Characterisation of a novel paralog of scavenger receptor class B member I (SCARB1) in Atlantic salmon (Salmo salar)

<p>Abstract</p> <p>Background</p> <p>Red flesh colour is a unique trait found in some salmonid genera. Carotenoid pigments are not synthesized <it>de novo </it>in the fish, but are provided by dietary uptake. A better understanding of the molecular mechanisms underlying the cellular uptake and deposition of carotenoids could potentially be used to improve the low muscle deposition rate that is typically found in farmed Atlantic salmon. In addition, from an evolutionary point of view, the establishment and maintenance of this trait is still poorly understood. It has been demonstrated in several species that scavenger receptor class B, member 1 (<it>SCARB1</it>) is involved in intestinal absorption of carotenoids, which makes this gene a possible source of genetic variation in salmonid flesh pigmentation.</p> <p>Results</p> <p>In this study, a novel paralog of <it>SCARB1 (SCARB1-2) </it>was detected through screening for genetic variation in Atlantic salmon <it>SCARB1</it>. Full length <it>SCARB1-2 </it>encodes a protein with 89% identity to Atlantic salmon <it>SCARB1</it>, except for the C-terminal cytoplasmic tail that shows only 12% identity. The most prominent site of <it>SCARB1 </it>mRNA expression was in the mid gut, while a five-fold lower level was detected in Atlantic salmon skeletal muscle and liver. The <it>SCARB1-2 </it>mRNA was equally expressed in liver, muscle and mid gut, and at a lower level than <it>SCARB1 </it>mRNA. A total of seven different <it>SCARB1-2 </it>alleles comprising repetitive enhancer of zeste motifs (EZH2) were identified in the founding parents of a resource Atlantic salmon population. We mapped the <it>SCARB1-2 </it>paralog to a region on Atlantic salmon chromosome 1, containing a putative QTL for flesh colour. Addition of the <it>SCARB1-2 </it>marker increased the significance of this QTL, however the large confidence interval surrounding the QTL precludes confirmation of <it>SCARB1-2 </it>as a causative gene underlying variation in this trait.</p> <p>Conclusion</p> <p>We have characterised a novel paralog of <it>SCARB1 (SCARB1-2)</it>, have mapped it to Atlantic salmon chromosome 1 and have described its expression in various tissues. Mapping with <it>SCARB1-2 </it>alleles added further evidence for a QTL affecting flesh colour on this chromosome, however further studies are needed to confirm a functional role for this gene in flesh colour pigmentation.</p

A linkage map of transcribed single nucleotide polymorphisms in rohu (Labeo rohita) and QTL associated with resistance to Aeromonas hydrophila

Background Production of carp dominates world aquaculture. More than 1.1 million tonnes of rohu carp, Labeo rohita (Hamilton), were produced in 2010. Aeromonas hydrophila is a bacterial pathogen causing aeromoniasis in rohu, and is a major problem for carp production worldwide. There is a need to better understand the genetic mechanisms affecting resistance to this disease, and to develop tools that can be used with selective breeding to improve resistance. Here we use a 6 K SNP array to genotype 21 full-sibling families of L. rohita that were experimentally challenged intra-peritoneally with a virulent strain of A. hydrophila to scan the genome for quantitative trait loci associated with disease resistance. Results In all, 3193 SNPs were found to be informative and were used to create a linkage map and to scan for QTL affecting resistance to A. hydrophila. The linkage map consisted of 25 linkage groups, corresponding to the number of haploid chromosomes in L. rohita. Male and female linkage maps were similar in terms of order, coverage (1384 and 1393 cM, respectively) and average interval distances (1.32 and 1.35 cM, respectively). Forty-one percent of the SNPs were annotated with gene identity using BLAST (cut off E-score of 0.001). Twenty-one SNPs mapping to ten linkage groups showed significant associations with the traits hours of survival and dead or alive (P <0.05 after Bonferroni correction). Of the SNPs showing significant or suggestive associations with the traits, several were homologous to genes of known immune function or were in close linkage to such genes. Genes of interest included heat shock proteins (70, 60, 105 and “small heat shock proteins”), mucin (5b precursor and 2), lectin (receptor and CD22), tributyltin-binding protein, major histocompatibility loci (I and II), complement protein component c7-1, perforin 1, ubiquitin (ligase, factor e4b isoform 2 and conjugation enzyme e2 c), proteasome subunit, T-cell antigen receptor and lymphocyte specific protein tyrosine kinase. Conclusions A panel of markers has been identified that will be validated for use with both genomic and marker-assisted selection to improve resistance of L. rohita to A. hydrophila

A Linkage Map of the Atlantic Salmon (Salmo salar) Based on EST-Derived SNP mMarkers

Background: The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, thespecies displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with fullgenome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it isimportant to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundredsingle nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage mapscontaining SNP and microsatellite markers. We also investigated further the distribution of male and femalerecombination events across the genome, and estimated levels of LD between pairs of markers.Results: The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which weresuccessfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicatingthat there is little overlap between regions in which male and female crossovers occur. The female map is likely to haveclose to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regionswhere male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodalfashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence ofrecent admixture in the population, the population being a \u27synthetic\u27 breeding population with contributions fromseveral distinct rivers. Levels of r2 dropped to half its maximum value (above baseline) within 15 cM, and were higherthan 0.2 above baseline for unlinked markers (\u27useful LD\u27) at inter-marker distances less than 5 cM.Conclusion: The linkage map presented here is an important resource for genetic, comparative, and physical mappingof the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the malemap length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparentlysmall physical regions where male crossovers occur. \u27Useful LD\u27 was found at inter-marker distances less than 5 cM

