71 research outputs found

    Estimation of additive and dominant variance of egg quality traits in pure-line layers

    Get PDF
    Improved performances are partly due to heterosis effects. One of the basis of heterosis is dominance, which cannot be inherited.However, it can be exploited to boost the total genetic merit of the animals. This has a special interest in avian selection schemeswhere commercial animals are crossbred. In this study, we have estimated additive and dominance genetic variances for severalegg quality traits in pure-line layers.Around 10,500 egg quality performances were used, collected from 1,148 female Rhode Island layers, phenotyped at 70 weeksold and genotyped using a 600K high density SNP chip. Five egg quality traits were analysed: egg weight (EW), egg shell color(ESC), egg shell strength (ESS), albumen height (AH) and egg shell shape (ESShape). Additive and dominance genetic varianceswere estimated via EM-REML with univariate models. That included an inbreeding coefficient and an additive and a dominancerandom effect. Dominance variance explained a small fraction of the phenotypic variance (between 2 to 4 % across all traits).However, it represented a relevant fraction of the total genetic variance for some of the traits (16%, 10%, 35%, 2.4% and 15% ofthe total genetic variance for EW, ESC, ESS, AH, ESShape, respectively).Further research will estimate additive and dominance genetic correlations between the traits to maximize the total genetic gainof these traits simultaneously. In addition, a genomic BLUP with dominance effects is envisaged for the joint analyses of purebredand crossbred performances, to evaluate the potential to generate superior crossbred performances

    Interest of Genotyping-by-Sequencing technologies as an alternative to low density SNP chips for genomic selection in layer chicken

    Get PDF
    To reduce the cost of genomic selection, low density SNP chip can be used in combination with imputation for genotyping the selection candidates instead of using high density (HD) SNP chip. Concurrently, next-generation sequencing (NGS) techniques has been increasingly used in livestock species but remain expensive to be routinely used in selection. An alternative and costefficient solution is the Genotyping by Genome Reducing and Sequencing (GGRS) techniques to sequence only a fraction of the genome by using restriction enzymes. This approach was simulated from sequences of 1027 individuals in a pure layer line, using four enzymes (EcoRI, TaqI, AvaII and PstI). Imputation accuracy on HD genotypes was assessed as the mean correlation between true and imputed genotypes. Egg weight, egg shell color, egg shell strength and albumen height were evaluated with single-step GBLUP methodology. The impact of imputation errors on the genomic estimated breeding values (GEBV) was also investigated.AvaII or PstI led to the detection of more than 10K SNPs in common with the HD SNP chip resulting in imputation accuracy higher than 0.97. The impact of imputation errors on the ranking of the selection candidates was reduced with Spearman correlation (between GEBV calculated on true and imputed genotypes) higher than 0.97 for AvaII and PstI. Finally, the GGRS approach can be an interesting alternative to low density SNP chip for genomic selection. However, with real data, heterogeneity between individuals with missing data has to be taken into account

    Letter from Sarah Forrer, Dayton, OH to Augusta Bruen, 1862 July 6

    Get PDF
    Use of data from crossbred animals for a genomic evaluation of pure line layer. XIth European symposium on poultry genetics (ESPG

    Etude du déséquilibre de liaison dans des lignées de poules de types génétiques "ponte" et "chair"

    Get PDF
    International audienceLa structure du déséquilibre de liaison (DL) au sein des populations en sélection impacte fortement la précision obtenue lors des études de cartographie de QTL ou lors de l'évaluation génomique des reproducteurs. Chez les oiseaux, la structure hétérogÚne du génome nécessite de décrire précisément le DL pour optimiser la sélection. L'utilisation des puces SNP haute densité pour le génotypage des populations de volailles est une opportunité pour approfondir notre connaissance de la structure du DL de ces populations. L'objectif de cette étude est d'acquérir une connaissance haute résolution de la structure du DL au sein de populations de poules de types ponte et chair. Nous avons analysé les génotypes (puce 600 K AffymetrixŸ AxiomŸ HD SNP) de 1541 animaux issus de 3 populations. L'étendue et le niveau du DL ont été estimés par le r 2 moyen à distance physique donnée entre SNP. Cette étude met en évidence des différences importantes de structure du DL entre lignées et entre chromosomes. L'étendue et le niveau du DL sont plus importants dans les lignées de type ponte ou pour les macro-chromosomes et le chromosome Z. Ce niveau important de DL peut faciliter la détection de QTL sur ces chromosomes, mais peut également compliquer la localisation fine de polymorphismes causaux. A l'inverse, le faible niveau de DL observé sur les micro-chromosomes nécessite l'utilisation d'une forte densité de SNP pour détecter une association avec un phénotype, mais devrait permettre la cartographie fine d'un polymorphisme causal. Ces différences sont à prendre en considération pour définir une stratégie de génotypage économique et efficace pour la cartographie fine de QTL ou l'évaluation génomique. ABSTRACT A Linkage disequilibrium study in layers and broiler commercial chicken populations. Knowledge of the linkage disequilibrium (LD) pattern is useful in animal genetic studies as it underlies mapping studies and genomic selection. This is all the more important in birds given the heterogeneous structure of the avian karyotype. Recently, the availability of the high density 600 K AffymetrixŸ AxiomŸ HD SNP genotyping array allowed to assess an in-depth knowledge of the LD pattern in chicken genome. The aim of the present study was to assess a higher resolution of the LD pattern in chicken genome in layer and broiler lines. In this study, we analyzed genotypes of 1541 animals from layers and broiler commercial populations to characterize their LD pattern. LD was measured by the average r 2 value at a given physical distance between SNP. LD extended over a larger region for layer lines than for broiler line. Most differences between lines appeared at small interval distances (< 0.5Mb). LD extent and decay differed considerably between chromosomes categories. Average r 2 values were higher for Z chromosome than for macro, intermediates and micro-chromosomes. The extent of useful LD observed for autosomal chromosomes was at least tenfold longer for layer lines than for broiler. Finally, this study shed light on high LD for Z chromosome. The differences in LD pattern observed between chromosomes and chicken lines should be taken into account to define an economically efficient genotyping strategy

    Genotypic variability enhances the reproducibility of an ecological study

    Get PDF
    Many scientific disciplines are currently experiencing a “reproducibility crisis” because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduces reproducibility by amplifying impacts of lab-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. We tested this hypothesis using a multi-laboratory microcosm study in which the same ecological experiment was repeated in 14 laboratories across Europe. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the “reproducibility crisis”, deliberately including genetic variation may be a simple solution for increasing the reproducibility of ecological studies performed in controlled environments

    Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

    Get PDF
    RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≄60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

    COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

    Get PDF
    Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≀ 18 years: 69, 48, 23; 85%), older adults (≄ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P &lt; 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

    Étude fonctionnelle de variants gĂ©nĂ©tiques identifiĂ©s chez des patients atteints d’érythrocytoses hĂ©rĂ©ditaires

    No full text
    Introduction – L’érythrocytose hĂ©rĂ©ditaire est une maladie rare caractĂ©risĂ©e par un excĂšs de globules rouges. Elle peut ĂȘtre de type primaire lorsqu’elle est causĂ©e par des dĂ©fauts intrinsĂšques des progĂ©niteurs Ă©rythroĂŻdes ou secondaire lors de l’activation de gĂšnes de la voie de l’hypoxie qui entraine une surproduction de globules rouges. Selon le gĂšne et le type de mutation en cause, les patients peuvent dĂ©velopper des complications, notamment un risque accru de dĂ©veloppement de tumeurs (phĂ©ochromocytome). Pourtant, la cause reste inconnue dans plus de 70% des cas, ce qui signifie que ni un diagnostic correct, ni des informations adĂ©quates sur le pronostic ou le traitement ne peuvent ĂȘtre fournis au patient et Ă  sa famille.Objectifs – Le projet pour lequel j’ai Ă©tĂ© recrutĂ©, pour ces 3 annĂ©es de recherche, avait pour but d’étudier des variants gĂ©nĂ©tiques identifiĂ©s chez des patients atteints d’érythrocytose hĂ©rĂ©ditaire suite Ă  un sĂ©quençage nouvelle gĂ©nĂ©ration d’un panel de gĂšnes candidats. A ce jour 250 patients ont Ă©tĂ© sĂ©quencĂ©s, et 35 variants retrouvĂ©s dans les gĂšnes impliquĂ©s dans la voie de l’hypoxie (PHD1, PHD2, HIF1α, HIF2α, SH2B3, EPO, FH) ont Ă©tĂ© sĂ©lectionnĂ©s pour une Ă©tude fonctionnelle approfondie.MatĂ©riels/MĂ©thodes – AprĂšs une analyse in silico de ces variants, des Ă©tudes fonctionnelles ont Ă©tĂ© mises en place. Si le variant Ă  un potentiel impact sur l’épissage un test rapporteur d’épissage est rĂ©alisĂ©. Cette technique est ensuite complĂ©tĂ©e par une analyse transcriptomique d’iPS de patients diffĂ©renciĂ©es en cellules productrices d’érythropoiĂ©tine (EPO). Dans le cas oĂč le mutant induit une perte ou un gain de fonction nous Ă©tudions l’activitĂ© fonctionnelle du mutant (test rapporteur lucifĂ©rase, Ă©tude de l’activation du rĂ©cepteur Ă  l’EPO).RĂ©sultats – Une collection unique de constructions de plasmides d’expression et de minigĂšnes a Ă©tĂ© rĂ©alisĂ©e (39 constructions). Nous avons pu rĂ©aliser l’étude fonctionnelle approfondie de variants des gĂšnes VHL, PHD2, FH et HIF3A. Nous avons notamment identifiĂ© un Ă©pissage alternatif liĂ© Ă  la mutation c.14-26A>G de l’EPO. Ce variant d’épissage entraine la production d’une EPO modifiĂ©e que nous avons purifiĂ©e et commencer Ă  caractĂ©riser. Nous pourrions avoir identifiĂ© une nouvelle EPO avec un gain de fonction.Conclusion – Nous avons mis en Ă©vidence une altĂ©ration de la fonction de plusieurs variants gĂ©nĂ©tiques chez des patients ayant une Ă©rythrocytose, que nous pouvons donc classer dans la catĂ©gorie "mutation causale". Les patients vont donc pouvoir bĂ©nĂ©ficier d’un diagnostic prĂ©cis (avec Ă©largissement du diagnostic Ă  l’ensemble des membres de la famille), d’un traitement adaptĂ© et d’un suivi clinique appropriĂ© (surveillance des complications associĂ©es au gĂšne mutĂ©)

    CrĂ©ation d’une puce basse-densitĂ© pour la sĂ©lection gĂ©nomique en poule pondeuse

    No full text
    La sĂ©lection gĂ©nomique utilise des informations sur les polymorphismes de l’ADN, notamment SNP, en complĂ©ment des mesures de performances, afin de choisir les futurs reproducteurs parmi un ensemble de candidats Ă  la sĂ©lection. Depuis 2013, une puce commerciale de gĂ©notypages Ă  haute densitĂ© (600 000 marqueurs) de l’espĂšce poule a permis le dĂ©veloppement de la sĂ©lection gĂ©nomique dans les filiĂšres ponte et chair. Toutefois, les coĂ»ts de gĂ©notypages avec cette puce restent Ă©levĂ©s pour une utilisation en routine sur un grand nombre de candidats Ă  la sĂ©lection. Un des enjeux actuels de la sĂ©lection gĂ©nomique est donc le dĂ©veloppement de puces de gĂ©notypage de basse densitĂ© (dites puces LD) Ă  plus faible coĂ»t. Il s’agit pour cela de sĂ©lectionner un panel de marqueurs SNP permettant une imputation (prĂ©diction) des gĂ©notypes manquants sur puce haute densitĂ© (puce HD). Dans cette optique, diffĂ©rentes Ă©tudes ont Ă©tĂ© menĂ©es afin de choisir la stratĂ©gie de gĂ©notypages basse densitĂ© la mieux adaptĂ©e Ă  une lignĂ©e de poule pondeuse. DiffĂ©rentes densitĂ©s de gĂ©notypages, plusieurs scenarii de populations et deux logiciels ont Ă©tĂ© testĂ©s. Les puces basse densitĂ© ont Ă©tĂ© construites selon deux stratĂ©gies : choix des SNP selon un clustering basĂ© sur un seuil de dĂ©sĂ©quilibre de liaison ou choix de SNP Ă  intervalles rĂ©guliers. Trois critĂšres d’efficacitĂ© des imputations ont Ă©tĂ© comparĂ©s : taux d’erreur gĂ©notypique, taux d’erreur allĂ©lique et corrĂ©lation entre gĂ©notypes imputĂ©s et rĂ©els. Le taux d’erreur gĂ©notypique s’est rĂ©vĂ©lĂ© un critĂšre plus discriminant que les autres. Le logiciel FImpute apparaĂźt plus intĂ©ressant que le logiciel Beagle car c’est un meilleur compromis entre efficacitĂ© de l’imputation et temps de calcul. L’étude des diffĂ©rentes puces basse densitĂ© montre que les imputations sont meilleures lorsque la densitĂ© des SNP augmente, lorsque le seuil de DL augmente et lorsque des SNP avec une faible MAF (FrĂ©quence AllĂ©lique Mineure) sont pris en compte. Les Ă©tudes de populations montrent que les imputations sont meilleures lorsque la taille de la population de rĂ©fĂ©rence augmente. L’influence du degrĂ© d’apparentement entre population de rĂ©fĂ©rence et candidats ainsi que l’impact sur la prĂ©cision des Ă©valuations gĂ©nomiques restent Ă  approfondir.Genomic selection uses information on DNA polymorphisms, in particular SNP, in addition of performance measures, in order to choose breeders of the next generation among a set of selection candidates. Since 2013, a commercial high density genotyping chip (600000 markers) for chicken allowed the implementation of genomic selection in layer and broiler breeding. However, genotyping costs with this chip still remain high for a routine use on a large number of selection candidates. Consequently, one of the current stakes of genomic selection is the development at a lower cost of low density genotyping chips (LD chips). To do so, a set of SNP markers has to be selected to enable an imputation (prediction) of missing genotypes on a high density chip (HD chip). [br/] In this regard, various studies were conducted to choose the low density genotyping strategy the best suited to laying hens line. Different genotyping densities, several population scenarii and two software were tested. Low density genotyping chips were built according to two strategies: a choice of SNP depending on a clustering based on linkage disequilibrium threshold or a choice of SNP at regular intervals. Three criteria of imputation accuracy were compared: genotypic error rate, allelic error rate and correlation. The genotypic error rate appeared to be a criterion more discriminating than the others. FImpute software is preferred to Beagle software because FImpute is a better compromise between imputation accuracy and calculation time. The study of different low density genotyping chips shows that imputations improve with SNP density, when the LD threshold increases and when SNP with low MAF (Minor Allele Frequency) are considered. Population studies show that imputations are better when the size of the reference population increases. The influence of the kinship degree between reference population and target population, and the impact on accuracy of genomic evaluations still remain to be deepened
    • 

    corecore