| 1. |
- Brännäs, Eva, et al.
(författare)
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Arctic charr farming : production of juveniles; a manual
- 2011
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- 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
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| 2. |
- Jeuthe, Henrik
(författare)
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Brood-stock management and early hatchery rearing of Arctic charr (Salvelinus alpinus(Linnaeus))
- 2020
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Ingår i: Reviews in Aquaculture. - : Wiley. - 1753-5123 .- 1753-5131. ; 12, s. 1595-1623
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Tidskriftsartikel (refereegranskat)abstract
- Arctic charr (Salvelinus alpinus(Linnaeus)) is a stenothermic cold-water fish, which has been cultured in Northern Europe and North America since the 1980s. The industry has remained relatively small with an annual production between 6000 and 10 000 tonnes, and is still challenged by an unreliable offspring production. This review focuses on offspring production in Arctic charr aquaculture including holding conditions for brood-stock, fertilisation and egg rearing until hatch. Brood-stock requires low temperatures during summer (<12 degrees C) with the optimum still unknown. The temperature maximum for egg incubation lies between 6 and 8 degrees C. The composition of an optimal brood-stock diet is debated regarding fatty acids. A demand for a freshwater-based diet rich in omega-6 fatty acids is indicated, but results remain inconclusive. Extensive knowledge has been gained on the timing of spawning and its manipulation through photoperiod, temperature and hormone treatments; spawning can be induced by short-day photoperiod; and temperature drops to 5 degrees C. Eggs are fertilised dry in ovarian fluid. Egg quality is highly variable and positively related to egg size and energy density. Contrary, little information is available on sperm quality and its impact on egg survival. There may also be profound differences between Arctic charr of stationary or anadromous origin regarding requirements for holding conditions of brood-stock and their diet. However, these differences have received little attention, and direct comparative studies are in demand.
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| 3. |
- Jeuthe, Henrik, et al.
(författare)
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DNA fragmentation and membrane integrity in sperm of farmed Arctic charr (Salvelinus alpinus)
- 2022
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 547
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Tidskriftsartikel (refereegranskat)abstract
- Despite the relatively long history of captive breeding, the Arctic charr still exhibits a generally low, but highly variable reproductive performance in aquaculture. A recent publication exposed potential paternal factors influencing the reproductive outcome of Arctic charr broodstock from the Swedish breeding program. Interestingly, the paternal factor appeared to be more closely connected to embryo survival than to fertilisation rates. This lead to speculations on whether e.g. chromatin related issues, potentially related to oxidative stress could be involved. In order to investigate this hypothesis the present study assessed the levels of DNA fragmentation, using the SCD-method, and membrane integrity, using flow cytometry, in sperm of farmed Arctic charr. Moreover, the existence of associations was tested between DNA fragmentation and membrane integrity in individual semen samples and viability of their resulting progeny. We found high levels of DNA fragmentation in sperm from the Arctic charr sires, ranging from 24% to 86% with a median of 67%. Membrane integrity values were high, with individual levels of 93.1% to 99.6% viable sperm cells, median 98.8%. DNA fragmentation and membrane integrity values were moderately correlated (r = 0.304, p < 0.05). Fertilisation rates and proportions of eyed eggs showed substantial individual variation and were correlated (r = 0.497, p < 0.05). However, large differences between proportion of eyed eggs and fertilisation rate, median 52% and 81.6% respectively, highlight that the main loss occurred due to embryo mortality rather than failed fertilisation. No correlation was found between either DNA fragmentation or membrane integrity and the resulting reproductive outcome (fertilisation rate and eyed eggs) of the individual Arctic charr sires. Overall, our study identified very high levels of DNA fragmentation, which could influence the fertility of the broodstock in question and thereby be a mitigating mechanism involved in the low reproductive success most often observed in farmed Arctic charr. Further exploration of this relationship would be needed, though.
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| 4. |
- Jeuthe, Henrik, et al.
