Benchmark Animal Health (United Kingdom)

ABSTRACT MicroRNAs (miRNAs) are key post-transcriptional regulators of antiviral immunity, controlling gene expression by targeting 3’ UTRs of immune-related transcripts. Despite their importance, the role of miRNAs in viral nervous necrosis (VNN) resistance in European seabass ( Dicentrarchus labrax ) is unexplored. Here, we characterized for the first time the brain miRNome of seabass from three VNN-resistance genotypes (susceptible, intermediate, resistant) across two genetically distinct seabass clusters. Differential expression analyses revealed cluster-specific patterns, with susceptible fish consistently showing overexpression of the differently expressed miRNAs (DEmiRNAs) as compared to the resistant fish. Considering the two genetic clusters in the study, miR–199–5p was differentially expressed between the VNN susceptible and resistant fish. This miRNA was found to be less expressed in the resistant individuals. Functional characterization of the miRNA predicted that it binds to two distinct miRNA recognition elements (MREs) within the ifi27l2a 3’ UTR. These MREs flank a SNP (Chr3:10,082,380) previously associated with VNN survival. A strong negative correlation (r= -0.840) between miR–199–5p expression and ifi27l2a mRNA abundance further supports a post–transcriptional repression mechanism. Together, these results propose a regulatory model in which miR–199–5p modulates ifi27l2a expression, contributing to phenotypic variation in VNN resistance and positioning it as a promising biomarker for seabass aquaculture breeding.

The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices. In a commercial setting, we explore the genetic structure of growth characteristics, measure genotype-environment interactions (GxE) in salmon smolts, and examine genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net-pens and RAS. After an 8-week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re-ranking for whole-body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented.

ABSTRACTBackgroundSalmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown.ResultsWe characterised the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12h, 24h, 36h, 48h, and 60h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite.ConclusionOur results highlight the key role of keratinocytes to coho salmon’s sea lice resistance, and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

BackgroundFlavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease that affects rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of the host resistance. However, genomic selection is expensive partly because of the cost of genotyping large numbers of animals using high-density single nucleotide polymorphism (SNP) arrays. The objective of this study was to assess the efficiency of genomic selection for resistance to F. columnare using in silico low-density (LD) panels combined with imputation. After a natural outbreak of columnaris disease, 2874 challenged fish and 469 fish from the parental generation (n = 81 parents) were genotyped with 27,907 SNPs. The efficiency of genomic prediction using LD panels was assessed for 10 panels of different densities, which were created in silico using two sampling methods, random and equally spaced. All LD panels were also imputed to the full 28K HD panel using the parental generation as the reference population, and genomic predictions were re-evaluated. The potential of prioritizing SNPs that are associated with resistance to F. columnare was also tested for the six lower-density panels.ResultsThe accuracies of both imputation and genomic predictions were similar with random and equally-spaced sampling of SNPs. Using LD panels of at least 3000 SNPs or lower-density panels (as low as 300 SNPs) combined with imputation resulted in accuracies that were comparable to those of the 28K HD panel and were 11% higher than the pedigree-based predictions.ConclusionsCompared to using the commercial HD panel, LD panels combined with imputation may provide a more affordable approach to genomic prediction of breeding values, which supports a more widespread adoption of genomic selection in aquaculture breeding programmes.

Background: Flavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease affecting rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of host resistance. However, genomic selection is expensive partly due to the cost of genotyping high numbers of animals using high-density SNP arrays. The objective of this study was to assess the efficiency of genomic selection for resistance to F. columnare using in silico low-density (LD) panels combined with imputation. After a natural outbreak of columnaris disease, 2,874 challenged fish and 469 fish from the parental generation (n=81 parents) were genotyped with 27,907 SNPs. The efficiency of genomic prediction using LD-panels was assessed for panels of 10 different densities, created in silico using two sampling methods, random and equally spaced. All LD-panels were also imputed to the full 28K HD-panel using the parental generation as the reference population, and genomic predictions were reevaluated. The potential of prioritizing SNPs showing association with resistance to F. columnare was also tested for the six lower densities. Results: Similar results were obtained with random and equally spaced sampling of SNPs for accuracy of both imputation and genomic predictions. Using LD-panels of at least 3,000 makers or lower density panels (as low as 300 markers) combined with imputation resulted in comparable accuracy to the 28K HD-panel and 11% higher accuracy than pedigree-based predictions. Conclusions: Compared to using the commercial HD-panel, LD-panels with imputation may provide a more affordable route to genomic prediction of breeding values, supporting wider adoption of genomic selection in aquaculture breeding programmes.

Intraperitoneal (i.p.) injection vaccination is considered effective to protect European sea bass (Dicentrarchus labrax) from economically important diseases. Water-based as well as oil-adjuvanted vaccine formulations are being widely used. The oil adjuvants used to potentiate antigen effects lead to higher and more prolonged immune response but also to chronic peritoneal inflammatory reactions, regarded as adverse or side-effects. During a three-year field study conducted throughout Greek mariculture, the intra-abdominal lesions were assessed on fish sampled prior to, and at different times post i.p. injection with different oil-adjuvanted vaccine formulations. The scope was to create a macroscopic side-effect intensity scale for sea bass in line with those applicable to salmonids (Salmo salar, Oncorhynchus mykiss) and cod (Gadus morhua). The diversity of lesions observed ranged from none (presumably non-injected; score 0) to widespread, strong adhesions with granuloma, pigmented or not (score 6). The occurrence of small nodules apparently containing vaccine remains, encapsulated by layers of connective tissue is described. The proposed scoring system is described and illustrated, intended to guide farm staff to evaluate the intensity of post-injection vaccination side-effects by necropsy on site.

Digit amputation is a commonly performed surgery in cattle practice. The most frequent reason for digit amputation is septic pedal arthritis, but other indications include severe trauma, pedal osteitis, non-healing sole, wall or toe ulcers, osteomyelitis of P2, septic tenosynovitis of the distal digital flexor tendons and other infectious processes of the deep digital structures. The procedure is considered a salvage procedure, but good rates of success are reported. The size of the patient is one of the key determinants of prognosis, with reported success rates varying between bulls, cows and calves. Reported complications include haemorrhage, avascular necrosis of the phalangeal fragments, wound infection and fracture of the partner claw. In this case report the authors describe digit amputation under regional and general anaesthesia for the treatment of proximal interphalangeal septic arthritis and the subsequent wound management in the face of a multidrug resistant Pseudomonas aeruginosa infection.