0000000000970811
AUTHOR
Marte Sodeland
MOESM2 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Additional file 2: Table S2. Primer sequences used for the reverse transcription qPCR (RT-qPCR).
Local recruitment of Atlantic cod and putative source spawning areas in a coastal seascape
Abstract Increased knowledge on connectivity is crucial to our understanding of the population dynamics, genetic structure, and biogeography of many coastal species. In coastal marine populations, the main factor for structuring is thought to be the degree of isolation and confinement, limiting genetic exchange between populations. However, many offshore populations use the coastal areas as nursery grounds, but venture back to natal spawning grounds as adults. Therefore, increased knowledge on the connectivity between coastal and offshore populations is crucial to ensure correct assessment of coastal living resources. Here, we combine genetic assignment data of Atlantic cod recruits sampled…
Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod
Abstract The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist i…
Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13
Background Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle. Milk fatty acid composition was predicted from the nation-wide recording scheme using Fourier tr…
Who is fishing on what stock: population-of-origin of individual cod (Gadus morhua) in commercial and recreational fisheries
AbstractAtlantic cod (Gadus morhua) in Skagerrak are structured into distinct ecotypes or stock components that have been severely depleted over the past decades. To improve our understanding of how local commercial and recreational fisheries influence cod stocks, we investigated whether these user groups target different stock components of cod. Cod were sampled from the recreational rod and line fishery and from commercial shrimp trawlers catching cod as by-catch. Based on a large set of single nucleotide polymorphisms (SNPs), we defined a subset of 27 semi-diagnostic SNPs designed to discriminate between two cod stock components: “inner fjord” cod and “North Sea” cod, designated by their…
Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod
AbstractIdentification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. In Atlantic cod – historically a major marine resource – Northeast-Arctic- and Norwegian coastal cod are recognized by fundamental differences in migratory and non-migratory behavior, respectively. However, the genomic architecture underlying such behavioral ecotypes is unclear. Here, we have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of sev…
Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
Gene flow shapes spatial genetic structure and the potential for local adaptation. Among marine animals with nonmigratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats is expected to influence the distribution of biological populations and their connectivity patterns. We used whole genome sequencing to study demographic history and reduced representation (double-digest restriction associated DNA) sequencing data to analyse spatial genetic structure in broadnosed pipefish (Syngnathus typhle). Its main habitat is eelgrass beds…
Coastal Research Seen Through an Early Career Lens—A Perspective on Barriers to Interdisciplinarity in Norway
The value of interdisciplinarity for solving complex coastal problems is widely recognized. Many early career researchers (ECRs) therefore actively seek this type of collaboration through choice or necessity, for professional development or project funding. However, establishing and conducting interdisciplinary research collaborations as an ECR has many challenges. Here, we identify these challenges through the lens of ECRs working in different disciplines on a common ecosystem, the Norwegian Skagerrak coast. The most densely populated coastline in Norway, the Skagerrak coast, is experiencing a multitude of anthropogenic stressors including fishing, aquaculture, eutrophication, climate chan…
Stabilizing selection on Atlantic cod supergenes through a millennium of extensive exploitation
Life on Earth has been characterized by recurring cycles of ecological stasis and disruption, relating biological eras to geological and climatic transitions through the history of our planet. Due to the increasing degree of ecological abruption caused by human influences many advocate that we now have entered the geological era of the Anthropocene, or “the age of man.” Considering the ongoing mass extinction and ecosystem reshuffling observed worldwide, a better understanding of the drivers of ecological stasis will be a requisite for identifying routes of intervention and mitigation. Ecosystem stability may rely on one or a few keystone species, and the loss of such species could potentia…
Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Background Clinical mastitis is an inflammation of the mammary gland and causes significant costs to dairy production. It is unfavourably genetically correlated to milk production, and, thus, knowledge of the mechanisms that underlie these traits would be valuable to improve both of them simultaneously through breeding. A quantitative trait locus (QTL) that affects both clinical mastitis and milk production has recently been fine-mapped to around 89 Mb on bovine chromosome 6 (BTA6), but identification of the gene that underlies this QTL was not possible due to the strong linkage disequilibrium between single nucleotide polymorphisms (SNPs) within this region. Our aim was to identify the gen…
Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients
The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene–environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in norther…
MOESM3 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Additional file 3: Figure S1. Further description of the procedure for estimating DBP protein levels. Detailed description of the protocol for estimating the DBP levels in serum from 50 NR cows. Figure S1 gives a schematic explanation of vitamin D3 metabolism.
Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales
Abstract Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analysed genetic origin of 6,483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two gene…
Mixed origin of juvenile Atlantic cod (Gadus morhua) along the Swedish west coast
AbstractCryptic population structure in exploited fish species poses a major challenge for fisheries management. Atlantic cod (Gadus morhua) is a species in which the presence of sympatric ecotypes has been known for a long time, for instance off the coast of Northern Norway. More recently, two sympatric ecotypes of cod have also been documented in the Skagerrak and Kattegat; one ecotype is of an apparent offshore origin and undertakes spawning migrations to the North Sea, and the other is resident at the coast throughout its life. However, their relative contributions of juveniles to the Swedish west coast remain poorly understood. The lack of adult cod along the Skagerrak and Kattegat coa…
"Islands of divergence" in the Atlantic cod genome represent polymorphic chromosomal rearrangements
- In several species genetic differentiation across environmental gradients or between geographically separate populations has been reported to center at “genomic islands of divergence,” resulting in heterogeneous differentiation patterns across genomes. Here, genomic regions of elevated divergence were observed on three chromosomes of the highly mobile fish Atlantic cod (Gadus morhua) within geographically fine-scaled coastal areas. The “genomic islands” extended at least 5, 9.5, and 13 megabases on linkage groups 2, 7, and 12, respectively, and coincided with large blocks of linkage disequilibrium. For each of these three chromosomes, pairs of segregating, highly divergent alleles were id…
Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe
Understanding the biological processes involved in genetic differentiation and divergence between populations within species is a pivotal aim in evolutionary biology. One particular phenomenon that requires clarification is the maintenance of genetic barriers despite the high potential for gene flow in the marine environment. Such patterns have been attributed to limited dispersal or local adaptation, and to a lesser extent to the demographic history of the species. The corkwing wrasse (Symphodus melops) is an example of a marine fish species where regions of particular strong divergence are observed. One such genetic break occurred at a surprisingly small spatial scale (FST ~0.1), over a s…
Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color
AbstractRed coloration of muscle tissue (flesh) is a unique trait in several salmonid genera, including Atlantic salmon. The color results from dietary carotenoids deposited in the flesh, whereas the color intensity is affected both by diet and genetic components. Herein we report on a genome-wide association study (GWAS) to identify genetic variation underlying this trait. Two SNPs on ssa26 showed strong associations to the flesh color in salmon. Two genes known to be involved in carotenoid metabolism were located in this QTL- region: beta-carotene oxygenase 1 (bco1) and beta-carotene oxygenase 1 like (bco1l). To determine whether flesh color variation is caused by one, or both, of these g…
MOESM1 of Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13
Additional file 1: Table S1. SNPs genotyped for the candidate gene map, with rs numbers, positions in base pairs and primer sequences.
MOESM6 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Additional file 6: Table S5. Results for General Linear Model (GLM) analyses of effect of rs110675140 genotype on DBP, ALB, 25(OH)D2, 25(OH)D3 and total 25(OH)D; free 25(OH)D2, 25(OH)D3 and total 25(OH)D; bioavailable (i.e., free and ALB-bound) 25(OH)D2, 25(OH)D3 and total 25(OH)D; DBP-bound total 25(OH)D; and ALB-bound total 25(OH)D serum concentrations. Detailed results of GLM analyses of genotype effect on several serum protein levels in 50 NR cows.
Data from: Can we rely on selected genetic markers for population identification? evidence from coastal Atlantic cod
The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist in coastal…
MOESM5 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Additional file 5: Table S4. Results for single marker association analyses of CM1, CM4, CM6, kg milk, kg protein and kg fat on imputed full sequence data. Positions in basepairs, rs numbers, â log10(p value), minor allele frequency, SNP effects, alleles, putative consequences of the variants on the protein sequence and nearest gene for the imputed full sequence SNPs. The file contains six sheets, one for each tested trait.
MOESM1 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Additional file 1: Table S1. SNP genotype, pregnancy status, age, lactation number and lactation status for the cows used for analyses of protein concentrations and ligand binding.
MOESM4 of Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13
Additional file 4: Table S4. Results from single-marker association analyses on BTA13 data from the BovineHD BeadChip.
Data from: Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales
Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification, and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analyzed genetic origin of 6483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two genetically d…
MOESM2 of Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13
Additional file 2: Table S2. Results for calibration of FTIR-spectra against GC-FID reference data, correlations between each FA and total fat percentage, and estimates of variance components with standard errors.
MOESM3 of Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13
Additional file 3: Table S3. GWAS results.
MOESM5 of Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13
Additional file 5: Table S5. Results from single-marker association analyses on SNPs in the candidate gene region.
MOESM4 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Additional file 4: Table S3. Results for single marker association analyses of seven mastitis traits and five milk traits on BTA6 markers from the Illumina BovineHD BeadChip. rs numbers, positions in basepairs, â log10(p value), SNP effects and alleles for all markers on BTA6 on the Illumina BovineHD BeadChip. The file contains twelve sheets, one for each trait.