Applying genetic technologies to combat infectious diseases in aquaculture.

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon.

Genomic selection has a great potential in aquaculture breeding since many important traits are not directly measured on the candidates themselves. However, its implementation has been hindered by staggering genotyping costs because of many individual genotypes. In this study, we explored the potential of DNA pooling for creating a reference population as a tool for genomic selection of a binary trait. Two datasets from the SalmoBreed population challenged with salmonid alphavirus, which causes pancreas disease, were used. Dataset-1, that includes 855 individuals (478 survivors and 377 dead), was used to develop four DNA pool samples (i.e., 2 pools each for dead and survival). Dataset-2 includes 914 individuals (435 survivors and 479 dead) belonging to 65 full-sibling families and was used to develop in-silico DNA pools. SNP effects from the pool data were calculated based on allele frequencies estimated from the pools and used to calculate genomic breeding values (GEBVs). The correlation between SNP effects estimated based on individual genotypes and pooled data increased from 0.3 to 0.912 when the number of pools increased from 1 to 200. A similar trend was also observed for the correlation between GEBVs, which increased from 0.84 to 0.976, as the number of pools per phenotype increased from 1 to 200. For dataset-1, the accuracy of prediction was 0.71 and 0.70 when the DNA pools were sequenced in 40× and 20×, respectively, compared to an accuracy of 0.73 for the SNP chip genotypes. For dataset-2, the accuracy of prediction increased from 0.574 to 0.691 when the number of in-silico DNA pools increased from 1 to 200. For this dataset, the accuracy of prediction using individual genotypes was 0.712. A limited effect of sequencing depth on the correlation of GEBVs and prediction accuracy was observed. Results showed that a large number of pools are required to achieve as good prediction as individual genotypes; however, alternative effective pooling strategies should be studied to reduce the number of pools without reducing the prediction power. Nevertheless, it is demonstrated that pooling of a reference population can be used as a tool to optimize between cost and accuracy of selection.

Raman and near Infrared Spectroscopy for Quantification of Fatty Acids in Muscle Tissue-A Salmon Case Study.

The aim of the present study was to critically evaluate the potential of using NIR and Raman spectroscopy for prediction of fatty acid features and single fatty acids in salmon muscle. The study was based on 618 homogenized salmon muscle samples acquired from Atlantic salmon representing a one year-class nucleus, fed the same high fish oil feed. NIR and Raman spectra were used to make regression models for fatty acid features and single fatty acids measured by gas chromatography. The predictive performance of both NIR and Raman was good for most fatty acids, with R2 above 0.6. Overall, Raman performed marginally better than NIR, and since the Raman models generally required fewer components than respective NIR models to reach high and optimal performance, Raman is likely more robust for measuring fatty acids compared to NIR. The fatty acids of the salmon samples co-varied to a large extent, a feature that was exacerbated by the overlapping peaks in NIR and Raman spectra. Thus, the fatty acid related variation of the spectroscopic data of the present study can be explained by only a few independent principal components. For the Raman spectra, this variation was dominated by functional groups originating from long-chain polyunsaturated FAs like EPA and DHA. By exploring the independent EPA and DHA Raman models, spectral signatures similar to the respective pure fatty acids could be seen. This proves the potential of Raman spectroscopy for single fatty acid prediction in muscle tissue.

Genomic and Phenotypic Agreement Defines the Use of Microwave Dielectric Spectroscopy for Recording Muscle Lipid Content in European Seabass (Dicentrarchus labrax).

Recording the fillet lipid percentage in European seabass is crucial to control lipid deposition as a means toward improving production efficiency and product quality. The reference method for recording lipid content is solvent lipid extraction and is the most accurate and precise method available. However, it is costly, requires sacrificing the fish and grinding the fillet sample which limits the scope of applications, for example grading of fillets, recording live fish or selective breeding of fish with own phenotypes are all limited. We tested a rapid, cost effective and non-destructive handheld microwave dielectric spectrometer (namely the Distell fat meter) against the reference method by recording both methods on 313 European seabass (Dicentrarchus labrax). The total method agreement between the dielectric spectrometer and the reference method was assessed by Lin's concordance correlation coefficient (CCC), which was low to moderate CCC = 0.36-0.63. We detected a significant underestimation in accuracy of lipid percentage 22-26% by the dielectric spectrometer and increased imprecision resulting in the coefficient of variation (CV) doubling for dielectric spectrometer CV = 40.7-46% as compared to the reference method 27-31%. Substantial genetic variation for fillet lipid percentage was found for both the reference method (h 2 = 0.59) and dielectric spectroscopy (h 2 = 0.38-0.58), demonstrating that selective breeding is a promising method for controlling fillet lipid content. Importantly, the genetic correlation (r g) between the dielectric spectrometer and the reference method was positive and close to unity (r g = 0.96), demonstrating the dielectric spectrometer captures practically all the genetic variation in the reference method. These findings form the basis of defining the scope of applications and experimental design for using dielectric spectroscopy for recording fillet lipid content in European seabass and validate its use for selective breeding.