(författare)
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Effects of egg size, maternal age and temperature on egg, viability of farmed Arctic charr
- 2013
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 408, s. 70-77
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Tidskriftsartikel (refereegranskat)abstract
- The present study aims to analyze several biological and environmental variables to explain the unpredictable reproductive success at the main aquaculture facility involved in the Swedish Arctic charr breeding program. Data from 540 egg batches, collected from the years 2000 to 2011, were analyzed for the effects of factors such as temperature conditions, female age and egg size on egg viability (% of eyed eggs). An exploratory factor analysis (EFA) reduced 12 variables into 4 factors. Factor 1 mainly explains the negative relationship between high temperature in summer and egg viability. Factor 2 mainly explains a significant relationship between increasing temperatures in autumn (September to November) and decreased egg viability. Factor 3 explains that an early stripping date and increased temperature during stripping and egg incubation together have a negative, although not statistically significant, relationship to egg viability. Factor 4 explains a significant positive relationship between female age and egg size on the proportion of eyed eggs. The most relevant factors in explaining egg viability identified by the EFA analysis were evaluated further, indicating how farming conditions need to be improved. The broodstocks have been subjected to critically high water temperatures during July and August, resulting in decreased egg viability. Access to sufficiently cool water during summer is crucial. Based on the negative correlations found between incubation temperature and egg survival we suggest that a more moderate water heating may be beneficial. Most females were used as broodfish for several years. By applying individual tagging, data on the individual reproductive performance of females for up to 5 consecutive years could be analyzed. In this analysis, both egg size and the proportion of eyed eggs increased with the mean female age. There was also a strong age-unrelated positive correlation between egg size and survival. (C) 2013 Elsevier B.V. All rights reserved.
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| 5. |
- Jeuthe, Henrik, et al.
(författare)
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Effects of variable egg incubation temperatures on the embryonic development in Arctic charr Salvelinus alpinus
- 2016
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Ingår i: Aquaculture Research. - : Hindawi Limited. - 1355-557X .- 1365-2109. ; 47, s. 3753-3764
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Tidskriftsartikel (refereegranskat)abstract
- An evaluation of different thermal regimes during incubation of Arctic charr Salvelinus alpinus L. egg was conducted with regard to embryo survival and development. The study consisted of two major parts: In experiment A, a range of commonly used thermal regimes, constant and variable ranging from 2.7 degrees C to 7 degrees C, were tested for differences in embryo survival and developmental status of newly hatched alevins. Experiment B assessed the timing of a shift from autumn (6 degrees C) to winter temperature (2.5 degrees C) and its effect on embryo survival and the occurrence of spinal deformities in newly hatched alevins. In general, incubations that were initiated at temperatures below 3 degrees C resulted in significantly higher mortality rates and spinal deformity frequencies than other treatments. Hence, Arctic charr eggs require an initial warmer period for unimpaired embryonic development. A general negative correlation was found between the duration of this warmer period (6 degrees C) and both mortality rates and frequency of spinal deformities. The total absence of the 6 degrees C period had the most detrimental effect, with deformity frequencies at least four times higher than all treatments with an initial warmer period. The upper incubation temperature threshold was not reached in the study. The highest temperature tested (7 degrees C) did not result in excess mortality or increased deformity frequency. Higher incubation temperature resulted in less developed alevins at hatching, i.e. alevins were smaller with more yolk remaining. However, measurements on alevins from incubations at variable temperatures revealed different temperature effects on growth and yolk consumption during different parts of embryonic development.
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| 6. |
- Jeuthe, Henrik, et al.
