Svein-Erik Fevolden

Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection

BackgroundThe Atlantic cod (Gadus morhua) is a groundfish of great economic value in fisheries and an emerging species in aquaculture. Genetic markers are needed to identify wild stocks in order to ensure sustainable management, and for marker-assisted selection and pedigree determination in aquaculture. Here, we report on the development and evaluation of a large number of Single Nucleotide Polymorphism (SNP) markers from the alignment of Expressed Sequence Tag (EST) sequences in Atlantic cod. We also present basic population parameters of the SNPs in samples of North-East Arctic cod and Norwegian coastal cod obtained from three different localities, and test for SNPs that may have been targeted by natural selection.ResultsA total of 17,056 EST sequences were used to find 724 putative SNPs, from which 318 segregating SNPs were isolated. The SNPs were tested on Atlantic cod from four different sites, comprising both North-East Arctic cod (NEAC) and Norwegian coastal cod (NCC). The average heterozygosity of the SNPs was 0.25 and the average minor allele frequency was 0.18. FSTvalues were highly variable, with the majority of SNPs displaying very little differentiation while others had FSTvalues as high as 0.83. The FSTvalues of 29 SNPs were found to be larger than expected under a strictly neutral model, suggesting that these loci are, or have been, influenced by natural selection. For the majority of these outlier SNPs, allele frequencies in a northern sample of NCC were intermediate between allele frequencies in a southern sample of NCC and a sample of NEAC, indicating a cline in allele frequencies similar to that found at the Pantophysin I locus.ConclusionThe SNP markers presented here are powerful tools for future genetics work related to management and aquaculture. In particular, some SNPs exhibiting high levels of population divergence have potential to significantly enhance studies on the population structure of Atlantic cod.

Natural selection and the genetic differentiation of coastal and Arctic populations of the Atlantic cod in northern Norway: a test involving nucleotide sequence variation at the pantophysin (PanI) locus

To examine the role of contemporary selection in maintaining significant allele frequency differences at the pantophysin (PanI) locus among populations of the Atlantic cod, Gadus morhua, in northern Norway, we sequenced 127 PanIA alleles sampled from six coastal and two Barents Sea populations. The distributions of variable sites segregating within the PanIA allelic class were then compared among the populations. Significant differences were detected in the overall frequencies of PanIA alleles among populations within coastal and Arctic regions that was similar in magnitude to heterogeneity in the distributions of polymorphic sites segregating within the PanIA allelic class. The differentiation observed at silent sites in the PanIA allelic class contradicts the predicted effects of widescale gene flow and suggests that postsettlement selection acting on cohorts cannot be responsible for the genetic differences described between coastal and Arctic populations. Our results suggest that the marked differences observed between coastal and Arctic populations of G. morhua in northern Norway at the PanI locus reflect the action of recent diversifying selection and that populations throughout the region may be more independent than suggested by previous studies.

Selection response of cortisol and lysozyme in rainbow trout and correlation to growth

Abstract Progeny groups of rainbow trout ( Oncorhynchus mykiss Walbaum) selected for high or low post-stress levels of plasma cortisol, or similarly for high or low post-stress lysozyme activity, have been tested for their response to the selection. In four of the four stress exposures, individuals from the line selected for high cortisol responsiveness displayed significantly higher levels of post-stress cortisol than individuals of the low responding line. Phenotypic correlations of cortisol response between samplings, irrespective of line, were highly significant. The realised heritability of cortisol was 0.50, which is very similar to the estimated h 2 based on the parental generation. Only in the last two of the four stress experiments did the high lysozyme selected line exhibit significantly higher lysozyme activity than the low lysozyme line. The timing of vaccination may cause this, since the vaccine is known to affect lysozyme activity. Breeding values of parents were based on vaccinated fish only. The phenotypic correlations between samplings of lysozyme response were weaker than for cortisol, though still significant. The realised heritability of lysozyme was 0.32, which is also in agreement with the previously estimated h 2 . The phenotypic correlations between cortisol and lysozyme in individual samplings were in cases of significance negative. There is qualified support for better growth performance in the low cortisol responding line as compared to the high responding line. The data are not conclusive as to establishing whether selection for altered post-stress lysozyme activity affects growth. In conclusion, the present data confirm that the progeny inherit stress-related traits identified in the parents; the response to selection for both cortisol and lysozyme is encouraging. The practical implications or gain of selecting for either trait under aquacultural conditions is still being resolved.