The heritable landscape of near-infrared and Raman spectroscopic measurements to improve lipid content in Atlantic salmon fillets.

BACKGROUND: Product quality and production efficiency of Atlantic salmon are, to a large extent, influenced by the deposition and depletion of lipid reserves. Fillet lipid content is a heritable trait and is unfavourably correlated with growth, thus genetic management of fillet lipid content is needed for sustained genetic progress in these two traits. The laboratory-based reference method for recording fillet lipid content is highly accurate and precise but, at the same time, expensive, time-consuming, and destructive. Here, we test the use of rapid and cheaper vibrational spectroscopy methods, namely near-infrared (NIR) and Raman spectroscopy both as individual phenotypes and phenotypic predictors of lipid content in Atlantic salmon. RESULTS: Remarkably, 827 of the 1500 individual Raman variables (i.e. Raman shifts) of the Raman spectrum were significantly heritable (heritability (h2) ranging from 0.15 to 0.65). Similarly, 407 of the 2696 NIR spectral landscape variables (i.e. wavelengths) were significantly heritable (h2 = 0.27-0.40). Both Raman and NIR spectral landscapes had significantly heritable regions, which are also informative in spectroscopic predictions of lipid content. Partial least square predicted lipid content using Raman and NIR spectra were highly concordant and highly genetically correlated with the lipid content values ([Formula: see text] = 0.91-0.98) obtained with the reference method using Lin's concordance correlation coefficient (CCC = 0.63-0.90), and were significantly heritable ([Formula: see text] = 0.52-0.67). CONCLUSIONS: Both NIR and Raman spectral landscapes show substantial additive genetic variation and are highly genetically correlated with the reference method. These findings lay down the foundation for rapid spectroscopic measurement of lipid content in salmonid breeding programmes.

Management of Genetic Diversity in the Era of Genomics.

Management of genetic diversity aims to (i) maintain heterozygosity, which ameliorates inbreeding depression and loss of genetic variation at loci that may become of importance in the future; and (ii) avoid genetic drift, which prevents deleterious recessives (e.g., rare disease alleles) from drifting to high frequency, and prevents random drift of (functional) traits. In the genomics era, genomics data allow for many alternative measures of inbreeding and genomic relationships. Genomic relationships/inbreeding can be classified into (i) homozygosity/heterozygosity based (e.g., molecular kinship matrix); (ii) genetic drift-based, i.e., changes of allele frequencies; or (iii) IBD-based, i.e., SNPs are used in linkage analyses to identify IBD segments. Here, alternative measures of inbreeding/relationship were used to manage genetic diversity in genomic optimal contribution (GOC) selection schemes. Contrary to classic inbreeding theory, it was found that drift and homozygosity-based inbreeding could differ substantially in GOC schemes unless diversity management was based upon IBD. When using a homozygosity-based measure of relationship, the inbreeding management resulted in allele frequency changes toward 0.5 giving a low rate of increase in homozygosity for the panel used for management, but not for unmanaged neutral loci, at the expense of a high genetic drift. When genomic relationship matrices were based on drift, following VanRaden and as in GCTA, drift was low at the expense of a high rate of increase in homozygosity. The use of IBD-based relationship matrices for inbreeding management limited both drift and the homozygosity-based rate of inbreeding to their target values. Genetic improvement per percent of inbreeding was highest when GOC used IBD-based relationships irrespective of the inbreeding measure used. Genomic relationships based on runs of homozygosity resulted in very high initial improvement per percent of inbreeding, but also in substantial discrepancies between drift and homozygosity-based rates of inbreeding, and resulted in a drift that exceeded its target value. The discrepancy between drift and homozygosity-based rates of inbreeding was caused by a covariance between initial allele frequency and the subsequent change in frequency, which becomes stronger when using data from whole genome sequence.

