Multivariate restricted maximum likelihood estimation of genetic parameters for growth, carcass and meat quality traits in French Large White and French Landrace pigs

Genetic parameters of 7 traits measured in central test stations - average daily gain (ADG1), feed conversion ratio (FCR) and backfat thickness (ABT) measured on candidates for selection, and average daily gain (ADG2), dressing percentage (DP), estimated carcass lean content (ECLC) and meat quality index (MQI) measured in slaughtered relatives - were estimated for the Large White (LW) and French Landrace (LR) breeds using a derivative free restricted maximum likelihood (DF-REML) procedure applied to a multiple trait individual animal model. The data consisted of 2 sets of records (3 671 and 3 630 candidates, 3 039 and 2 695 slaughtered animals in, respectively, LW and LR breeds) collected at 3 different stations from 1985-1990 (LW) or 1980-1990 (LR). The models included additive genetic value, common environment of birth litter and residual random effects, a fixed year x station x batch or year x station x slaughter date effect and, for traits measured in slaughtered animals, a fixed sex effect and a covariable (weight at the beginning or at the end of the test period). Heritabilities of ADG1, ABT, FCR, ADG2, DP, ECLC and MQI were respectively 0.30, 0.64, 0.22, 0.52, 0.39, 0.60, 0.33 in the LW and 0.34, 0.56, 0.25, 0.46, 0.31, 0.68, 0.23 in the LR breed. Common litter effects ranged from 5% (ABT in LW breed) to 16% (ADG2 in LR breed) of phenotypic variance. Growth traits and FCR exhibited favourable genetic correlations, but were unfavourably correlated to DP and carcass lean content. MQI also showed unfavourable though generally low genetic correlations with all the other traits. These antagonisms were apparent in both breeds, but tended to be larger in the LW than in the LR breed.Les paramètres génétiques de sept caractères mesurés dans les stations publiques de contrôle de performance - le gain moyen quotidien (GMQ1), l’indice de consommation (IC) et l’épaisseur de lard (ELD) mesurés sur les candidats à la sélection ainsi que le gain moyen quotidien (GMQ2), le rendement de carcasse (RDT), le pourcentage de muscle (PM) et l’indice de qualité de la viande (IQV) mesurés sur des apparentés abattus - ont été estimés pour les races Large White (LW) et Landrace français (LR) à l’aide du maximum de vraisemblance restreinte appliqué à un modèle animal multicaractères. Deux fichiers de tailles comparables (3 671 et 3 630 candidats, 3 039 et 2 695 animaux abattus, respectivement, pour les races LW et LR) ont été constitués à partir des données collectées dans trois stations au cours des périodes 1985-90 (LW) et 1980-90 (LR). Les modèles d’analyse incluaient les effets aléatoires de la valeur génétique additive de l’animal, du milieu commun de la portée de naissance, l’effet fixé de l’année x station x bande ou de l’année x station x date d’abattage et, pour les caractères mesurés chez les animaux abattus, l’effet fixé du sexe et une covariable (poids au début ou à la fin du contrôle). Les valeurs d’héritabilité de GMQ1, ELD, IC, GMQ2, RDT, PM et IQV s’élèvent respectivement à 0,30; 0,64; 0,22; 0,52; 0,39; 0,60; 0,33 en race LW et 0,34; 0,56; 0,25; 0,46; 0,31; 0,68; 0,23 en race LR. Les effets de milieu commun de la portée de naissance représentent de 5% (ELD en race LW) à 16% (GMQ2 en race GR) de la variance phénotypique. La croissance et l’indice de consommation présentent entre eux des corrélations génétiques favorables, mais sont corrélés de façon défavorable au rendement et au taux de muscle de la carcasse. L’IQV présente également des corrélations génétiques défavorables, bien qu’en général faibles, avec l’ensemble des autres caractères. Ces antagonismes existent dans les deux races, mais tendent à être plus marqués en race LW que LR

TORRENTIAL RAIN EVENTS OVER THE CÉVENNES-VIVARAIS REGION

High resolution numerical simulations of recent flash-flood events that have occurred over Mediterranean coasts are used to underline the physical mechanisms leading to the stationary of the precipitating systems and the predictability associated with such events. Three cases, including the two last extreme flash-flood events over Southeastern France, have been simulated : the 12-13 November 1999 catastrophe over the Aude region (MAP IOP16), the 8-9 September 2002 flash-flood over the Gard region and the less paroxysmal event of 13-14 October 1995 over the Cévennes-Vivarais relief. Sensitivity to the initial conditions, to the Massif Central relief and to the Sea Surface Temperature (SST) has been studied