(författare)
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Evaluation of gamete quality indicators for Arctic charr Salvelinus alpinus
- 2019
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 504, s. 446-453
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Tidskriftsartikel (refereegranskat)abstract
- The reproductive performance of farmed Arctic charr exhibits substantial individual variation. The causes behind this variation have not yet been properly explained, despite the species relatively long history in aqua-culture. The aim of the present study was to provide better understanding of the issue by evaluating parent and gamete traits in relation to fertility and offspring viability under routine hatchery conditions. Are losses mainly due to failed fertilisation or mortality? Are maternal or paternal factor more predominant? The study covered sex hormone status of the broodstock, egg traits (egg size and wateriness of egg batches), milt traits (volume, density, and sperm motility characteristics), and symmetry of early cell division.We found that the majority of offspring loss occurred as embryo mortality, although a significant additional loss could be assigned fertilisation failure. Fertilisation and mortality rates were not inter-correlated. Neither of the evaluated egg traits, egg size and wateriness of newly stripped egg batches, proved to be useful indicators of egg quality. With regard to sperm traits, milt density as well as several computer assisted sperm analysis (CASA) parameters, i.e. swimming speed (VAP, VSL, and VCL) and beat cross frequency (BCF), were correlated with reproductive performance and could potentially be used as quality indicators for Arctic charr. Together, male 17,20β-P levels and BCF explained 69.5% of the between male variation in proportion of successfully eyed eggs.The results support previous indications that post-ovulatory aging of oocytes is contributing to the impairment of reproductive performance in farmed Arctic charr. In addition, a significant paternal factor to this impairment has been exposed. However, the cause and mechanism involved are still far from clear.
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| 7. |
- Jeuthe, Henrik, et al.
(författare)
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Mal i Båven 2017 – Inventeringsstudier i lekområden
- 2018
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Fram till 1800-talets mitt var malen (Silurus glanis) allmänt förekom-mande i Sverige, men idag är utbredningen begränsad till ett fåtal vat-ten i sydöstra delarna av landet. Malen är rödlistad som sårbar, och 21 november 2017 fastställdes ett nytt åtgärdsprogram för arten. Ett av de huvudsakliga hoten som listas är brist på reproduktionsområden. För att kunna åtgärda detta måste kunskap finnas kring malens exakta preferenser för lekplatser, d.v.s. vilka typer av miljöer som måste skyddas och utvecklas. Det är även så att dagens inventerings-metodik och därmed beståndsuppskattningar är bristfälliga.Den föreliggande rapporten presenterar arbetet som utförts av SLU Aqua inom två projekt riktat mot mal i nordvästra Båven. Fokus låg på att öka förståelsen kring malens reproduktionsbiologi men omfat-tade även tester av nya inventeringsmetoder. Vuxna malars rörelse-mönster och beteende kartlades med hjälp av radiotelemetri och sonarkamera (ARIS). Försök gjordes även att fånga in malyngel med elfiskebåt för att ta reda på var och i vilken omfattning lek och yngel-produktion skett under den gångna säsongen (2017).Projekten omfattar även två studentarbeten som i skrivande stund ännu är under arbete. Denna rapport innehåller därför endast utdrag ur resultaten från fältstudien. För detaljerade resultat hänvisas till respektive stu-dentarbete som ska finnas tillgängliga januari 2018.Radiopejling av märkta individer visade att huvuddelen av tiden spenderades under eller i närheten av gungflyn. En del aktivitet regi-strerades även ute på öppet vatten. Ett stort antal malar (ett hundratal) i storleksordningen 0,5–2 meter kunde lokaliseras och studeras i Kvarnsjön, Lillsjön och Hornsundssjön med hjälp av ARIS. ARIS vi-sade därmed stor potential för att användas som ett nytt verktyg för inventering av vuxna malar. Den absoluta majoriteten av malarna hit-tades under gungflyn. Ofta fanns många malar samlade på samma ställe. Som mest kunde ett 20-tal malar observeras längs en gungfly-sträcka på ca 30 meter.Ingen lek eller yngelproduktion kunde påvisas under reproduktions-säsongen år 2017, vare sig genom direkt observation av lek eller fynd av årsyngel. Malarnas beteende under gungflyn kunde framgångsrikt studeras med ARIS, men inget beteende som direkt kan kopplas tilllek observerades. Ingen mal, oavsett storlek, fångades vid båtelfisket. Anledningen till malynglens frånvaro är ännu oklar. Det kan vara så att reproduktionen misslyckades detta år. Det kan också handla om bris-ter i inventeringsmetodiken. Klart är att det kvarstår många fråge-tecken kring malens reproduktion och arbetet med att räta ut dessa fortsätter.
