| 1. |
- De Koning, Dirk-Jan, et al.
(författare)
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Growth performance of five different strains of Nile tilapia (Oreochromis niloticus) introduced to Tanzania reared in fresh and brackish waters
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Five introduced strains of Nile tilapia (Oreochromis niloticus) were tested for growth performance both in fresh- and brackish-water (2 salinity units) environments for 56 days. The BIG NIN, GIFT, Chitralada, "Ruvu Farm" and Silver YY strains with initial mean average weight (+/- standard error) of 96.4 +/- 6.90 g, 104.1 +/- 7.19 g, 137.2 +/- 7.21 g, 53.2 +/- 6.98 g and 95.3 +/- 7.11 g, respectively were used. Individuals were tagged and pooled in hapas (12 mx8.5 mx2 m each), aligned into different ponds (20 mx20 m each). Stocking density of 5 fish/m(2) and 350 g/kg crude protein diet were used. Overall, the average weight gain for GIFT strain was 7.5%, 32%, 45% and 86.5% higher than BIG NIN, Chitralada, "Ruvu Farm" and Silver YY strains, respectively, across both environments. All strains performed significantly better (p<0.05) when reared in brackish-water than their respective counterparts in freshwater, except for the BIG NIN strain. The morphometric correlations for all strains in both environments ranged from moderate (0.50) to strong positive (0.92). The GIFT strain demonstrated superior growth and genotype by environment interaction was weak and not important to be prioritized in breeding programs.
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| 2. |
- Jeuthe, Henrik, et al.
(författare)
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DNA fragmentation and membrane integrity in sperm of farmed Arctic charr (Salvelinus alpinus)
- 2022
-
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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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
- 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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| 7. |
- Lopes Pinto, Fernando A, et al.
(författare)
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Characterizing the genetic structure of introduced Nile tilapia (Oreochromis niloticus) strains in Tanzania using double digest RAD sequencing
- 2020
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Ingår i: Aquaculture International. - : Springer Science and Business Media LLC. - 0967-6120 .- 1573-143X. ; 28, s. 477-492
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Tidskriftsartikel (refereegranskat)abstract
- Tilapia hatcheries in Tanzania rely heavily on importing germplasm. Nevertheless, the genetic structure of the imported stocks is poorly understood. In the current study, the level of genetic diversity and differentiation of eight populations of Nile tilapia (Oreochromis niloticus) strains imported in Tanzania was investigated. Four of the studied strains originated from Thailand, three from Uganda, and one from the Netherlands. Double-digest restriction site-associated DNA sequencing (ddRAD-seq) was applied to identify and genotype single nucleotide polymorphisms (SNPs). In total, 2214 SNPs passed all the quality control steps and were utilized for downstream analysis. Mean heterozygosity estimates were higher for the Thailand strains (Ho, 0.23) compared with the strains from Uganda (Ho, 0.12). Low genetic distance was observed amongst populations from the same geographic origin (Fst, 0.01-0.04). However, genetic distance between populations from different geographic origins was substantial (Fst, 0.24-0.44). Bayesian model-based clustering (STRUCTURE) and discriminant analysis of principal components (DAPC) grouped the studied animals into three distinct clusters. A cross-validation approach (where 25% of animals from each population were considered of unknown origin) was conducted in order to test the efficiency of the SNP dataset for identifying the population of origin. The cross-validation procedure was repeated 10 times resulting in approximately 97% of the tested animals being allocated to the correct geographic population of origin. The breeding history and hatchery practices used to manage these stocks prior and after import appear to be the main factors for the genetic diversity observed in this study. Our study will help inform hatchery stock management and future breeding program designs in Tanzania.
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| 8. |
- Nyinondi, Christer Simon, et al.
(författare)
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Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing
- 2020
-
Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 10, s. 10044-10056
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Tidskriftsartikel (refereegranskat)abstract
- Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all-male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double-digest restriction-site-associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs;n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (F-st) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (F-st = 0.34). Isolation-by-distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05;p-value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross-validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.
