scholarly journals Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 899
Author(s):  
Fotis Pappas ◽  
Christos Palaiokostas
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Cost Effective ◽  
Limiting Factors ◽  
Phenotypic Traits ◽  
Production Volume ◽  
High Coverage ◽  
Genomic Relationships ◽  
Low Coverage

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.

scholarly journals Multivariate distributions of behavioural, morphological, and ontogenetic traits in hybrids bring new insights into the divergence of sympatric Arctic charr morphs

2020 ◽  
Author(s):  
Quentin J.B. Horta-Lacueva ◽  
Sigurður S. Snorrason ◽  
Michael B. Morrissey ◽  
Camille A. Leblanc ◽  
Kalina H. Kapralova
Keyword(s):  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Common Garden ◽  
Covariance Structures ◽  
Adaptive Divergence ◽  
Phenotypic Traits ◽  
Phenotypic Variance ◽  
Multivariate Distributions ◽  
Phenotypic Novelty ◽  
Trait Covariance

AbstractStudying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour, life-history) remain largely unknown in this context. In a common garden setup, we conducted an extensive examination of phenotypic traits suspected to be involved in the divergence of two recently evolved morphs of Arctic charr (Salvelinus alpinus), and investigated the consequences of potential patterns of trait covariance on the phenotype of their hybrids. We observed differences among morphs in overall phenotypic variance and in trait correlations. Phenotypic contrainsts also tended to be reduced in the hybrids, which corroborates the narrative of hybridization facilitating adaptive divergence by relaxing trait covariance. However, the hybrids were associated with reduced phenotypic variance at different scales (i.e. at the scale of the entire P matrix and in different parts of the multivariate space), and we identified stronger correlations between several ontogenetic and morphological traits in the hybrids than in both morphs. These findings suggest a limited potential for hybridization to generate phenotypic novelty, and emphasise the need for multivariate approaches conciliating ontogenetic, morphological and behavioural processes to study the processes of adaptive divergence and speciation.

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

2020 ◽  
Vol 10 (6) ◽  
pp. 2069-2078 ◽  
Author(s):  
Christos Palaiokostas ◽  
Shannon M. Clarke ◽  
Henrik Jeuthe ◽  
Rudiger Brauning ◽  
Timothy P. Bilton ◽  
...  
Keyword(s):  
Principal Components ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Genotyping By Sequencing ◽  
Breeding Value ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genomic Relationship ◽  
Value Estimation ◽  
Low Coverage

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

scholarly journals Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

2018 ◽  
Author(s):  
Roger Ros-Freixedes ◽  
Battagin Mara ◽  
Martin Johnsson ◽  
Gregor Gorjanc ◽  
Alan J Mileham ◽  
...  
Keyword(s):  
Sequence Data ◽  
Cost Effective ◽  
Reference Allele ◽  
High Coverage ◽  
Sequencing Errors ◽  
Percentage Points ◽  
Low Coverage ◽  
The Impact ◽  
Genotype Concordance

AbstractBackgroundInherent sources of error and bias that affect the quality of the sequence data include index hopping and bias towards the reference allele. The impact of these artefacts is likely greater for low-coverage data than for high-coverage data because low-coverage data has scant information and standard tools for processing sequence data were designed for high-coverage data. With the proliferation of cost-effective low-coverage sequencing there is a need to understand the impact of these errors and bias on resulting genotype calls.ResultsWe used a dataset of 26 pigs sequenced both at 2x with multiplexing and at 30x without multiplexing to show that index hopping and bias towards the reference allele due to alignment had little impact on genotype calls. However, pruning of alternative haplotypes supported by a number of reads below a predefined threshold, a default and desired step for removing potential sequencing errors in high-coverage data, introduced an unexpected bias towards the reference allele when applied to low-coverage data. This bias reduced best-guess genotype concordance of low-coverage sequence data by 19.0 absolute percentage points.ConclusionsWe propose a simple pipeline to correct this bias and we recommend that users of low-coverage sequencing be wary of unexpected biases produced by tools designed for high-coverage sequencing.

scholarly journals A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr ( Salvelinus alpinus )

2021 ◽  
Author(s):  
Christos Palaiokostas ◽  
Anam Anjum ◽  
Henrik Jeuthe ◽  
Khrystyna Kurta ◽  
Fernando Lopes Pinto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Performance Traits

scholarly journals Genetic insights into the management and conservation of Arctic charr in North Wales

2021 ◽  
Author(s):  
Samantha V. Beck ◽  
Gary R. Carvalho ◽  
Ian McCarthy ◽  
Walter Hanks ◽  
Robert Evans ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Long Term Effects ◽  
Effective Population ◽  
Isolated Populations ◽  
Anthropogenic Pressures ◽  
Southern Limit ◽  
North Wales ◽  
Native Populations

AbstractAquatic species throughout the world are threatened by extinction in many parts of their range, particularly in their most southerly distributions. Arctic charr (Salvelinus alpinus) is a Holarctic species with a distribution that includes the glacial lakes of North Wales, towards it southern limit. To date, no genetic studies have been conducted to determine the genetic health of the three remaining native Arctic charr populations in North Wales, despite exposure to stocking and adverse environmental and ecological conditions. We used seven microsatellite loci to determine whether: 1) genetic differentiation existed between native populations; 2) translocated populations from Llyn Peris were genetically similar to the historically connected Llyn Padarn population; and 3) hatchery supplementation negatively impacted genetic diversity in Llyn Padarn. All three native populations retained their genetic integrity, with Llyn Bodlyn showing high levels of divergence (FST = 0.26 ± 0.02SD) as well as low genetic diversity (HO 0.30) compared to remaining populations (HO 0.64 ± 0.14SD). Although evidence suggests that stocking increased the effective population size of Llyn Padarn in the short term without impacting genetic diversity, the long term effects of such practices are yet to be seen. Results provide baseline data for conservation management, and highlight the need for protection of small isolated populations that are being negatively impacted by the processes of genetic drift due to escalating anthropogenic pressures. Continual monitoring of both Arctic charr and their habitats using a combination of methods will increase the likelihood that these threatened and iconic populations will persist in the future.

