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Importance du phénotypage pour maintenir la précision des prédictions génomiques des caractères mesurés en station

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Céline Carillier-Jacquin (Inrae) et al., 52es Journées de la Recherche Porcine (FRA), 4 et 5 février 2020, poster

Poster.

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2020

Impact de l’information génomique sur les choix de reproducteurs préconisés par la méthode des contributions optimales appliquée à une population Landrace

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Eva Reucheron (Ifip / Ecole Supérieure d'Agricultures,d'Angers), 52e Journées de la Recherche Porcine (FRA), 4 et 5 février 2020, p. 47-48, poster

Poster.

La méthode de sélection selon les contributions génétiques optimales (OCS) développée par Meuwissen (1997) fait consensus dans la communauté scientifique pour préserver au mieux la diversité génétique dans les populations sélectionnées tout en maximisant le progrès génétique réalisé. Cette méthode, basée sur un algorithme d’optimisation, recommande un nombre d’accouplements à réaliser pour chaque reproducteur qui maximise le progrès génétique attendu dans la descendance en respectant une contrainte d’augmentation de la consanguinité. Aujourd’hui, tous les reproducteurs utilisés dans le schéma de sélection Landrace sont génotypés. Cette nouvelle information pourrait permettre d’affiner les choix de reproducteurs avec l’OCS et favoriser l’utilisation des individus contribuant le plus à la diversité génétique. Cette étude propose ainsi d’évaluer les conséquences d’intégrer l’information génomique pour estimer les contributions génétiques optimales (OCSGeno) des reproducteurs de la population Landrace de l’entreprise de sélection Nucléus par rapport à un scénario de référence dans lequel le pedigree est utilisé (OCSPed).

ENG

Poster.

Impact of genomic information on choices of breeding animals when applying optimal contribution selection to a Landrace population

Optimal contribution selection (OCS) is a method that estimates the optimal number of matings for each breeding animal to maximize genetic gain while limiting the increase in inbreeding to a given level. The objective of this study was to assess the effect of including genomic data in the OCS method on usage recommendationsfor breeding animals in a Landrace population. The OCS method was applied considering 975 top breeding females and 102 breeding boars using at first only pedigree data to evaluate kinship among all breeding animals, and then genomic data. In both cases, the breeding values used in the optimization were those from routine genomic evaluations. The same limit in the increase in inbreeding was considered (0.1%/5 months). Including genomic data in the OCS changed the list of boars to be used only marginally: 38 in the pedigree OCS vs. 37 in the genomic OCS. The number of recommended matings was identical for 31 of the boars, which represented 83% of the matings. Three boars were used only in the genomic OCS, while 4 boars were used only in the pedigree OCS. Finally, only three boars had different contributions when genomic data were integrated in OCS. Both OCS scenarios led to the same expected genetic level of progeny. To conclude, the impact of including genomic data in the OCS is negligible in this Landrace population given the set of constraints considered. Further research is needed to assess if genomic OCS would be more relevant if higher levels of constraint are placed on preserving genetic diversity.

2020

Importance du phénotypage pour maintenir la précision des prédictions génomiques des caractères mesurés en station

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Céline Carillier-Jacquin (Inrae) et al., 52e Journée de la Recherche Porcine (FRA), 4 et 5 février 2020, Paris, p. 43-44, poster

Poster.

L’évaluation génomique dans les lignées porcines maternelles françaises a été mise en place en 2016 et a permis d’augmenter le progrès génétique, notamment pour les caractères de reproduction. Cependant, des problèmes calculatoires sont apparus pour l’évaluation génomique de certains caractères de production mesurés en station, dont la capacité de phénotypage est limitée. Cela concerne particulièrement les candidats génotypés des élevages de sélection qui ne disposent pas de phénotypes en station et peu d’apparentés phénotypés. La structure de données pour ce type de caractère (i.e. porcs génotypés (candidats) non phénotypés et porcs phénotypés (animaux station) non génotypés) pourrait être responsable des problèmes de convergence observés pour la prédiction des valeurs génomiques. Dans cette étude, nous avons simulé, à partir de phénotypes réels mesurés sur l’ensemble des candidats à la sélection, différents scénarios pour mimer la situation de phénotypage partiel rencontrée dans le cas des caractères mesurés en station et évaluer l’impact d’une augmentation du nombre de porcs phénotypés sur la précision des valeurs génomiques obtenues.