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| 9. |
- 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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| 10. |
- 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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| 11. |
- 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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| 12. |
- Palaiokostas, Christos
(författare)
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Genetic parameters and genomic prediction of resistance to koi herpesvirus disease using a low-density SNP panel on two Amur mirror carp populations
- 2023
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Ingår i: Aquaculture Reports. - 2352-5134. ; 30
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Tidskriftsartikel (refereegranskat)abstract
- Koi herpesvirus disease (KHVD), caused by Cyprinid herpesvirus-3 (CyHV-3), is one of the most serious threats to carp farming. In the present study, we investigated the efficiency of a low-density (LD) SNP panel for estimating genetic parameters and breeding values to KHVD resistance in the Amur mirror carp (AMC). Two populations (Pop 1 and Pop 2) of AMC generated from unrelated parents were created using a partial factorial design. One-year old fish (Pop 1 = 1500 individuals.; Pop 2 = 1200 individuals) were challenged with CyHV-3 and phe-notyped to KHVD resistance. 218 SNPs originating from a medium genotyping platform previously applied to Pop 1 (15615 SNPs; denoted as MD panel) with the highest association to KHVD resistance were used as a LD panel to genotype individuals of Pop 2. Genetic parameters and estimated pedigree-based BLUP (EBV) and genomic-based GBLUP (GEBV_MD and GEBV_LD) breeding values were calculated and obtained for Pop 1 using either pedigree, MD or LD panel and for Pop 2 using either pedigree or the LD panel. The heritability estimates of KHVD resistance were very high for both populations ranging from 0.42 to 0.96. Selection for KHVD resistance in Pop 2 using the LD panel would have led to a relative increase of similar to 7% in prediction accuracy compared to the pedigree-based selection. Pearson correlation coefficients between pedigree-based and genomic-based estimated breeding values (EBV vs. GEBV_MD; EBV vs. GEBV_LD; GEBV_MD vs. GEBV_LD) showed a strong association for both populations (0.79 - 0.91). In addition, the concordance rate of individuals selected by pedigree-based (EBV) and genomic-based breeding values (GEBV_MD and GEBV_LD) within selection pressures of 5%, 10% and 20% were not statistically different in most cases. In conclusion, the low-density SNP panel could be useful for a selection program focused on the genetic improvement of KHVD resistance.
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| 13. |
- Palaiokostas, Christos
(författare)
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Genetic relationship between koi herpesvirus disease resistance and production traits inferred from sibling performance in Amur mirror carp
- 2020
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 520
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Tidskriftsartikel (refereegranskat)abstract
- Koi herpesvirus disease (KHVD) is currently the most serious threat to global carp farming. Prevention is a sensible strategy for tackling this disease and improved genetic resistance of carp strains is a desirable breeding goal. To study the potential for multitrait selection, the objective of the current study was to estimate the genetic correlations between KHVD resistance and production traits in Amur mirror carp. A total of 1500 fingerlings from four factorial crosses of five dams and ten sires were challenged with Koi herpesvirus (KHV). Juvenile growth-related traits were collected on the same individuals before the challenge test. Production traits were measured on siblings of the challenged population at different life stages (yearling to market size). The estimated heritability for resistance to KHVD was 0.43 +/- 0.08 on the observed scale and 0.72 +/- 0.13 on the underlying liability scale. Most genetic correlations between KHVD resistance and important production traits were insignificant, showing that selection for improved production traits would not increase susceptibility to KHV and vice versa. However, resistance to KHVD was negatively correlated with Fulton's condition factor (FC) after the second overwintering and relative head length (RHL), relative body height (RBH) and relative body width (RBW) from the second growing season to the market size, with a more prolonged body shape of Amur mirror carp (genes from Amur wild scaly carp, Cyprinus rubrofuscus) being associated with higher KHVD resistance. Intermediate favorable genetic correlations between KHVD resistance and log-log residuals of headless carcass yield (0.37 +/- 0.14) and fillet yield (0.44 +/- 0.13) at market size suggested that selection for improved yields of edible body parts might indirectly lead to a slight improvement in KHVD resistance and vice versa.