A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

<p>Abstract</p> <p>Background</p> <p>The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers.</p> <p>Results</p> <p>The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r²increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r²dropped to half its maximum value (above baseline) within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM.</p> <p>Conclusion</p> <p>The linkage map presented here is an important resource for genetic, comparative, and physical mapping of the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the male map length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparently small physical regions where male crossovers occur. 'Useful LD' was found at inter-marker distances less than 5 cM.</p

The Atlantic salmon genome provides insights into rediploidization

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.publishedVersio

Natural climate solutions for the United States

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Science Advances 4 (2018): eaat1869, doi:10.1126/sciadv.aat1869.Limiting climate warming to <2°C requires increased mitigation efforts, including land stewardship, whose potential in the United States is poorly understood. We quantified the potential of natural climate solutions (NCS)—21 conservation, restoration, and improved land management interventions on natural and agricultural lands—to increase carbon storage and avoid greenhouse gas emissions in the United States. We found a maximum potential of 1.2 (0.9 to 1.6) Pg CO2e year−1, the equivalent of 21% of current net annual emissions of the United States. At current carbon market prices (USD 10 per Mg CO2e), 299 Tg CO2e year−1 could be achieved. NCS would also provide air and water filtration, flood control, soil health, wildlife habitat, and climate resilience benefits.This study was made possible by funding from the Doris Duke Charitable Foundation. C.A.W. and H.G. acknowledge financial support from NASA’s Carbon Monitoring System program (NNH14ZDA001N-CMS) under award NNX14AR39G. S.D.B. acknowledges support from the DOE’s Office of Biological and Environmental Research Program under the award DE-SC0014416. J.W.F. acknowledges financial support from the Florida Coastal Everglades Long-Term Ecological Research program under National Science Foundation grant no. DEB-1237517

Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar)

<p>Abstract</p> <p>Background</p> <p>Flesh colour and growth related traits in salmonids are both commercially important and of great interest from a physiological and evolutionary perspective. The aim of this study was to identify quantitative trait loci (QTL) affecting flesh colour and growth related traits in an F2 population derived from an isolated, landlocked wild population in Norway (Byglands Bleke) and a commercial production population.</p> <p>Methods</p> <p>One hundred and twenty-eight informative microsatellite loci distributed across all 29 linkage groups in Atlantic salmon were genotyped in individuals from four F2 families that were selected from the ends of the flesh colour distribution. Genotyping of 23 additional loci and two additional families was performed on a number of linkage groups harbouring putative QTL. QTL analysis was performed using a line-cross model assuming fixation of alternate QTL alleles and a half-sib model with no assumptions about the number and frequency of QTL alleles in the founder populations.</p> <p>Results</p> <p>A moderate to strong phenotypic correlation was found between colour, length and weight traits. In total, 13 genome-wide significant QTL were detected for all traits using the line-cross model, including three genome-wide significant QTL for flesh colour (Chr 6, Chr 26 and Chr 4). In addition, 32 suggestive QTL were detected (chromosome-wide P < 0.05). Using the half-sib model, six genome-wide significant QTL were detected for all traits, including two for flesh colour (Chr 26 and Chr 4) and 41 suggestive QTL were detected (chromosome-wide P < 0.05). Based on the half-sib analysis, these two genome-wide significant QTL for flesh colour explained 24% of the phenotypic variance for this trait.</p> <p>Conclusions</p> <p>A large number of significant and suggestive QTL for flesh colour and growth traits were found in an F2 population of Atlantic salmon. Chr 26 and Chr 4 presented the strongest evidence for significant QTL affecting flesh colour, while Chr 10, Chr 5, and Chr 4 presented the strongest evidence for significant QTL affecting growth traits (length and weight). These QTL could be strong candidates for use in marker-assisted selection and provide a starting point for further characterisation of the genetic components underlying flesh colour and growth.</p

Many Labs 5:Testing pre-data collection peer review as an intervention to increase replicability

Replication studies in psychological science sometimes fail to reproduce prior findings. If these studies use methods that are unfaithful to the original study or ineffective in eliciting the phenomenon of interest, then a failure to replicate may be a failure of the protocol rather than a challenge to the original finding. Formal pre-data-collection peer review by experts may address shortcomings and increase replicability rates. We selected 10 replication studies from the Reproducibility Project: Psychology (RP:P; Open Science Collaboration, 2015) for which the original authors had expressed concerns about the replication designs before data collection; only one of these studies had yielded a statistically significant effect (p < .05). Commenters suggested that lack of adherence to expert review and low-powered tests were the reasons that most of these RP:P studies failed to replicate the original effects. We revised the replication protocols and received formal peer review prior to conducting new replication studies. We administered the RP:P and revised protocols in multiple laboratories (median number of laboratories per original study = 6.5, range = 3?9; median total sample = 1,279.5, range = 276?3,512) for high-powered tests of each original finding with both protocols. Overall, following the preregistered analysis plan, we found that the revised protocols produced effect sizes similar to those of the RP:P protocols (?r = .002 or .014, depending on analytic approach). The median effect size for the revised protocols (r = .05) was similar to that of the RP:P protocols (r = .04) and the original RP:P replications (r = .11), and smaller than that of the original studies (r = .37). Analysis of the cumulative evidence across the original studies and the corresponding three replication attempts provided very precise estimates of the 10 tested effects and indicated that their effect sizes (median r = .07, range = .00?.15) were 78% smaller, on average, than the original effect sizes (median r = .37, range = .19?.50)