ENG

Poster.

Importance of phenotyping to maintain the accuracy of genomic predictions of traits measured in a test station

Genomic evaluation of French maternal lines, set up in 2016, has helped increase genetic progress, especially for reproductive traits. However, computational problems have emerged for genomic evaluation of certain production traits for which phenotyping capacity is limited. This particularly concerns genotyped candidates on breeding farms that have no phenotypes and only a few phenotyped relatives. This data structure seems to pose convergence problems for predicting genomic breeding values. To check this hypothesis, we simulated such a situation, based on a set of actual phenotype data measured for all farm candidates and genotypes. The simulation consisted of deleting phenotypes of the animals measured on-farm in order to reproduce the data structure encountered for the traitsrecorded at the FGPorc/INRAE test station in Le Rheu. Phenotypes were then progressively added in different scenarios to identify whether prediction accuracy improved and to estimate the number of phenotypes required. The simulations showed that the unbalanced structure between genotypes and phenotypes was responsible for the computational problems that led to low accuracy of genomic predictions. Phenotyping 12% of all pigs phenotyped at 100 kg each year made it possible to solve the computational problems observed and to recover 61% of the maximum expected accuracy. In conclusion, these results highlight the importance of collecting large-scale phenotypes in the context of genomic selection schemes. Further studies will be conducted to study the impact of genotyping animals measured at the station.

2020

Impact de l’information génomique sur les choix de reproducteurs préconisés par la méthode des contributions optimales appliquée à une population Landrace

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Eva Reucheron (Ifip / Ecole Supérieure d'Agricultures,d'Angers), 52e Journées de la Recherche Porcine (FRA), 4 et 5 février 2020, poster

Poster.

La préservation de la diversité génétique des populations en sélection est indispensable pour maintenir le progrès génétique sur le long terme. La méthode de sélection selon les contributions optimales (ou OCS) fait référence pour maximiser le progrès génétique tout en limitant l’augmentation de la consanguinité. La disponibilité de données génomiques pour l’ensemble des reproducteurs en sélection pourrait être valorisée dans la méthode OCS pour affi ner les choix de reproducteurs et leur utilisation en sélection. 

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2020

Dynamique temporelle de la diversité génétique dans des lignées commerciales de porc

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Simon Boitard (Inrae) et al., 3rd International Seminar of CRB-Anim Infrastructure Domestic Animals, Biobanks and Biodiversity, 26 Novembre 2019 

La détection des locus sous sélection positive dans le génome d'une population est une alternative intéressante aux approches de détection de QTLs. Elle permet d’identifier des zones du génome fonctionnellement importantes sans a priori sur le phénotype concerné. Cette détection se base le plus souvent sur des données génétiques observées chez des individus contemporains et consiste à rechercher des régions du génome présentant une diversité génétique atypique, peu compatible avec une évolution sous neutralité. Cependant, l’analyse rétrospective d’échantillons conservés en cryobanque permet d’accéder plus directement à la dynamique temporelle récente des fréquences alléliques. La détection mais aussi l’annotation des événements de sélection sont ainsi améliorées. Nous présentons ici les résultats d’une analyse rétrospective de ce type dans le cas des lignées commerciales françaises de porcs Large White lignée mâle et Large White lignée femelle, créées en 1995 à partir d’une même population et sélectionnées depuis avec des objectifs différents. Dans le cadre du projet LW_DivSeq financé par CRB Anim, nous avons séquençé le génome de 13 animaux contemporains (nés entre 2012 et 2016) dans chacune de ceslignées et de 10 animaux nés en 1977 issus de la population ancestrale. En comparant les génotypes de ces différents échantillons, nous avons évalué l’érosion de la diversité génétique intervenue dans les deux lignées depuis 1977 et avons identifié 30 régions sous sélection. Plusieurs de ces régions semblent avoir été sélectionnées de manière convergente dans les deux lignées, comme par exemple la région du gène IGF2. D’autres montrent des signatures de sélection spécifiques à une lignée. Dans quelques rares régions, comme par exemple celle du gène SOX5, la sélection semble avoir été divergente avec un haplotype différentsélectionné dans chaque lignée. Une analyse plus détaillée des gènes inclus dans les régions candidates est actuellement en cours ; la comparaison de ces gènes avec les objectifs de sélection poursuivis depuis 1977 devrait permettre d’affiner l’annotation fonctionnelle de ces régions..

