Special features of RAD Sequencing data:implications for genotyping

Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

BackgroundDense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. ResultsSNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. ConclusionsThis manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection

Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild.

Evolutionary adaptation is generally thought to occur through incremental mutational steps, but large mutational leaps can occur during its early stages. These are challenging to study in nature due to the difficulty of observing new genetic variants as they arise and spread, but characterizing their genomic dynamics is important for understanding factors favoring rapid adaptation. Here, we report genomic consequences of recent, adaptive song loss in a Hawaiian population of field crickets (Teleogryllus oceanicus). A discrete genetic variant, flatwing, appeared and spread approximately 15 years ago. Flatwing erases sound-producing veins on male wings. These silent flatwing males are protected from a lethal, eavesdropping parasitoid fly. We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a flatwing quantitative trait locus covering a large region of the X chromosome. Gene expression profiling showed that flatwing is associated with extensive genome-wide effects on embryonic gene expression. We found that flatwing male crickets express feminized chemical pheromones. This male feminizing effect, on a different sexual signaling modality, is genetically associated with the flatwing genotype. Our findings suggest that the early stages of evolutionary adaptation to extreme pressures can be accompanied by greater genomic and phenotypic disruption than previously appreciated, and highlight how abrupt adaptation might involve suites of traits that arise through pleiotropy or genomic hitchhiking

Impact of vaccination on the association of COVID-19 with cardiovascular diseases: An OpenSAFELY cohort study

AbstractInfection with SARS-CoV-2 is associated with an increased risk of arterial and venous thrombotic events, but the implications of vaccination for this increased risk are uncertain. With the approval of NHS England, we quantified associations between COVID-19 diagnosis and cardiovascular diseases in different vaccination and variant eras using linked electronic health records for ~40% of the English population. We defined a ‘pre-vaccination’ cohort (18,210,937 people) in the wild-type/Alpha variant eras (January 2020-June 2021), and ‘vaccinated’ and ‘unvaccinated’ cohorts (13,572,399 and 3,161,485 people respectively) in the Delta variant era (June-December 2021). We showed that the incidence of each arterial thrombotic, venous thrombotic and other cardiovascular outcomes was substantially elevated during weeks 1-4 after COVID-19, compared with before or without COVID-19, but less markedly elevated in time periods beyond week 4. Hazard ratios were higher after hospitalised than non-hospitalised COVID-19 and higher in the pre-vaccination and unvaccinated cohorts than the vaccinated cohort. COVID-19 vaccination reduces the risk of cardiovascular events after COVID-19 infection. People who had COVID-19 before or without being vaccinated are at higher risk of cardiovascular events for at least two years.</jats:p

Associations between weight change and biomarkers of cardiometabolic risk in South Asians:secondary analyses of the PODOSA trial

Background/Objectives: The association of weight changes with cardiometabolic biomarkers in South Asians has been sparsely studied. Subjects/Methods: We measured cardiometabolic biomarkers at baseline and after 3 years in the Prevention of Diabetes and Obesity in South Asians Trial. We investigated the effect of a lifestyle intervention on biomarkers in the randomized groups. In addition, treating the population as a single cohort, we estimated the association between change in weight and change in biomarkers. Results: Complete data were available at baseline and after 3 years in 151 participants. At 3 years, there was an adjusted mean reduction of 1·44 kg (95% confidence interval (95% CI): 0.18–2.71) in weight and 1.59 cm (95% CI: 0.08–3.09) in waist circumference in the intervention arm as compared with the control arm. There was no clear evidence of difference between the intervention and control arms in change of mean value of any biomarker. As a single cohort, every 1 kg weight reduction during follow-up was associated with a reduction in triglycerides (−1.3%, P=0.048), alanine aminotransferase (−2.5%, P=0.032), gamma-glutamyl transferase (−2.2%, P=0.040), leptin (−6.5%, P&lt;0.0001), insulin (−3.7%, P=0.0005), fasting glucose (−0.8%, P=0.0071), 2-h glucose (−2.3%, P=0.0002) and Homeostatic Model Assessment of insulin resistance (HOMA-IR: −4.5%, P=0.0002). There was no evidence of associations with other lipid measures, tissue plasminogen activator, markers of inflammation or blood pressure. Conclusions: We demonstrate that modest weight decrease in SAs is associated with improvements in markers of total and ectopic fat as well as insulin resistance and glycaemia in South Asians at risk of diabetes. Future trials with more intensive weight change are needed to extend these findings

Metallurgical and mechanical analysis from thixoforging steel shape

Since always, Industry minimizes manufacturing process plan and increases mechanical behaviour. In this topic, the thixoforging process offers important perspectives especially steel thixoforging. It is on the way of industrial development between casting and forging process. Previous works have illustrated the importance many parameters such as steel grade, slide speed, slug and tool temperature on the geometry from thixoforging part and of the forming load. This paper completes the previous results. It presents an analysis from mechanical resistance of samples extracted of from thixo-extrusion parts on a high speed hydraulic press. This strength investigation is correlated with metallurgical analysis. Macrograph analyses allow identifying the material yield during the process and the different phases

Effects of alimentary whole proteins versus their small peptide hydrolysates on liver and skeletal muscle during the acute inflammation phase in the rat

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Data from: Special features of RAD Sequencing data: implications for genotyping

RAD Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases, and that most RAD loci will be accurately genotyped by existing tools

RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region

How loss of genetic exchanges (recombination) evolves between sex chromosomes is a long-standing question. Suppressed recombination may evolve when a sexually antagonistic (SA) polymorphism occurs in a partially sex-linked ‘pseudoautosomal’ region (or ‘PAR’), maintaining allele frequency differences between the two sexes, and creating selection for closer linkage with the fully sex-linked region of the Y chromosome in XY systems, or the W in ZW sex chromosome systems. Most evidence consistent with the SA polymorphism hypothesis is currently indirect, and more studies of the genetics and population genetics of PAR genes are clearly needed. The sex chromosomes of the plant Silene latifolia are suitable for such studies, as they evolved recently and the loss of recombination could still be ongoing. Here, we used RAD sequencing to genetically map sequences in this plant, which has a large genome (c. 3 gigabases) and no available whole-genome sequence. We mapped 83 genes on the sex chromosomes, and comparative mapping in the related species S. vulgaris supports previous evidence for additions to an ancestral PAR and identified at least 12 PAR genes. We describe evidence that recombination rates have been reduced in meiosis of both sexes, and differences in recombination between S. latifolia families suggest ongoing recombination suppression. Large allele frequency differences between the sexes were found at several loci closely linked to the PAR boundary, and genes in different regions of the PAR showed striking sequence diversity patterns that help illuminate the evolution of the PAR.We thank NBAF project 494 for funding the RAD sequencing and the Leverhulme trust for funding (RPG-2013-110). S. G-R was supported by a Beatriu de Pinós postdoctoral fellowship (AGAUR; 2010 BP_A 00438).Peer reviewe