Identification and Genomic Localization of Autosomal sdY Locus in a Population of Atlantic Salmon (Salmo salar).

The determination of sex in salmonid fishes is controlled by genetic mechanisms, with males being the heterogametic sex. The master sex-determining gene, the sexually dimorphic gene on the Y chromosome (sdY), is a conserved gene across various salmonid species. Nevertheless, variations in the genomic location of sdY have been observed both within and between species.

Identification of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant in Atlantic Salmon ( L.) that can Cause High Mortality Even in Genetically Resistant Fish.

Infectious pancreatic necrosis (IPN) is an important viral disease of salmonids that can affect fish during various life cycles. In Atlantic salmon, selecting for genetically resistant fish against IPN has been one of the most highly praised success stories in the history of fish breeding. During the late 2000s, the findings that resistance against this disease has a significant genetic component, which is mainly controlled by variations in a single gene, have helped to reduce the IPN outbreaks to a great extent.

Identification of genetic loci associated with higher resistance to pancreas disease (PD) in Atlantic salmon (Salmo salar L.).

Background: Pancreas disease (PD) is a contagious disease caused by salmonid alphavirus (SAV) with significant economic and welfare impacts on salmon farming. Previous work has shown that higher resistance against PD has underlying additive genetic components and can potentially be improved through selective breeding. To better understand the genetic basis of PD resistance in Atlantic salmon, we challenged 4506 smolts from 296 families of the SalmoBreed strain.

Genome-Wide Association Study Confirms Previous Findings of Major Loci Affecting Resistance to in Atlantic Salmon ( L.).

Cardiomyopathy syndrome is a viral disease of Atlantic salmon, mostly affecting fish during the late stages of production, resulting in significant losses to the industry. It has been shown that resistance to this disease has a strong genetic component, with quantitative trait loci (QTL) on chromosomes 27 (Ssa27) and Ssa12 to explain most of the additive genetic variance. Here, by analysing animals from a different year-class and a different population, we further aimed to confirm and narrow down the locations of these QTL.

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.

Genome-Wide Association Study of Piscine Myocarditis Virus (PMCV) Resistance in Atlantic Salmon (Salmo salar).

Cardiomyopathy syndrome is a severe, viral disease of Atlantic salmon that mostly affects farmed animals during their late production stage at sea. Caused by piscine myocarditis virus (PMCV), over the past few years outbreaks due to this disease have resulted in significant losses to the aquaculture industry. However, there is currently no vaccine that has proven effective against this virus.

Early Developmental Stress Affects Subsequent Gene Expression Response to an Acute Stress in Atlantic Salmon: An Approach for Creating Robust Fish for Aquaculture?

Stress during early life has potential to program and alter the response to stressful events and metabolism in later life. Repeated short exposure of Atlantic salmon to cold water and air during embryonic (E), post-hatch (PH) or both phases of development (EPH) has been shown to alter the methylome and transcriptome and to affect growth performance during later life compared to untreated controls (CO). The aim of this study was to investigate how the transcriptome of these fish responds to subsequent acute stress at the start feeding stage, and to describe methylation differences that might steer these changes.

Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon ( L.).

Amoebic gill disease (AGD) is one of the most important parasitic diseases of farmed Atlantic salmon. It is a source of major economic loss to the industry and poses significant threats to animal welfare. Previous studies have shown that resistance against this disease has a moderate, heritable genetic component, although the genes and the genetic pathways that contribute to this process have yet to be elucidated.

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.

Lack of Truncated IFITM3 Transcripts in Cells Homozygous for the rs12252-C Variant That is Associated With Severe Influenza Infection.

Interferon-induced transmembrane 3 (IFITM3) is known to restrict the entry of a range of enveloped viruses. The single nucleotide polymorphism rs12252-C within IFITM3 has been shown to be associated with severe influenza A virus infection. It has been suggested that rs12252-C results in expression of a truncated IFITM3 protein lacking the first 21 amino acids.

Impacts of Early Life Stress on the Methylome and Transcriptome of Atlantic Salmon.

Exposure to environmental stressors during early-life stages can change the rate and timing of various developmental processes. Epigenetic marks affecting transcriptional regulation can be altered by such environmental stimuli. To assess how stress might affect the methylome and transcriptome in salmon, fish were treated using cold-shock and air-exposure from the eye-stage until start-feeding.

Gene expression profiling in melanised sites of Atlantic salmon fillets.

Black spots, which deteriorate quality of Atlantic salmon fillets represent a significant problem for commercial aquaculture. These areas are characterized with accumulation of melanomacrophages, occasional formation of granulomas and substitution of skeletal muscle with connective tissue. A number of possible causative agents have been suggested including vaccination and infection with piscine reovirus (PRV).

The Atlantic Bonito (Sarda sarda, Bloch 1793) transcriptome and detection of differential expression during larvae development.

The Atlantic bonito (Sarda sarda, Bloch 1793) belongs to the important marine fish species with a wide geographical distribution covering the Atlantic Ocean, the Mediterranean and its bordering seas. Aquaculture practices for this species are still in their infancies and scientific studies are seldom undertaken, mainly because of difficulties in sampling. Thus for small tuna species like the Atlantic bonito only little is known about its biology and regarding the molecular background even less information is available.

The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome.