ENG

Time trends in genomic variation for commercial pig lines

Detecting the loci under positive selection in a population is a promising alternative to QTL detection approaches, which allows identifying functionally relevant genomic regions without focusing on a pre‐defined phenotype. Such detection is generally based on the observation of genetic data from contemporary individuals and looks for genomic regions whose genetic diversity is not consistent with neutral evolution. However, the retrospective analysis of samples stored in cryobanks provides a more direct access to the recent temporal dynamics of allele frequencies, which improves the detection and the annotation of past selection events. Here we illustrate this approach by considering the case of the French dam and sire Large White breeding lines, which have been created in 1995 from a single ancestral population and have been selected since then using different objectives. Whole genome sequences from 13 contemporary animals of each line (born from 2012 to 2016) and 10 animals from the ancestral population (born in 1977) were produced thanks to a CRBAnim funding (project LW_DivSeq). The comparison of genotypes from these three populations allowed quantifying the decrease of genetic diversity from 1977 to current lines and detecting 30 regions under selection. Several of these regions, including the one around IGF2, showed a signature of convergent selection between lines. Some other were most likely selected only in one line. Finally, a few regions including the one around SOX5 showed evidence of divergent selection with distinct haplotypes selected in the two lines. A more detailed study of the genes included in candidate regions is ongoing; the comparison of these genes with the selection objectives applied in the two Large White lines is expected to improve the functional annotation of these regions.

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2019

Use of mate allocation in pig crossbreeding schemes: a simulation study

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González-Diéguez D et al., 70th Annual meeting of the European Federation of Animal science (EAAP), 26-30 août 2019, Ghent, Belgique, visuels d'intervention

One of the main goals in a crossbreeding scheme is to improve the performance of crossbred population by exploiting heterosis and breed complementarity. Dominance is one of the likely genetic bases of heterosis and, nowadays, estimating dominance effects in genetic evaluations has become feasible in a genomic selection context. Mate allocation strategies that account for inbreeding and/or dominance can be of interest for maximizing the crossbred performance. The objective of this study was to simulate scenarios including or not mate allocation strategies in two-breed pig crossbreeding schemes. The different crossbreeding scenarios have been compared in terms of genetic gain (within-breed) and total genetic value in crossbred populations. The benchmark scenario is a crossbreeding scheme where within-line selection is performed on purebred genomic estimated breeding values and crossbreds come from random matings of the best purebreds. The other subsequent scenarios are conceived to evaluate the potential benefits of accounting for inbreeding, dominance and crossbred performances in the genetic evaluation model. Genomic mate allocation is a promising strategy to improve the crossbred performance.

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2019

Additive and dominance genomic parameters for backfat thickness in purebred and crossbred pigs

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Mohammadpanah M (Shahid Bahonar University of Kerman, Iran) et al., 70th Annual meeting of the European Federation of Animal science (EAAP), 26-30 août 2019, Ghent, Belgique, p. 291, poster

In pig crossbreeding programs, genetic evaluation has been based predominantly on purebred data accounting only for additive genetic effects, whereas improving crossbred performance is the ultimate goal. Theoretically, a combined crossbred and purebred selection method is advised if genetic correlation between purebred and crossbred populations differ from unity. If dominance effects are large enough, assortative mating strategies can enhance the total genetic values of the offspring. Hence, estimates of genetic parameters for purebreds and crossbreds are needed to assess the best selection crossbreeding scheme strategies. In this study, additive and dominance genetic variance components and additive and dominance genotypic correlations between a Piétrain and a Piétrain × Large White populations were estimated for backfat thickness (BFT). A total of 607 purebreds and 620 crossbred BFT records were analysed with a genotypic bivariate model that included hot carcass weight and inbreeding coefficient as covariates, an additive and a dominance genotypic effects, and a pen nested within batch random effect. Genetic parameters were estimated with EM-REML plus an additional iteration of AIREML to obtain the asymptotic standard deviations of the estimates. The additive genotypic correlation between purebreds and crossbreds was high, 0.82, indicating that the genetic progress attained in the purebreds can mostly be transferred to the crossbreds. Dominance genetic variance represented about 10% of the BFT phenotypic variance in both populations, suggesting that assortative matings could slightly enhance both purebred and crossbred performances. However, the underlying genetic mechanisms responsible for the dominance effects could differ between populations since dominance genotypic correlation was 0.49.

