Reproductive performance of farmed Arctic charr

The production of farmed Arctic charr (Salvelinus alpinus) has increased rapidly over the last decade, and the industry is predicted to continue to grow in the coming years. One major bottleneck for this future expansion concerns the supply of viable eggs and juveniles. Hatching rates of Arctic charr eggs in aquaculture are generally much lower than for other farmed salmonids, and exhibit a large variation between individuals and years. The aim of this thesis is to evaluate current hatchery conditions and to deepen the understanding on how environmental and biological factors affect the reproductive performance of Arctic charr in routine farming. The thesis comprises four separate studies. In paper I, records of biological and environmental variables and individual egg survival data from an Arctic charr hatchery, covering a period of 12 years, were analysed in an attempt to find single and combined factors that can explain some of the variation in egg survival. Rearing temperature during summer was identified as the most critical factor for reproductive success of the current broodstock. The study also revealed strong positive relationships between female age, egg size, and egg viability, most likely enhanced by the thermal stress experienced by the broodstock. Paper II assessed broodstock rearing temperature and egg viability over a period of 28 years with focus on thermal stress in a changing climate. Mean summer water temperatures in the hatchery increased by approximately 2°C from 1986 to 2010. The temperature increase was most evident in July but was also apparent in May, August, and September. Egg survival was most closely linked to September temperatures, which indicates that it is not necessarily the warmest days that are the most detrimental. Paper III is a study on egg incubation temperature, and the first, to my knowledge, to show that the initial stages of embryogenesis in Arctic charr are much more cold-sensitive than later in the incubation period. Incubations initiated at low temperature (2.3°C to 2.8°C) resulted in significantly higher mortality and deformity rates. Paper IV is a case study which assessed hormonal status and gamete quality of male and female Arctic charr during routine artificial fertilisation. Female plasma levels of maturation inducing hormone during stripping indicated that post-ovulation aging of oocytes can explain part of the egg loss. The results also suggest that the paternal effect on reproductive performance of the current broodstock is considerable

Evaluating the potential of improving sperm quality traits in farmed Arctic charr (Salvelinus alpinus) using selective breeding

Arctic charr (Salvelinus alpinus) is a high-value species for the Nordic aquaculture. The highly variable reproductive performance that is commonly observed in commercial farms is hindering the expansion of the Arctic charr industry in Sweden. Traits related to sperm motility (total motility; curvilinear velocity; average path velocity; straight-line velocity) and concentration can play a pivotal role in male fertility. Selective breeding practices could offer solutions and contribute to improving male fertility. The current study aimed to investigate the magnitude of genetic variance for sperm quality traits in a selectively bred population of Arctic charr from Sweden and evaluate the possibility of their improvement through selection. Sperm motility and concentration were recorded using a computer-assisted semen analysis (CASA) system and a NucleoCounter, respectively, in over 400 males from year-class 2017. Double digest restriction-site associated DNA sequencing (ddRAD-seq) was applied in a subset of the recorded animals (n = 329), resulting in the detection of over 5000 single nucleotide polymorphisms (SNPs). Moderate heritability estimates were obtained for the recorded semen traits using both pedigree (0.21-0.32; SE 0.09) and genomic (0.23-0.26; SE 0.09) relationship matrices. A genome-wide association study (GWAS) detected a single SNP significantly associated (P < 1e-05) with total sperm motility on chromosome LG7 in relatively close proximity (500 Kb) to PTPN11 a gene previously associated with sperm quality traits in mammals. Moreover, weighted single-step genomic best linear unbiased prediction (WssGBLUP) pinpointed genomic regions explaining more than 3 % of the additive genetic variance for both the motility traits and the sperm concentration. Finally, the efficiency of genomic prediction was tested using a 3-fold cross-validation scheme. Higher prediction accuracy for total motility and velocities (both curvilinear and average path) was obtained using genomic information (0.26-0.29, SE 0.03-0.06) compared to pedigree (0.20-0.28, SE 0.04-0.07), while for sperm concentration a pedigree-based model (0.22 SE 0.03) was more efficient than the genomic model (0.14 SE 0.04). Overall, our results indicate that the recorded sperm quality traits are heritable, and could be improved through selective breeding practices

Insights from the early generations of the Swedish rainbow trout (Oncorhynchus mykiss) breeding program

This study aimed to gain insights about the status of the Swedish breeding program through studying key phenotypic traits. In total, 133 and 73 full-sib families were formed during the reproductive seasons of 2016 and 2019, respectively. Growth-related recordings were available from two occasions: & SIM; 9 and 24-27 months post-hatch. A preliminary descriptive analysis of the fecundity and early embryo survival identified substantial differences in favor of G0 (year class 2016) which was partly explained by the fact that first-time 3-year-old spawners were used in G1 (year class 2019). Moderate to high heritability values (0.23-0.49) were obtained for body length and weight across both time points and generations. Furthermore, the prediction accuracy of the estimated breeding values was & SIM;0.65, while the expected genetic gain was 36 g per year. Overall, our results demonstrate the positive performance of the Swedish rainbow trout breeding program