Carcass conformation and fat cover scores in beef cattle: A comparison of threshold linear models vs grouped data models

Background: Beef carcass conformation and fat cover scores are measured by subjective grading performed by trained technicians. The discrete nature of these scores is taken into account in genetic evaluations using a threshold model, which assumes an underlying continuous distribution called liability that can be modelled by different methods. Methods: Five threshold models were compared in this study: three threshold linear models, one including slaughterhouse and sex effects, along with other systematic effects, with homogeneous thresholds and two extensions with heterogeneous thresholds that vary across slaughterhouses and across slaughterhouse and sex and a generalised linear model with reverse extreme value errors. For this last model, the underlying variable followed a Weibull distribution and was both a log-linear model and a grouped data model. The fifth model was an extension of grouped data models with score-dependent effects in order to allow for heterogeneous thresholds that vary across slaughterhouse and sex. Goodness-of-fit of these models was tested using the bootstrap methodology. Field data included 2,539 carcasses of the Bruna dels Pirineus beef cattle breed. Results: Differences in carcass conformation and fat cover scores among slaughterhouses could not be totally captured by a systematic slaughterhouse effect, as fitted in the threshold linear model with homogeneous thresholds, and different thresholds per slaughterhouse were estimated using a slaughterhouse-specific threshold model. This model fixed most of the deficiencies when stratification by slaughterhouse was done, but it still failed to correctly fit frequencies stratified by sex, especially for fat cover, as 5 of the 8 current percentages were not included within the bootstrap interval. This indicates that scoring varied with sex and a specific sex per slaughterhouse threshold linear model should be used in order to guarantee the goodness-of-fit of the genetic evaluation model. This was also observed in grouped data models that avoided fitting deficiencies when slaughterhouse and sex effects were score-dependent. Conclusions: Both threshold linear models and grouped data models can guarantee the goodness-of-fit of the genetic evaluation for carcass conformation and fat cover, but our results highlight the need for specific thresholds by sex and slaughterhouse in order to avoid fitting deficiencies

Genetic parameters for social effects on survival in cannibalistic layers: Combining survival analysis and a linear animal model

<p>Abstract</p> <p>Background</p> <p>Mortality due to cannibalism in laying hens is a difficult trait to improve genetically, because censoring is high (animals still alive at the end of the testing period) and it may depend on both the individual itself and the behaviour of its group members, so-called associative effects (social interactions). To analyse survival data, survival analysis can be used. However, it is not possible to include associative effects in the current software for survival analysis. A solution could be to combine survival analysis and a linear animal model including associative effects. This paper presents a two-step approach (2STEP), combining survival analysis and a linear animal model including associative effects (LAM).</p> <p>Methods</p> <p>Data of three purebred White Leghorn layer lines from Institut de Sélection Animale B.V., a Hendrix Genetics company, were used in this study. For the statistical analysis, survival data on 16,780 hens kept in four-bird cages with intact beaks were used. Genetic parameters for direct and associative effects on survival time were estimated using 2STEP. Cross validation was used to compare 2STEP with LAM. LAM was applied directly to estimate genetic parameters for social effects on observed survival days.</p> <p>Results</p> <p>Using 2STEP, total heritable variance, including both direct and associative genetic effects, expressed as the proportion of phenotypic variance, ranged from 32% to 64%. These results were substantially larger than when using LAM. However, cross validation showed that 2STEP gave approximately the same survival curves and rank correlations as LAM. Furthermore, cross validation showed that selection based on both direct and associative genetic effects, using either 2STEP or LAM, gave the best prediction of survival time.</p> <p>Conclusion</p> <p>It can be concluded that 2STEP can be used to estimate genetic parameters for direct and associative effects on survival time in laying hens. Using 2STEP increased the heritable variance in survival time. Cross validation showed that social genetic effects contribute to a large difference in survival days between two extreme groups. Genetic selection targeting both direct and associative effects is expected to reduce mortality due to cannibalism in laying hens.</p

Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction

<p>Abstract</p> <p>Background</p> <p>The purpose of this work was to study the impact of both the size of genomic reference populations and the inclusion of a residual polygenic effect on dairy cattle genetic evaluations enhanced with genomic information.</p> <p>Methods</p> <p>Direct genomic values were estimated for German Holstein cattle with a genomic BLUP model including a residual polygenic effect. A total of 17,429 genotyped Holstein bulls were evaluated using the phenotypes of 44 traits. The Interbull genomic validation test was implemented to investigate how the inclusion of a residual polygenic effect impacted genomic estimated breeding values.</p> <p>Results</p> <p>As the number of reference bulls increased, both the variance of the estimates of single nucleotide polymorphism effects and the reliability of the direct genomic values of selection candidates increased. Fitting a residual polygenic effect in the model resulted in less biased genome-enhanced breeding values and decreased the correlation between direct genomic values and estimated breeding values of sires in the reference population.</p> <p>Conclusions</p> <p>Genetic evaluation of dairy cattle enhanced with genomic information is highly effective in increasing reliability, as well as using large genomic reference populations. We found that fitting a residual polygenic effect reduced the bias in genome-enhanced breeding values, decreased the correlation between direct genomic values and sire's estimated breeding values and made genome-enhanced breeding values more consistent in mean and variance as is the case for pedigree-based estimated breeding values.</p

β blockers and mortality after myocardial infarction in patients without heart failure: multicentre prospective cohort study

Objective: To assess the association between early and prolonged β blocker treatment and mortality after acute myocardial infarction. Design: Multicentre prospective cohort study. Setting: Nationwide French registry of Acute ST- and non-ST-elevation Myocardial Infarction (FAST-MI) (at 223 centres) at the end of 2005. Participants: 2679 consecutive patients with acute myocardial infarction and without heart failure or left ventricular dysfunction. Main outcome measures: Mortality was assessed at 30 days in relation to early use of β blockers (≤48 hours of admission), at one year in relation to discharge prescription, and at five years in relation to one year use. Results: β blockers were used early in 77% (2050/2679) of patients, were prescribed at discharge in 80% (1783/2217), and were still being used in 89% (1230/1383) of those alive at one year. Thirty day mortality was lower in patients taking early β blockers (adjusted hazard ratio 0.46, 95% confidence interval 0.26 to 0.82), whereas the hazard ratio for one year mortality associated with β blockers at discharge was 0.77 (0.46 to 1.30). Persistence of β blockers at one year was not associated with lower five year mortality (hazard ratio 1.19, 0.65 to 2.18). In contrast, five year mortality was lower in patients continuing statins at one year (hazard ratio 0.42, 0.25 to 0.72) compared with those discontinuing statins. Propensity score and sensitivity analyses showed consistent results. Conclusions: Early β blocker use was associated with reduced 30 day mortality in patients with acute myocardial infarction, and discontinuation of β blockers at one year was not associated with higher five year mortality. These findings question the utility of prolonged β blocker treatment after acute myocardial infarction in patients without heart failure or left ventricular dysfunction. Trial registration: Clinical trials NCT00673036

Early diagnosis of acute coronary syndrome.

The diagnostic evaluation of acute chest pain has been augmented in recent years by advances in the sensitivity and precision of cardiac troponin assays, new biomarkers, improvements in imaging modalities, and release of new clinical decision algorithms. This progress has enabled physicians to diagnose or rule-out acute myocardial infarction earlier after the initial patient presentation, usually in emergency department settings, which may facilitate prompt initiation of evidence-based treatments, investigation of alternative diagnoses for chest pain, or discharge, and permit better utilization of healthcare resources. A non-trivial proportion of patients fall in an indeterminate category according to rule-out algorithms, and minimal evidence-based guidance exists for the optimal evaluation, monitoring, and treatment of these patients. The Cardiovascular Round Table of the ESC proposes approaches for the optimal application of early strategies in clinical practice to improve patient care following the review of recent advances in the early diagnosis of acute coronary syndrome. The following specific 'indeterminate' patient categories were considered: (i) patients with symptoms and high-sensitivity cardiac troponin 99th percentile but without dynamic change; and (iv) patients with symptoms and high-sensitivity troponin >99th percentile and dynamic change but without coronary plaque rupture/erosion/dissection. Definitive evidence is currently lacking to manage these patients whose early diagnosis is 'indeterminate' and these areas of uncertainty should be assigned a high priority for research

The Evolution of Bat Vestibular Systems in the Face of Potential Antagonistic Selection Pressures for Flight and Echolocation

PMCID: PMC3634842This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited