evolve more slowly in S. aurata due to stronger functional constraints. [ABSTRACT FROM AUTHOR]

Background: Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90–100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1–49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values. Results: The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28–16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19–24% increase when using genomic information. Conclusion: The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs. [ABSTRACT FROM AUTHOR]

A correction to the article "Genotype data from SNP array are available in Dryad" that was published in the previous issue is presented.