Microbiome structure of milt and ovarian fluid in farmed Arctic charr (Salvelinus alpinus)

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 be-tween the Shannon diversity index and sperm motility-related traits. Additionally, a fungal operational taxo-nomic 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 di-versity 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

Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus)

Background Substantial variation in male fertility is regularly observed in farmed Arctic charr. However, detailed investigations of its fluctuation during a reproductive season and across years are lacking. Furthermore, information about the effect of underlying genetic factors influencing sperm quality is scarce. The current study focused on seasonal and age-related factors that may affect sperm quality characteristics in males reared in natural and delayed photoperiods. Animals were sampled three times for two consecutive years, and sperm quality parameters were recorded using a computer-assisted sperm analysis (CASA) system. Thereafter, high-throughput sequencing technologies were applied, aiming to identify genomic regions related to the variation of sperm quality throughout the reproductive season.Results An across-season variation in the recorded sperm quality parameters was evident. Overall, 29% and 42% of males from the natural and delayed spawning groups had a highly variable total progressive motility. Males at four years of age showed significantly higher sperm motility and velocities during the early October and November recordings compared to the following year when the same animals were five years of age. On the other hand, the opposite was observed regarding sperm concentration during the last sampling. A genome-wide F-ST scan detected SNP differentiation among males with high and low variability in total progressive motility (PM) on eight chromosomes (F-ST > 0.17), Genome wide windows with the highest F-ST contained SNPs in proximity (within 250 kb up- and downstream distance) to 16 genes with sperm quality biological functions in mammalian species.Conclusion Our findings provide a detailed view of seasonal, age-related, and genetic effects on sperm quality and can be used to guide decisions on broodstock selection and hatchery management

Field demonstration of a novel towed, area bubble-plume zooplankton (Calanus sp.) harvesting approach

SINTEF post https://www.sintef.no/en/publications/publication/?pubid=CRIStin+1097811.This paper presents field experiment results of using a new technology to harvest copepods (Calanus sp.) in the ocean by bubble upwelling. Two largo-scale bubble rafts, a 21 m2 and a flexible 75 m2 bubble raft with tow parallel and perpendicular sparger elements, respectively, were field tested in areas with high, upper 25-m water column Calanus densities. Measured bubble-driven upwelling velocities (Vup) at different air flows (Q) and depths (z0), found Vup-(f21 under stratified marine conditions, in agreement with other results for stratified conditions. Bubble trawls significantly enhanced Calanus concentrations in the upper water column, as much as 1416% integrated over the upper 2·m, with the best results for the tow-transverse raft, which also was tested under unstratified seas. Bubble trawl perfonnance aJso was related to stratification with the highest enhancement for the lowest stratification. Catch species analysis showed reduced bycatch. Thus, this new harvesting technology showed a potential to develop an economically robust, environmentally benign, and sustainable fishery on a renewable resource at lower trophic levels in the food web, within the context of ecosystem-based managemen

Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia

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 similar to 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

Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data

Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low-throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double-digest restriction-site-associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the F-ST fixation index was similar to 0.01 between the industry populations and similar to 0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (N-e) and inbreeding (based on runs of homozygosity; F-ROH) were similar amongst the three populations (N-e approximate to 50-80; median F-ROH approximate to 0.11). Finally, the haplotype-based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management

Arctic charr farming

The Arctic charr (Salvelinus alpinus L.) is a holarctic salmonid fish species with both landlocked and anadromous populations. In Scandinavia it is mainly found in the mountain area, but it also appears in deep and large lake further south, i.e. in the Alps. It is the northernmost freshwater fish and A. charr is generally regarded as the most cold-adapted freshwater fish. A. charr has been commercially farmed since the early 90ths and today, the total production is 3000, 2300 and 700 tonnes/year in Iceland, Sweden and Norway, respectively. Both in Sweden and Iceland, there are selective breeding programs in effect and the bulk of the farming production is conducted using offspring from the national breeding programs in each country. A. charr is renowned for its ability of high growth rate at low temperature and is therefore especially suitable for farming at high latitudes and altitudes. Moreover, due to the success of the breeding programs, the charr used in farms today grow faster and mature at a larger size and age than the original wild charr. Hence, although being a fairly small industry at present, A. charr farming is predicted to grow in all three countries. This booklet summarises up-to-date knowledge on A. charr farming production cycle, from brood stock to juvenile on-growing stage (Fig. 1). It is intended to be useful for people taking their first steps in A. charr culture but also to serve as a farming manual for more experienced farm staff. Therefore, the booklet is divided in to two chapters. The first chapter (Arctic charr farming in practice) provides a straight forward introduction to each production step from brood stock to juveniles. The second chapter (theory and background) presents some details and research data on the background of specific farming practices and procedures

Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus)

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, F-ST 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