Genomic selection strategies to improve maternal traits in Norwegian White Sheep.

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.

Genetic Variation, GWAS and Accuracy of Prediction for Host Resistance to Sparicotyle chrysophrii in Farmed Gilthead Sea Bream (Sparus aurata).

Gilthead sea bream (Sparus aurata) belongs to a group of teleost which has high importance in Mediterranean aquaculture industry. However, industrial production is increasingly compromised by an elevated outbreak of diseases in sea cages, especially a disease caused by monogeneans parasite Sparicotyle chrysophrii. This parasite mainly colonizes gill tissues of host and causes considerable economical losses with mortality and reduction in growth. The aim of current study was to explore the genetics of host resistance against S. chrysophrii and investigate the potential for genomic selection to possibly accelerate genetic progress. To achieve the desired goals, a test population derived from the breeding nucleus of Andromeda Group was produced. This experimental population was established by crossing of parents mated in partial factorial crosses of ∼8 × 8 using 58 sires and 62 dams. The progeny obtained from this mating design was challenged with S. chrysophrii using a controllable cohabitation infection model. At the end of the challenge, fish were recorded for parasite count, and all the recorded fish were tissue sampled for genotyping by sequencing using 2b-RAD methodology. The initial (before challenge test) and the final body weight (after challenge test) of the fish were also recorded. The results obtained through the analysis of phenotypic records (n = 615) and the genotypic data (n = 841, 724 offspring and 117 parents) revealed that the resistance against this parasite is lowly heritable (h 2 = 0.147 with pedigree and 0.137 with genomic information). We observed moderately favorable genetic correlation (R g = -0.549 to -0.807) between production traits (i.e., body weight and specific growth rate) and parasite count, which signals a possibility of indirect selection. A locus at linkage group 17 was identified that surpassed chromosome-wide Bonferroni threshold which explained 22.68% of the total genetic variance, and might be playing role in producing genetic variation. The accuracy of prediction was improved by 8% with genomic information compared to pedigree.

Strong selection pressures maintain divergence on genomic islands in Atlantic cod (Gadus morhua L.) populations.

BACKGROUND: Two distinct populations have been extensively studied in Atlantic cod (Gadus morhua L.): the Northeast Arctic cod (NEAC) population and the coastal cod (CC) population. The objectives of the current study were to identify genomic islands of divergence and to propose an approach to quantify the strength of selection pressures using whole-genome single nucleotide polymorphism (SNP) data. After applying filtering criteria, information on 93 animals (9 CC individuals, 50 NEAC animals and 34 CC × NEAC crossbred individuals) and 3,123,434 autosomal SNPs were used. RESULTS: Four genomic islands of divergence were identified on chromosomes 1, 2, 7 and 12, which were mapped accurately based on SNP data and which extended in size from 11 to 18 Mb. These regions differed considerably between the two populations although the differences in the rest of the genome were small due to considerable gene flow between the populations. The estimates of selection pressures showed that natural selection was substantially more important than genetic drift in shaping these genomic islands. Our data confirmed results from earlier publications that suggested that genomic islands are due to chromosomal rearrangements that are under strong selection and reduce recombination between rearranged and non-rearranged segments. CONCLUSIONS: Our findings further support the hypothesis that selection and reduced recombination in genomic islands may promote speciation between these two populations although their habitats overlap considerably and migrations occur between them.

Dietary Fish Oil Alters DNA Methylation of Genes Involved in Polyunsaturated Fatty Acid Biosynthesis in Muscle and Liver of Atlantic Salmon (Salmo salar).