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2019

Towards the quantitative characterisation of piglets’ robustness to weaning: A modelling approach

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M Revilla et al., Animal, 2019, volume 16, mai, 11 pages

Weaning is a critical transition phase in swine production in which piglets must cope with different stressors that may affect their health. During this period, the prophylactic use of antibiotics is still frequent to limit piglet morbidity, which raises both economic and public health concerns such as the appearance of antimicrobial-resistant microbes. With the interest of developing tools for assisting health and management decisions around weaning, it is key to provide robustness indexes that inform on the animals’ capacity to endure the challenges associated with weaning. This work aimed at developing a modelling approach for facilitating the quantification of piglet resilience to weaning. A total of 325 Large White pigs weaned at 28 days of age were monitored and further housed and fed conventionally during the post-weaning period without antibiotic administration. Body weight and diarrhoea scores were recorded before and after weaning, and blood was sampled at weaning and 1 week later for collecting haematological data. A dynamic model was constructed based on the Gompertz–Makeham law to describe live weight trajectories during the first 75 days after weaning, following the rationale that the animal response is partitioned in two time windows (a perturbation and a recovery window). Model calibration was performed for each animal. Our results show that the transition time between the two time windows, as well as the weight trajectories are characteristic for each individual. The model captured the weight dynamics of animals at different degrees of perturbation, with an average coefficient of determination of 0.99, and a concordance correlation coefficient of 0.99. The utility of the model is that it provides biologically meaningful parameters that inform on the amplitude and length of perturbation, and the rate of animal recovery. Our rationale is that the dynamics of weight inform on the capability of the animal to cope with the weaning disturbance. Indeed, there were significant correlations between model parameters and individual diarrhoea scores and haematological traits. Overall, the parameters of our model can be useful for constructing weaning robustness indexes by using exclusively the growth curves. We foresee that this modelling approach will provide a step forward in the quantitative characterisation of robustness.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/18FBD3614BA779E09D061744323CF5DD/S1751731119000843a.pdf/towards_the_quantitative_characterisation_of_piglets_robustness_to_weaning_a_modelling_approach.pdf

2019

Evaluations génétiques et génomiques des populations porcines

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Sandrine Schwob, Alban Bouquet et Pauline Brenaut, Bilan 2018, éditions IFIP, avril 2019, p. 84

Le travail de sélection a pour but d’améliorer le niveau moyen des performances des populations porcines sur des caractères d’intérêt économique pour l’ensemble de la filière porcine française. Ce travail d’amélioration génétique consiste à repérer les meilleurs individus d’une génération pour les garder comme reproducteurs. Pour cela, des modèles statistiques prédisent la valeur génétique (VG) des candidats à la sélection à partir de leurs performances propres et de celles de leurs apparentés et contemporains. L’information du génome des animaux est également prise en compte dans les lignées femelles Large White (LW) et Landrace français (LF). Chaque semaine, les meilleurs candidats LW et LF sont génotypés sur puces ADN basse densité. Puis les génotypages haute densité sont reconstitués par imputation, permettant ainsi d’optimiser les coûts. Pour consolider les populations de référence, les reproducteurs les plus utilisés en sélection sont de nouve

PDF icon Sandrine Schwob, Alban Bouquet et Pauline Brenaut, Bilan 2018, éditions IFIP, avril 2019, p. 84
2019

Etude de la composante génétique du défaut « jambon déstructuré »

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Sandrine Schwob, bilan 2018, éditions IFIP, avril 2019, p. 57

Le défaut « jambon déstructuré » constitue un handicap majeur dans la technologie de fabrication du jambon cuit. Actuellement, il n’est détectable qu’après désossage du jambon, ce qui complique son élimination. Cette étude a pour objectif de mieux comprendre l’origine génétique du défaut afin de réduire la fréquence d’apparition par la voie génétique.

PDF icon Sandrine Schwob, bilan 2018, éditions IFIP, avril 2019, p. 57
2019

Optiviande - Prédiction de la qualité technologique de la viande de poulet : apport de nouvelles approches de phénotypage et des analyses biologiques et génomiques à haut-débit

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M. Bourin et al., Innovations Agronomiques (FRA), 2019, volume 71, février, p. 323-337

Même si la viande est de plus en plus consommée sous forme élaborée, les consommateurs sont sensibles à la naturalité des produits. Cette tendance est largement prise en compte par les industriels de l’agroalimentaire qui cherchent à limiter l’ajout d’additifs (exhausteurs de goût ou agents texturants) ou de conservateurs (en particulier le sel). Ceci montre l’importance de maîtriser dès l’amont la qualité de la matière première destinée aux produits élaborés. Cette problématique touche particulièrement la viande de poulet, majoritairement consommée sous forme découpée ou transformée mais dont la qualité technologique est très variable. L’objectif du projet CASDAR OPTIVIANDE était de développer de nouveaux outils de phénotypage ainsi que des marqueurs biologiques ou génétiques pouvant être utilisés à des fins de sélection ou d’évaluation de l’impact des facteurs d’élevage. Les approches mises en œuvre concernaient l’utilisation de la spectrométrie dans le proche infrarouge (SPIR) ainsi que des analyses biologiques et génomiques à haut-débit. L’étude s’est appuyée sur un modèle animal original constitué de deux lignées de poulet sélectionnées de manière divergente sur le pH ultime du filet et dont les caractéristiques technologiques et sensorielles de la viande sont très différentes. La spectrométrie dans le proche infrarouge est rapide à mettre en œuvre et permet de prédire plusieurs critères de qualité technologique tel que le pH ultime, les pertes d’eau lors du stockage et la dureté après cuisson. Les analyses transcriptomique et métabolomique ont permis le développement de premiers modèles de prédiction basés sur un nombre restreint de métabolites (sanguins et musculaires) ou de transcrits musculaires. Au niveau génétique, les analyses ont permis d’identifier les principales régions contrôlant le pH ultime du filet et révéler plusieurs gènes d’intérêt. En conclusion, le projet a conduit à des avancées significatives pour la compréhension des mécanismes génétiques et physiologiques impliqués dans la mise en place des défauts de qualité chez le poulet. Il ouvre des perspectives d’application grâce au développement d’outils de prédiction et d’aide à la sélection dont la généricité devra être validée sur d’autres populations et en conditions de production. 

https://www6.inra.fr/ciag/content/download/6606/48428/file/Vol71-22-Bourin%20et%20al.pdf

ENG 

Predicting the technological quality of chicken meat : new approaches of phenotyping and high-throughput biological and genomic analyzes 

Even though meat is increasingly consumed in elaborated form, consumers are sensitive to naturality of the products. This trend is largely taken into account by agribusiness company seeking to reduce additives (flavor enhancers or texturizing agents) or preservatives (in particular salt). This shows the importance of upstream control of quality of the raw material for elaborated products. This issue particularly affects chicken meat, mostly consumed in cut or processed but whose technological quality is highly variable. The objective of the CASDAR OPTIVIANDE project was to develop new phenotyping tools and biological or genetic markers that could be used for selection or evaluation of the impact of breeding factors. The approaches implemented concerned the use of near-infrared spectrometry (NIRS) as well as high-throughput biological and genomic analyzes. The study was based on an original animal model composed of two chicken lines selected in a divergent manner on the ultimate pH of the filet and whose technological and sensory characteristics of meat were very different. Near-infrared spectrometry is fast to implement and makes it possible to predict several technological quality criteria such as ultimate pH, water loss during storage and hardness after cooking. Transcriptomic and metabolomics analyzes made it possible to develop first prediction models based on a limited number of metabolites (blood and muscle) or muscle transcripts. At the genetic level, analyzes made possible to identify the main regions controlling the ultimate pH of the filet and revealed several genes of interest. In conclusion, the project led to significant advances in understanding the genetic and physiological mechanisms involved in the establishment of quality defects in chicken. It opens perspectives of application thanks to the development of prediction tools for selection whose genericity will have to be validated on other populations and in conditions of production. 

https://www6.inra.fr/ciag/content/download/6606/48428/file/Vol71-22-Bourin%20et%20al.pdf

2019

Genomic data reveals large similarities among Canadian and French maternal pig lines

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Raphaël Boré et al., Canadian Journal of Animal Science, volume 98, n° 4, décembre, p. 809-817