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| 14. |
- Palaiokostas, Christos
(författare)
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Genomics Era on Breeding Aquaculture Stocks
- 2019
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Ingår i: Organic aquaculture : impacts and future developments. - Cham : Springer International Publishing. - 9783030056025 ; , s. 65-77
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Bokkapitel (refereegranskat)
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| 15. |
- Palaiokostas, Christos
(författare)
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Mapping and Sequencing of a Significant Quantitative Trait Locus Affecting Resistance to Koi Herpesvirus in Common Carp
- 2018
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 8, s. 3507-3513
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Tidskriftsartikel (refereegranskat)abstract
- Cyprinids are the most highly produced group of fishes globally, with common carp being one of the most valuable species of the group. Koi herpesvirus (KHV) infections can result in high levels of mortality, causing major economic losses, and is listed as a notifiable disease by the World Organization for Animal Health. Selective breeding for host resistance has the potential to reduce morbidity and losses due to KHV. Therefore, improving knowledge about host resistance and methods of incorporating genomic data into breeding for resistance may contribute to a decrease in economic losses in carp farming. In the current study, a population of 1,425 carp juveniles, originating from a factorial cross between 40 sires and 20 dams was challenged with KHV. Mortalities and survivors were recorded and sampled for genotyping by sequencing using Restriction Site-Associated DNA sequencing (RADseq). Genome-wide association analyses were performed to investigate the genetic architecture of resistance to KHV. A genome-wide significant QTL affecting resistance to KHV was identified on linkage group 44, explaining approximately 7% of the additive genetic variance. Pooled whole genome resequencing of a subset of resistant (n = 60) and susceptible animals (n = 60) was performed to characterize QTL regions, including identification of putative candidate genes and functional annotation of associated polymorphisms. The TRIM25 gene was identified as a promising positional and functional candidate within the QTL region of LG 44, and a putative premature stop mutation in this gene was discovered.
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| 16. |
- Palaiokostas, Christos
(författare)
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Optimizing Genomic Prediction of Host Resistance to Koi Herpesvirus Disease in Carp
- 2019
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Genomic selection (GS) is increasingly applied in breeding programs of major aquaculture species, enabling improved prediction accuracy and genetic gain compared to pedigree-based approaches. Koi Herpesvirus disease (KHVD) is notifiable by the World Organization for Animal Health and the European Union, causing major economic losses to carp production. GS has potential to breed carp with improved resistance to KHVD, thereby contributing to disease control. In the current study, Restriction-site Associated DNA sequencing (RAD-seq) was applied on a population of 1,425 common carp juveniles which had been challenged with Koi herpes virus, followed by sampling of survivors and mortalities. GS was tested on a wide range of scenarios by varying both SNP densities and the genetic relationships between training and validation sets. The accuracy of correctly identifying KHVD resistant animals using GS was between 8 and 18% higher than pedigree best linear unbiased predictor (pBLUP) depending on the tested scenario. Furthermore, minor decreases in prediction accuracy were observed with decreased SNP density. However, the genetic relationship between the training and validation sets was a key factor in the efficacy of genomic prediction of KHVD resistance in carp, with substantially lower prediction accuracy when the relationships between the training and validation sets did not contain close relatives.
