Search

Arctic charr (Salvelinus alpinus) is a niche‐market high‐value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole‐genome re‐sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era. [ABSTRACT FROM AUTHOR]

Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise Fst values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner. [ABSTRACT FROM AUTHOR]

The Arctic charr breeding programme has been a main driving force for developing the aquaculture industry in Sweden. Selection has been performed for almost 40 years using animals from a closed breeding nucleus. The aim of the current study was to evaluate the potential of further improving growth‐related traits taking into account the existence of genotype‐by‐environment interaction. Furthermore, we investigated the magnitude of the genetic component associated with survival to the eyed stage and potential associations with inbreeding coefficients. A preliminary heritability estimate of 0.23 (SE 0.20) was obtained for survival to the eyed stage using records spanning from 2000 to 2017 (n = 230). Moreover, moderate‐to‐high heritability estimates (0.27–0.49) were obtained for growth‐related traits (body weight and length), using animals from the latest generation of selection (year class 2017). Those animals (n = 2,776), originating from 55 full‐sib families, were split into two groups and reared in separate land‐based facilities of commercial fish farms in Sweden. The growth‐related traits were recorded twice in both sites when animals were of >1 and >2 years of age. Existence of sexual growth dimorphism was indicated with the males having on average 6%–8% higher total length and 22%–34% higher body weight. Furthermore, high genetic correlations regarding growth traits were obtained amongst animals reared at the two different sites (0.82–0.95). In addition, we assessed the accuracy of best linear unbiased prediction (BLUP)‐derived estimated breeding values (EBVs) when phenotypes from each rearing site were subsequently masked and used as a validation set. A mean prediction accuracy of 0.60 (length) and 0.64 (weight) were derived for both rearing sites. Overall, our results suggest that further growth improvements should be possible in the subsequent generations of selection. Finally, even though indications for the existence of an underlying genetic component(s) involved in survival to the eyed stage were obtained additional data will be required for elucidating its magnitude. [ABSTRACT FROM AUTHOR]

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, FST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program. [ABSTRACT FROM AUTHOR]

Limited knowledge exists about the residing microbiome in gamete-related samples in fish. A potential effect between the seminal microbiome composition and sperm quality traits has been previously suggested in humans and livestock. Using a metabarcoding approach, we aimed to gain insights into the structure of the residing prokaryotes and microbial eukaryotes in ovarian fluid (n = 10) and milt (n = 84) from farmed Arctic charr - a species with highly variable reproductive success in captivity. In addition, sperm quality traits were recorded on the sampled males to investigate potential associations with the residing seminal microbiome. Higher microbial diversity was found in the ovarian fluid compared to the milt habitat. Even though the residing microbiome showed distinct differences between the two habitats, substantial overlap was observed, with >70% of the milt core microbiome being found in the ovarian fluid habitat. Statistically significant associations were found between the Shannon diversity index and sperm motility-related traits. Additionally, a fungal operational taxonomic unit (OTU) potentially belonging to the Leotiomycetes class was associated with sperm concentration and motility. Overall, our study documents the microbiome structure of gamete-related samples from Arctic charr. Even though some associations were obtained between sperm quality parameters and either microbiome diversity or with a fungal OTU, follow-up studies on a larger scale with more tank replicates are needed to confirm the robustness and causality of these relationships. • First report of the residing microbiome structure in gamete-related samples on fish • Associations were found between the Shannon diversity index and sperm motility-related traits. • A fungal operational taxonomic unit was associated with sperm concentration and motility. [ABSTRACT FROM AUTHOR]