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| 8. |
- Jeuthe, Henrik
(författare)
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Reproductive performance of farmed Arctic charr
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 9. |
- Jeuthe, Henrik
(författare)
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Reproductive success of farmed Arctic charr (Salvelinus alpinus)
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The Swedish Arctic charr breeding programme was established in the early 1980's. Over 25 years of selective breeding has resulted in a fast-growing, late-maturing strain of charr called the Arctic Superior. However, the reproductive success of this strain is far from satisfactory. Egg hatching rates are erratic and often very low compared to other salmonid species in Scandinavian aquaculture. Securing a reliable supply of eggs and stocking fish is imperative to a continued expansion of the Swedish Arctic charr farming industry. The aim of this essay is to look into the biological and physical factors affecting gamete quality and offspring survival in fish and elucidate the most crucial of these factors concerning the Arctic Superior. I believe that physical factors regarding the holding conditions are the cause of the problem, rather than biological traits attained as by-products of the breeding process. I suggest high temperature to be the main factor behind the problems of poor reproductive success. However, it is unlikely the only explanation to the problem. Timing of spawning is an important part of the problem. Spawning period is often prolonged and poorly synchronised between sires and dams. This leads to increased handling and stress of the fish, over-ripening of eggs and difficulties with fertilisation, all contributing to lower reproductive success. Spawning period can be manipulated through altered photoperiod or hormonal treatment. Hormone implants can efficiently induce ovulation and spermiation, but may have detrimental effects on gamete quality. If the environmental holding conditions are right synchronised spawning and improved gamete quality should be achieved and the use of hormones should not be needed
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| 10. |
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| 11. |
- Jeuthe, Henrik, et al.
(författare)
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Thermal stress in Arctic charr Salvelinus alpinus broodstock: a 28 year case study
- 2015
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Ingår i: Journal of Fish Biology. - : Wiley. - 0022-1112 .- 1095-8649. ; 86, s. 1139-1152
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Tidskriftsartikel (refereegranskat)abstract
- Temperature and egg viability data from an Arctic charr Salvelinus alpinus hatchery covering a period of 28 years were analysed. During the study period, there was a significant increase in the mean water temperature in May, July, August and September of c. 2 degrees C. Independent of year, the egg viability showed a negative correlation with the mean monthly temperatures in July, August and September as well as with the temperature difference between October and November. The negative effect of high summer temperatures was further supported by a comparison of egg viability from replicate brood-stock reared at two sites differing mainly in summer water temperature. The eggs from the colder site were, on average, significantly larger (4.4 mm compared with 4.0 mm) and had higher hatching rates (57% compared with 37%). These results suggest that unfavourable temperature conditions during the summer and autumn can explain much of the excessive egg mortality experienced at the main facility used for the Swedish S. alpinus breeding programme. The main effect was supra-optimal temperatures during the period July to September, but there also appears to have been an effect from the temperature regime before and during spawning (October to November) that was unrelated to the summer temperatures. These findings emphasize the importance of site selection and sustainable management of aquaculture hatcheries in the light of the ongoing climate change. (C) 2015 The Fisheries Society of the British Isles
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| 12. |
- Kurta, Khrystyna, et al.
(författare)
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Evaluating the potential of improving sperm quality traits in farmed Arctic charr (Salvelinus alpinus) using selective breeding
- 2022
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Ingår i: Aquaculture Reports. - : Elsevier BV. - 2352-5134. ; 25
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 13. |
- Kurta, Khrystyna, et al.
(författare)
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Insights from the early generations of the Swedish rainbow trout (Oncorhynchus mykiss) breeding program
- 2023
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Ingår i: Acta Agriculturae Scandinavica, Section A - Animal Science. - 0906-4702 .- 1651-1972. ; 72, s. 88-99
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 14. |
- Kurta, Khrystyna, et al.
(författare)
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Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus)
- 2023
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Ingår i: BMC Genomics. - : BioMed Central (BMC). - 1471-2164. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 15. |
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| 16. |
- Longo, Alessio, et al.
(författare)
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Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data
- 2024
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Ingår i: Animal Genetics. - 0268-9146 .- 1365-2052. ; 55, s. 87-98
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 17. |
- Nilsson, Jan, et al.
(författare)
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Effects of age and rearing environment on genetic parameters of growth and body weight and heritability of skin pigmentation in Arctic charr (Salvelinus alpinus L.)
- 2016
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 453, s. 67-72
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Tidskriftsartikel (refereegranskat)abstract
- The Swedish breeding programme for Arctic charr aims to improve traits that are important for farming. Selection has been ongoing since the 1980s, and the aim of this study was to re-estimate the genetic parameters in the selected population. In addition, the genetics of skin pigmentation was studied, as previous work indicated a relationship between pigmentation and the ability to cope with stress.One hundred twenty-five full sib families of Arctic charr were hatched and reared separately until they were individually tagged (n = 12,266). In connection with the tagging, three replicates were formed, which were subsequently reared at different sites. The genetic relationships were known from a seven-generation pedigree. Body weight and length were at one site measured at six occasions until 27 months old, and these measurements were used to estimate the DGC (daily growth coefficient) and condition factor. At a second site fish were measured at 21 and 27 months age and at a third site at 27 months age.Skin pigmentation was measured using image analysis. The final weight at 27 months of age varied widely between rearing sites, ranging from 529 g to 1443 g. Weight heritability differed among the sites, at 0.45, 0.11, and 0.07. At one of the sites, where growth was followed closely, weight heritability varied among growth periods, ranging from 0.01 to 0.25, and similar results were obtained for the DGC. In contrast, condition factor heritability did not show such pronounced variations within and among sites. The magnitude of the differences in heritability of weight and growth among different sites that was observed here was not observed previously with this charr population. In particular, the low heritability among the fastest growing fish is unprecedented. Skin pigmentation showed a high heritability of 0.76, indicating a strong additive genetic component. At most ages, pigmentation showed a weak positive genetic correlation with growth. The genotype environment interaction (GEI) was estimated using genetic correlations among sites. For the final weight, genetic correlations were high, indicating weak GEI, although the presence of GEI was suggested from the DGC data.Statement of relevance: The ms will impact charr breeding for commercial farming. (C) 2015 Elsevier B.V. All rights reserved.
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| 18. |
- Palaiokostas, Christos, et al.
(författare)
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A genomic-based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus)
- 2022
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Ingår i: Evolutionary applications. - : Wiley. - 1752-4571. ; 15, s. 565-577
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Tidskriftsartikel (refereegranskat)abstract
- 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 F-st 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.
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| 19. |
- Palaiokostas, Christos, et al.
(författare)
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Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus)
- 2020
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 10, s. 2069-2078
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 20. |
- Palaiokostas, Christos, et al.
(författare)
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Assessing the potential of improving growth and survival to the eyed stage in selectively bred Arctic charr (Salvelinus alpinus)
- 2021
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 138, s. 326-337
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Tidskriftsartikel (refereegranskat)abstract
- 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 (SE0.20) 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.
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| 21. |
- Pappas, Fotis, et al.
(författare)
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Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia
- 2023
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Ingår i: Evolutionary applications. - : Wiley. - 1752-4571. ; 16, s. 797-813
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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