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| 17. |
- Palaiokostas, Christos
(författare)
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Predicting for disease resistance in aquaculture species using machine learning models
- 2021
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Ingår i: Aquaculture Reports. - : Elsevier BV. - 2352-5134. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Predicting disease resistance is one of the most prominent applications of aquaculture selective breeding. Reductions in genotyping costs have allowed the implementation of genomic selection in an abundance of aquaculture species and their related diseases showing promising results. Machine learning (ML) models can be of value for prediction purposes, as suggested by several studies in both plants and livestock. The current study aimed to test the efficiency of various ML models in predicting disease resistance using both simulated and real datasets. More specifically, models like decision trees (DT), support vector machines (SVM), random forests (RF), adaptive boosting (Adaboost) and extreme gradient boosting (XGB) were benchmarked against genomic best linear unbiased prediction for threshold traits backend by Markov chain Monte Carlo (GBLUP-MCMC) both in terms of prediction efficiency and required computational time. Moreover, the model ranking was tested in datasets where the ratio between the two observed phenotypes (resistant vs non-resistant) was unbalanced. Across all tested datasets, XGB ranked first with a slight advantage over GBLUP-MCMC, ranging between 1-4 %. SVM and RF delivered predictions in tight proximity with the ones from XGB and GBLUP-MCMC. In addition, predictions 3-4 % lower compared to GBLUP-MCMC were obtained with Adaboost. On the other hand, the predictions from DT were consistently low (-40 % lower compared to GBLUP-MCMC). All tested ML models had significantly reduced computational requirements than GBLUP-MCMC. In the case of XGB, the computational requirements were reduced more than 20-fold as opposed to GBLUP-MCMC under the settings of the current study. RF delivered both competitive predictions and was highly efficient in terms of the required computational time (-3 min). Overall, the results of the current study suggest that ML models can be valuable tools in aquaculture breeding studies for disease resistance.
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| 18. |
- Palaiokostas, Christos
(författare)
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The role of energy reserves in common carp performance inferred from phenotypic and genetic parameters
- 2021
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 541
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Tidskriftsartikel (refereegranskat)abstract
- In temperate zones, energy reserves of fish are closely related to survival during the first winter of their life. In this study, the genetic and phenotypic background of the accumulation, mobilization and utilization of energy reserves was investigated in Amur mirror carp. To achieve this, the role of traits related to energy reserves on fish performance during the first winter and further periods of rearing was investigated. The experimental stock was established by four full-factorial matings of 5 dams and 10 sires to generate up to 200 full-sibling families. The offspring were sampled before and after the first winter rearing period. Seasonal variation in direct and indirect measures of energy status was examined using Fulton's condition factor (FC), hepato-somatic index (HSI), visceral index (VSI_NO), glycogen, fat and protein in hepatopancreas (HP) and muscle fat content. Other performance traits were also recorded (weight, resistance to koi herpesvirus disease). All traits related to energy reserves, except HP protein, were significantly lower after the first winter. Overall, HP glycogen and fat from muscle, HP and viscera were mobilized during winter. However, genetic correlations between same traits recorded in autumn and spring were lower than 0.8 for most of the traits, implying that not all families responded to overwintering in a similar manner. Heritability also differed before and after the first winter. Before the first winter, all traits had low to medium heritability (0.05-0.35), but after the winter the same traits were moderately or highly heritable (0.22-0.58). Interestingly, HP glycogen traits, unlike HP fat and HP protein, and HSI recorded in yearlings were positively genetically correlated with survival during the third growing season (rg = 0.49-0.72). This study provides the first evidence of a genetically based strategy for energy mobilization related to overwintering of common carp. Measuring of FC and HSI could be used to monitor the energy status of common carp and to provide a supplementary tool for management of carp stocks.
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| 19. |
- Pappas, Fotis, et al.
(författare)
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Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)
- 2021
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Ingår i: Animals. - : MDPI AG. - 2076-2615. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Simple SummaryAnimal breeding in recent years has benefited greatly from the availability of large-scale genetic information. The most widely applied genomic tools in selective breeding are specialized arrays that use DNA hybridization. However, the high financial investments accompanying this practice impair the profitability of emerging aquaculture species, including Arctic charr. The aim of the current study was to assess and compare the potential of two cost-efficient genotyping strategies applicable in a variety of breeding-related tasks, such as pedigree verification, genetic diversity screening and detection of genomic regions that are associated with phenotypes of economic importance. Both strategies are based on reduced representation sequencing but differ in sequencing coverage (low and high). The low coverage strategy offers a higher density of DNA markers, but also presents a greater proportion of missing data in the marker set and is characterized by more uncertainty in determining heterozygosity compared to high coverage. Our results show that while high coverage genotyping performs better in genetic diversity and kinship analyses, a low coverage strategy is more successful in identifying genomic regions associated with phenotypic traits, leading to the conclusion that both strategies could be of value into selection schemes.Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.
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| 20. |
- 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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