We assembled a de novo transcriptome of short-read Illumina RNA-Seq data generated from telencephalon and diencephalon tissue samples from the Kentish plover, Charadrius alexandrinus. This is a species of considerable interest in behavioural ecology for its highly variable mating system and parental behaviour, but it lacks genomic resources and is evolutionarily distant from the few available avian draft genome sequences. We assembled and identified over 21,000 transcript contigs with significant expression in our samples, showing high homology to exonic sequences in avian draft genomes.

Trade-off between selection for dosage compensation and masculinization on the avian Z chromosome.

Following the suppression of recombination, gene expression levels decline on the sex-limited chromosome, and this can lead to selection for dosage compensation in the heterogametic sex to rebalance average expression from the X or Z chromosome with average autosomal expression. At the same time, due to their unequal pattern of inheritance in males and females, the sex chromosomes are subject to unbalanced sex-specific selection, which contributes to a nonrandom distribution of sex-biased genes compared to the remainder of the genome. These two forces act against each other, and the relative importance of each is currently unclear.

Characterization and 454 pyrosequencing of major histocompatibility complex class I genes in the great tit reveal complexity in a passerine system.

Background: The critical role of Major Histocompatibility Complex (Mhc) genes in disease resistance and their highly polymorphic nature make them exceptional candidates for studies investigating genetic effects on survival, mate choice and conservation. Species that harbor many Mhc loci and high allelic diversity are particularly intriguing as they are potentially under strong selection and studies of such species provide valuable information as to the mechanisms maintaining Mhc diversity. However comprehensive genotyping of complex multilocus systems has been a major challenge to date with the result that little is known about the consequences of this complexity in terms of fitness effects and disease resistance.

W chromosome expression responds to female-specific selection.

The W chromosome is predicted to be subject to strong female-specific selection stemming from its female-limited inheritance and therefore should play an important role in female fitness traits. However, the overall importance of directional selection in shaping the W chromosome is unknown because of the powerful degradative forces that act to decay the nonrecombining sections of the genome. Here we greatly expand the number of known W-linked genes and assess the expression of the W chromosome after >100 generations of different female-specific selection regimens in different breeds of chicken and in the wild ancestor, the Red Jungle Fowl.

Genome evolution in the fish family salmonidae: generation of a brook charr genetic map and comparisons among charrs (Arctic charr and brook charr) with rainbow trout.

Background: Salmonids are regarded as 4R derivative species, having experienced 4 whole genome duplication events in their ancestry. Many duplicated chromosome regions still share extensive homology with one another which is maintained primarily through male-based homeologous chromosome pairings during meiosis. The formation of quadrivalents during meiosis leads to pseudolinkage.

Genetic architecture of body weight, condition factor and age of sexual maturation in Icelandic Arctic charr (Salvelinus alpinus).

The high commercial value from the aquaculture of salmonid fishes has prompted many studies into the genetic architecture of complex traits and the need to identify genomic regions that have repeatable associations with trait variation both within and among species. We searched for quantitative trait loci (QTL) for body weight (BW), condition factor (CF) and age of sexual maturation (MAT) in families of Arctic charr (Salvelinus alpinus) from an Icelandic breeding program. QTL with genome-wide significance were detected for each trait on multiple Arctic charr (AC) linkage groups (BW: AC-4, AC-20; CF: AC-7, AC-20, AC-23, AC-36; MAT: AC-13/34, AC-39).

Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling.

Background: Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. Clock1 duplicates and copies of Clock3 and NPAS2-like genes were partially characterized (genomic sequencing) and mapped using family-based indels/SNPs in rainbow trout (RT)(Oncorhynchus mykiss), Arctic charr (AC)(Salvelinus alpinus), and Atlantic salmon (AS)(Salmo salar) mapping panels.

Results: Clock1 duplicates mapped to linkage groups RT-8/-24, AC-16/-13 and AS-2/-18.

Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss).

Background: Somatic growth is a complex process that involves the action and interaction of genes and environment. A number of quantitative trait loci (QTL) previously identified for body weight and condition factor in rainbow trout (Oncorhynchus mykiss), and two other salmonid species, were used to further investigate the genetic architecture of growth-influencing genes in this species. Relationships among previously mapped candidate genes for growth and their co-localization to identified QTL regions are reported.

Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout.

Background: Recent advances in the accumulation of genetic mapping and DNA sequence information from several salmonid species support the long standing view of an autopolyploid origin of these fishes (i.e., 4R).

Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon).

Background: Comparative genomic studies suggest that the modern day assemblage of ray-finned fishes have descended from an ancestral grouping of fishes that possessed 12-13 linkage groups. All jawed vertebrates are postulated to have experienced two whole genome duplications (WGD) in their ancestry (2R duplication). Salmonids have experienced one additional WGD (4R duplication event) compared to most extant teleosts which underwent a further 3R WGD compared to other vertebrates.

Determination of quantitative trait loci (QTL) for early maturation in rainbow trout (Oncorhynchus mykiss).

To identify quantitative trait loci (QTL) influencing early maturation (EM) in rainbow trout (Oncorhynchus mykiss), a genome scan was performed using 100 microsatellite loci across 29 linkage groups. Six inter-strain paternal half-sib families using three inter-strain F(1) brothers (approximately 50 progeny in each family) derived from two strains that differ in the propensity for EM were used in the study. Alleles derived from both parental sources were observed to contribute to the expression of EM in the progeny of the brothers.