Adequate dietary supply of eicosapentaenoic acid (20:5n-3) and docosahexaenoic acid (22:6n-3) is required to maintain health and growth of Atlantic salmon (Salmo salar). However, salmon can also convert α-linolenic acid (18:3n-3) into eicosapentaenoic acid (20:5n-3) and docosahexaenoic acid (22:6n-3) by sequential desaturation and elongation reactions, which can be modified by 20:5n-3 and 22:6n-3 intake. In mammals, dietary 20:5n-3 + 22:6n-3 intake can modify Fads2 expression (Δ6 desaturase) via altered DNA methylation of its promoter. Decreasing dietary fish oil (FO) has been shown to increase Δ5fad expression in salmon liver. However, it is not known whether this is associated with changes in the DNA methylation of genes involved in polyunsaturated fatty acid synthesis. To address this, we investigated whether changing the proportions of dietary FO and vegetable oil altered the DNA methylation of Δ6fad_b, Δ5fad, Elovl2, and Elovl5_b promoters in liver and muscle from Atlantic salmon and whether any changes were associated with mRNA expression. Higher dietary FO content increased the proportions of 20:5n-3 and 22:6n-3 and decreased Δ6fad_b mRNA expression in liver, but there was no effect on Δ5fad, Elovl2, and Elovl5_b expression. There were significant differences between liver and skeletal muscle in the methylation of individual CpG loci in all four genes studied. Methylation of individual Δ6fad_b CpG loci was negatively related to its expression and to proportions of 20:5n-3 and 22:6n-3 in the liver. These findings suggest variations in dietary FO can induce gene-, CpG locus-, and tissue-related changes in DNA methylation in salmon.

Individual differences in EPA and DHA content of Atlantic salmon are associated with gene expression of key metabolic processes.

The aim of this study was to explore how individual differences in content of the omega-3 fatty acids EPA and DHA in skeletal muscle of slaughter-sized Atlantic salmon, are associated with expression of genes involved in key metabolic processes. All experimental fish were fed the same diet throughout life and fasted for 14 days prior to slaughter. Still, there were relatively large individual variations in EPA and DHA content of skeletal muscle. Higher DHA content was concurrent with increased expression of genes of the glycolytic pathway and the production of pyruvate and lactate, whereas EPA was associated with increased expression of pentose phosphate pathway and glycogen breakdown genes. Furthermore, EPA, but not DHA, was associated with expression of genes involved in insulin signaling. Expression of genes specific for skeletal muscle function were positively associated with both EPA and DHA. EPA and DHA were also associated with expression of genes related to eicosanoid and resolvin production. EPA was negatively associated with expression of genes involved in lipid catabolism. Thus, a possible reason why some individuals have a higher level of EPA in the skeletal muscle is that they deposit - rather than oxidize - EPA for energy.

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish.

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.

Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing.

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.

Genetic effects of fatty acid composition in muscle of Atlantic salmon.

BACKGROUND: The replacement of fish oil (FO) and fishmeal with plant ingredients in the diet of farmed Atlantic salmon has resulted in reduced levels of the health-promoting long-chain polyunsaturated omega-3 fatty acids (n-3 LC-PUFA) eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) in their filets. Previous studies showed the potential of selective breeding to increase n-3 LC-PUFA levels in salmon tissues, but knowledge on the genetic parameters for individual muscle fatty acids (FA) and their relationships with other traits is still lacking. Thus, we estimated genetic parameters for muscle content of individual FA, and their relationships with lipid deposition traits, muscle pigmentation, sea lice and pancreas disease in slaughter-sized Atlantic salmon. Our aim was to evaluate the selection potential for increased n-3 LC-PUFA content and provide insight into FA metabolism in Atlantic salmon muscle. RESULTS: Among the n-3 PUFA, proportional contents of alpha-linolenic acid (ALA; 18:3n-3) and DHA had the highest heritability (0.26) and EPA the lowest (0.09). Genetic correlations of EPA and DHA proportions with muscle fat differed considerably, 0.60 and 0.01, respectively. The genetic correlation of DHA proportion with visceral fat was positive and high (0.61), whereas that of EPA proportion with lice density was negative. FA that are in close proximity along the bioconversion pathway showed positive correlations with each other, whereas the start (ALA) and end-point (DHA) of the pathway were negatively correlated (- 0.28), indicating active bioconversion of ALA to DHA in the muscle of fish fed high FO-diet. CONCLUSIONS: Since contents of individual FA in salmon muscle show additive genetic variation, changing FA composition by selective breeding is possible. Taken together, our results show that the heritabilities of individual n-3 LC-PUFA and their genetic correlations with other traits vary, which indicates that they play different roles in muscle lipid metabolism, and that proportional muscle contents of EPA and DHA are linked to body fat deposition. Thus, different selection strategies can be applied in order to increase the content of healthy omega-3 FAin the salmon muscle. We recommend selection for the proportion of EPA + DHA in the muscle because they are both essential FA and because such selection has no clear detrimental effects on other traits.