Improved interpretation of labelled fish otoliths: a cost-effective tool in sustainable fisheries management

2005 ◽  
Vol 56 (5) ◽  
pp. 705 ◽  
Author(s):  
T. Niva ◽  
P. Keränen ◽  
J. Raitaniemi ◽  
H. M. Berger
Keyword(s):  
Salmo Trutta ◽  
Lake Trout ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Cost Effective ◽  
Salvelinus Namaycush ◽  
Sander Lucioperca ◽  
Alizarin Red ◽  
Brown Trout Salmo Trutta

A total of 222 pairs of alizarin red S (ARS)-labelled and 75 pairs of unlabelled sagittal otoliths from six hatchery-reared species, including Arctic charr (Salvelinus alpinus (L.)), lake trout (Salvelinus namaycush (Walbaum)), salmon (Salmo salar L.), brown trout (Salmo trutta L.), whitefish (Coregonus sp.) and pikeperch (Sander lucioperca (L.)), were used in blind tests to determine whether sawing a 0.4-mm thick slice from the otolith would improve the interpretation of labelled otoliths. The fish were labelled in 1995–2002. Fish age at labelling varied from two weeks to three months, immersion time from three to six hours and concentration of ARS 50–100 ppm. Blind tests were arranged so that sawed slices were contrasted with entire otoliths using stereomicroscope under UV epi-illumination. According to blind tests, the accuracy of interpretation of ARS-labelled otoliths was 97.0% from the slices and 92.3% from entire otoliths. The role of different filters in detecting false marks owing to autofluorescence is discussed. Cost-benefits of the method are discussed briefly.

Impaired Swimming Performance of Acid-exposed Arctic Charr, Salvelinus Alpinus L.

1988 ◽  
Vol 23 (2) ◽  
pp. 301-307 ◽  
Author(s):  
L.A. Hunter ◽  
E. Scherer
Keyword(s):  
Dose Response ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Swimming Performance ◽  
Control Level ◽  
Ventilation Rates

Abstract Arctic charr (Salvelinus alpinus L.) were exposed to five levels of acidity between pH 6 and pH 3.8. Swimming performance as determined by critical swimming speeds was 67.5 cm · sࢤ1 or 4.4 body lengths per second for untreated fish (pH 7.8). Performance declined sharply below pH 4.5; at pH 3.8 it was reduced by 35% after 7 days of exposure. Tailbeat frequencies and ventilation rates showed no dose-response effects. At swimming speeds between 20 and 50 cm · sࢤ1, ventilation rates at all levels of acidity were higher than at the control level.

scholarly journals A seasonal comparison of trace metal concentrations in the tissues of Arctic charr (Salvelinus alpinus) in Northern Québec, Canada

Ecotoxicology ◽  
2020 ◽  
Vol 29 (9) ◽  
pp. 1327-1346
Author(s):  
Mackenzie Anne Clifford Martyniuk ◽  
Patrice Couture ◽  
Lilian Tran ◽  
Laurie Beaupré ◽  
Nastassia Urien ◽  
...  
Keyword(s):  
Trace Metal ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Metal Concentrations

scholarly journals Is an integrated model of school eye health delivery more cost-effective than a vertical model? An implementation research in Zanzibar

2021 ◽  
Vol 6 (1) ◽  
pp. e000561
Author(s):  
Ving Fai Chan ◽  
Fatma Omar ◽  
Elodie Yard ◽  
Eden Mashayo ◽  
Damaris Mulewa ◽  
...  
Keyword(s):  
Implementation Research ◽  
Cost Savings ◽  
Cost Effective ◽  
Integrated Model ◽  
Health Screening ◽  
High Coverage ◽  
Health Delivery ◽  
Screening Cost ◽  
Eye Health ◽  
The Cost

ObjectiveTo review and compare the cost-effectiveness of the integrated model (IM) and vertical model (VM) of school eye health programme in Zanzibar.Methods and analysisThis 6-month implementation research was conducted in four districts in Zanzibar. Nine and ten schools were recruited into the IM and VM, respectively. In the VM, teachers conducted eye health screening and education only while these eye health components were added to the existing school feeding programme (IM). The number of children aged 6–13 years old screened and identified was collected monthly. A review of project account records was conducted with 19 key informants. The actual costs were calculated for each cost categories, and costs per child screened and cost per child identified were compared between the two models.ResultsScreening coverage was 96% and 90% in the IM and VM with 297 children (69.5%) from the IM and 130 children (30.5%) from VM failed eye health screening. The 6-month eye health screening cost for VM and IM was US$6 728 and US$7 355. The cost per child screened for IM and VM was US$1.23 and US$1.31, and the cost per child identified was US$24.76 and US$51.75, respectively.ConclusionBoth models achieved high coverage of eye health screening with the IM being a more cost-effective school eye health delivery screening compared with VM with great opportunities for cost savings.

scholarly journals Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome

2020 ◽  
Vol 12 (11) ◽  
pp. 1953-1960
Author(s):  
Andrey A Yurchenko ◽  
Hans Recknagel ◽  
Kathryn R Elmer
Keyword(s):  
Linkage Map ◽  
Single Copy ◽  
Phenotypic Traits ◽  
Sequencing Data ◽  
High Coverage ◽  
Squamate Reptiles ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common ◽  
Chromosome Level

Abstract Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

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