Disease resistance in Atlantic salmon (Salmo salar) selected for high or low responses to stress

Abstract Two lines of Atlantic salmon, which had been selected for either high or low stress response following measurements of blood cortisol levels after a standardized stress, were challenged by three bacterial pathogens. The pathogenic agents were Aeromonas salmonicida , which causes furunculosis, Vibrio salmonicida , which causes cold-water vibriosis, and Renibacterium salmoninarum , which causes bacterial kidney disease (BKD). Following challenge with furunculosis bacteria, the mortality rates during the experiments, and the cumulative mortality at the end of the experiments, were significantly higher in the high than in the low stress response line of fish. In the course of the study it appeared that the fish challenged with cold-water vibriosis and BKD had also been previously infected with furunculosis bacteria. Following challenge with cold-water vibriosis, the high-stress line displayed a poorer performance than the low-stress line in this situation of double infection whereas there were no significant differences between the two lines following BKD challenge. The immunity of the parental generation of the challenged fish was assessed by measurements of serum haemolytic activity. The results indicated a significantly lowered immunity in fish of the high-stress response line.

Disease resistance and immune characteristics in rainbow trout (Oncorhynchus mykiss) selected for lysozyme activity

Abstract To evaluate the possibility of using serum lysozyme activity as a selection criterion to improve disease resistance in aquacultured fish, lines of rainbow trout ( Oncorhynchus mykiss ) selected for high- or low-serum lysozyme activity were tested for disease resistance against Aeromonas salmonicida and Vibrio anguillarum and for humoral immune response to these pathogens after vaccination. Two challenge experiments were undertaken by intraperitoneally injecting doses of each pathogen. Following injection with A. salmonicida , the mortality was significantly different between the two lines in both experiments, with higher mortality in the high-lysozyme line compared to the low-lysozyme line. The difference between lines was particularly pronounced during the first days after injection. Following injection with V. anguillarum , the mortality showed no significant difference between the lysozyme lines. After vaccination, the levels of antibodies against both A. salmonicida and V. anguillarum and total amount of IgM were significantly higher in the high-lysozyme line, whereas no difference between lines was seen before vaccination. Selection for lysozyme activity appears to affect both the immune system and the disease resistance of rainbow trout. The prospects of using lysozyme as a selection criterion to improve disease resistance is, however, complicated by the fact that the association between lysozyme activity and the disease traits seems to be highly influenced by the immune status of the fish at the actual moment of sampling blood for lysozyme assessments.

Ecological speciation in postglacial European whitefish: rapid adaptive radiations into the littoral, pelagic, and profundal lake habitats

Understanding how a monophyletic lineage of a species diverges into several adaptive forms has received increased attention in recent years, but the underlying mechanisms in this process are still under debate. Postglacial fishes are excellent model organisms for exploring this process, especially the initial stages of ecological speciation, as postglacial lakes represent replicated discrete environments with variation in available niches. Here, we combine data of niche utilization, trophic morphology, and 17 microsatellite loci to investigate the diversification process of three sympatric European whitefish morphs from three northern Fennoscandian lakes. The morphological divergence in the gill raker number among the whitefish morphs was related to the utilization of different trophic niches and was associated with reproductive isolation within and across lakes. The intralacustrine comparison of whitefish morphs showed that these systems represent two levels of adaptive divergence: (1) a consistent littoral–pelagic resource axis; and (2) a more variable littoral–profundal resource axis. The results also indicate that the profundal whitefish morph has diverged repeatedly from the ancestral littoral whitefish morph in sympatry in two different watercourses. In contrast, all the analyses performed revealed clustering of the pelagic whitefish morphs across lakes suggesting parallel postglacial immigration with the littoral whitefish morph into each lake. Finally, the analyses strongly suggested that the trophic adaptive trait, number of gill rakers, was under diversifying selection in the different whitefish morphs. Together, the results support a complex evolutionary scenario where ecological speciation acts, but where both allopatric (colonization history) and sympatric (within watercourse divergence) processes are involved.

Genetic and phenotypic parameters for cortisol and glucose stress response in Atlantic salmon and rainbow trout

Abstract Plasma cortisol and glucose levels were monitored in large numbers of hatchery-reared full- and half-sib families of Atlantic salmon (553 full-sib groups) and rainbow trout (281 full-sib groups) following a standardized confinement stress. The approximately normally distributed frequency of cortisol concentrations exhibited mean values in Atlantic salmon that were similar over the four year-classes examined and more than twice as high as in rainbow trout in two of three year-classes. The post-stress glucose levels were of the same order of magnitude in the two species and stable over year-classes. Heritability estimates ( h 2 ) for cortisol and glucose were low in Atlantic salmon (mean across year-classes 0.05 and 0.03); in rainbow trout cortisol levels exhibited heritability estimates of low to medium magnitude (mean 0.27), whereas h 2 of glucose was low (mean 0.07).

DNA HETEROZYGOSITY AND GROWTH RATE IN THE ATLANTIC COD GADUS MORHUA (L)

Relationships between growth rate and the degree of individual heterozygosity at ten nuclear RFLP loci were examined in two populations of the Atlantic cod, Gadus morhua, from northern Norway. A highly significant positive correlation was observed between growth rate and DNA heterozygosity in one population (Balsfjord) but not in the other (Barents Sea). Our results provide support for an important prediction of the associative overdominance hypothesis that heterozygosity‐fitness correlations can be detected at neutral genetic markers and suggest that environmental conditions might play a dominant role in the manifestation of the correlation.

Accuracy and precision in stock separation of north-east Arctic and Norwegian coastal cod by otoliths – comparing readings, image analyses and a genetic method

The distinction between north-east Arctic cod and Norwegian coastal cod, two major groups of Atlantic cod (Gadus morhua L.), has for many years been based on different distance and shape similarities between the two first translucent growth zones in the otoliths, subjectively decided by visual inspection in a binocular. To analyse the certainty of this technique, four independent readers have classified 263 cod otoliths in total from five different geographical areas. For three of the readers, between 82% and 89% of the classification results coincided with independent results based on genetic analyses. Further, 38 cod otoliths, where the readers were certain of the classification (21 north-east Arctic cod and 17 coastal cod) were classified by several image analysis methods. A complete separation was obtained by using the ratio of the circumferences of the two zones, providing a typical ratio of approximately 2 for coastal and 1.5 for north-east Arctic cod. The otolith method for separating the two types of cod has been considered adequately accurate in assessing the two stocks of cod. However, the method is sensitive to subjective interpretation, and action needs to be taken to minimise the difference in interpretation among otolith readers.

Mixed stock analysis and the power of different classes of molecular markers in discriminating coastal and oceanic Atlantic cod (Gadus morhua L.) on the Lofoten spawning grounds, Northern Norway

Atlantic cod (Gadus morhua) encompasses many different populations or stocks, which in part are managed separately. In the northeast Atlantic cod is divided into two main management units; northeast Arctic cod and coastal cod. These two groups have traditionally been separated by otolith classification. In this study, the power of different classes of genetic markers in separating the two cod groups was investigated. The variation in thirteen genetic markers, including allozymes, haemoglobin, the scDNA locus Pantophysin (Pan I) and a number of microsatellites was investigated, and mixed stock analysis and individual assignment tests were performed on samples comprising a mixture of individuals of putative coastal and oceanic type cod. The genetic analyses showed a large genetic differentiation between outer stations and stations located closer to the mainland shore. Mixed stock analysis and individual assignment tests used for estimation of stock proportions gave results similar to those obtained by otolith classification.