Mating structures for genomic selection breeding programs in aquaculture.

BACKGROUND: In traditional family-based aquaculture breeding, each sire is mated to two dams in order to separate the sire's genetic effect from other family effects. Factorial mating involves more mates per sire and/or dam and result in more but smaller full- and/or half-sib families. For traits measured on sibs of selection candidates, factorial mating increases intensity of selection between families when selection is on traditional best linear unbiased prediction (BLUP) estimated breeding values (TRAD-EBV). However, selection on genome-wide estimated breeding values (GW-EBV), uses both within- and between-family effects and the advantage of factorial mating is less obvious. Our aim was to compare by computer simulation the impact of various factorial mating strategies for truncation selection on TRAD-EBV versus GW-EBV on rates of inbreeding, accuracy of selection and genetic gain for two traits, i.e. one measured on selection candidates (CAND-TRAIT) and one on their sibs (SIB-TRAIT). RESULTS: Sire:dam mating ratios of 1:1, 2:2 or 10:10 were tested with 100, 200 or 1000 families produced from a constant number of parents (100 sires and 100 dams), and a mating ratio of 1:2 with 200 families produced from 100 sires and 200 dams. With GW-EBV, changing the mating ratio from 1:1 to 10:10 had a limited effect on genetic gain (less than 5 %) for both CAND-TRAIT and SIB-TRAIT, whereas with TRAD-EBV, selection intensity increased for SIB-TRAIT and genetic gain increased by 41 and 77 % for schemes with 3000 and 12,000 selection candidates, respectively. For both GW-EBV and TRAD-EBV, rates of inbreeding decreased by up to ~30 % when the mating ratio was changed from 1:1 to 10:10 for schemes with 3000 to 12,000 selection candidates. Similar results were found for alternative heritabilities of SIB-TRAIT and total number of tested sibs. CONCLUSIONS: Changing the sire:dam mating ratio from 1:1 to 10:10 increased genetic gain substantially with TRAD-EBV, mainly through increased selection intensity for the SIB-TRAIT, whereas with GW-EBV, it had a limited effect on genetic gain for both traits. Rates of inbreeding decreased for both selection methods.

Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod.

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.

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress.

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

Genetic heterogeneity of within-family variance of body weight in Atlantic salmon (Salmo salar).

BACKGROUND: Canalization is defined as the stability of a genotype against minor variations in both environment and genetics. Genetic variation in degree of canalization causes heterogeneity of within-family variance. The aims of this study are twofold: (1) quantify genetic heterogeneity of (within-family) residual variance in Atlantic salmon and (2) test whether the observed heterogeneity of (within-family) residual variance can be explained by simple scaling effects. RESULTS: Analysis of body weight in Atlantic salmon using a double hierarchical generalized linear model (DHGLM) revealed substantial heterogeneity of within-family variance. The 95% prediction interval for within-family variance ranged from ~0.4 to 1.2 kg2, implying that the within-family variance of the most extreme high families is expected to be approximately three times larger than the extreme low families. For cross-sectional data, DHGLM with an animal mean sub-model resulted in severe bias, while a corresponding sire-dam model was appropriate. Heterogeneity of variance was not sensitive to Box-Cox transformations of phenotypes, which implies that heterogeneity of variance exists beyond what would be expected from simple scaling effects. CONCLUSIONS: Substantial heterogeneity of within-family variance was found for body weight in Atlantic salmon. A tendency towards higher variance with higher means (scaling effects) was observed, but heterogeneity of within-family variance existed beyond what could be explained by simple scaling effects. For cross-sectional data, using the animal mean sub-model in the DHGLM resulted in biased estimates of variance components, which differed substantially both from a standard linear mean animal model and a sire-dam DHGLM model. Although genetic differences in canalization were observed, selection for increased canalization is difficult, because there is limited individual information for the variance sub-model, especially when based on cross-sectional data. Furthermore, potential macro-environmental changes (diet, climatic region, etc.) may make genetic heterogeneity of variance a less stable trait over time and space.