Combiner des populations de référence provenant de différents pays ou de différentes races peut être un moyen abordable d’agrandissement de la taille de la population de référence pour les prédictions génomiques. Par conséquent, les principaux objectifs de cette étude sont d’évaluer la diversité génomique entre et au sein des deux races porcines françaises et canadiennes (Landrace et Yorkshire) ainsi que l’apparentement des populations afin d’évaluer la faisabilité de combiner les populations de référence des deux pays en une population de référence commune pour la sélection génomique porcine. Un total de 14,756 animaux ont été génotypés sur deux puces à ADN commerciales (~ 65K SNPs). L’analyse en composantes principales discrimine clairement les deux races Landrace et Yorkshire, et dans une moindre mesure les populations de chacun des deux pays. Le déséquilibre de liaison (LD) entre les SNPs adjacents est similaire dans les populations Yorkshire. En revanche, les niveaux de LD sont légèrement différents pour les populations Landrace. La persistance de phase gamétique entre les populations Yorkshire est très élevée (0.96 à une distance de 0.05 Mb) et élevée entre les populations Landrace (0.88 à une distance de 0.05 Mb). Ces persistances de phase gamétique élevées suggèrent que les lignées maternelles canadiennes et françaises sont génétiquement proches les unes des autres. Ces résultats sont prometteurs et indiquent que la précision des valeurs génomiques estimées pourrait augmenter avec une population de référence commune entre le Canada et la France.

https://www.nrcresearchpress.com/doi/pdf/10.1139/cjas-2017-0103

Genomic data reveals large similarities among Canadian and French maternal pig lines

Combining reference populations from different countries and breeds could be an affordable way to enlarge the size of the reference populations for genomic prediction of breeding values. Therefore, the main objectives of this study were to assess the genetic diversity within and between two Canadian and French pig breeds (Landrace and Yorkshire) and the genomic relatedness among populations in order to evaluate the feasibility of an across-country reference population for pig genomic selection. A total of 14,756 pigs were genotyped on two SNP chip panels (~65K SNPs). A principal component analysis clearly discriminated Landrace and Yorkshire breeds, and also, but to a lesser extent, the Canadian and French purebred pigs of each breed. Linkage disequilibrium (LD) between adjacent SNPs was similar within Yorkshire populations. However, levels of LD were slightly different for Landrace populations. The consistency of gametic phase was very high between Yorkshire populations (0.96 at 0.05 Mb) and high for Landrace (0.88 at 0.05 Mb). Based on consistency of gametic phase, Canadian and French pig maternal lines are genetically close to each other.
These results are promising, as they indicate that the accuracy of estimated genomic breeding values may increase by combining reference populations from the two countries.

https://www.nrcresearchpress.com/doi/pdf/10.1139/cjas-2017-0103

2018

Diversity across major and candidate genes in European local pig breeds

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Maria Munoz et al., 2018, Plos One, 20 novembre, 30 pages

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population’s structure and relationships.

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0207475&type=printable

2018

Complete genome sequence of Salmonella enterica subsp. enterica Serotype Derby, associated with the pork sector in France

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Yann Sévellec et al., Microbiology Resource Announcements, volume 7, n° 12, septembre, 4 pages

In the European Union, Salmonella enterica subsp. enterica serovar Derby is the most abundant serotype isolated from pork. Recent studies have shown that this serotype is polyphyletic. However, one main genomic lineage, characterized by sequence type 40 (ST40), the presence of the Salmonella pathogenicity island 23, and showing resistance to streptomycin, sulphonamides, and tetracycline (STR-SSS-TET), is pork associated. Here, we describe the complete genome sequence of a strain from this lineage isolated in France.

https://mra.asm.org/content/ga/7/12/e01027-18.full-text.pdf

2018

Genomic mating allocation model with dominance to maximize overall genetic merit in Landrace pigs

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D. Gonzalez-Dieguez et al., 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018

Mating allocation strategies that account for dominance can be of interest for maximizing the overall genetic merit of future offspring. In a genomic context, accounting for dominance effects in genetic evaluations is easier than in a classical pedigree-based context. The objective of the present study was to evaluate, in terms of genetic gain, the efficiency of a genomic mating allocation model accounting for dominance in a Landrace pig population. Genetic variance components were estimated for three traits (age at 100 kg, backfat depth and average piglets weight per litter) using an additive and dominance GBLUP model with inbreeding. The estimated additive and dominance genetic variances were used to obtain additive and dominant SNP effects using a BLUP-SNP model. Then, additive breeding values (BV) and total genetic values (TGV, those including dominance) were predicted for the offspring of all possible matings between 40 boars and around 1,500 sows (the number of available sows depended on the trait). Following a traditional breeding scheme, the best matings resulting from 40 boars and 600 sows, were selected based either on BV or TGV using linear programming. The expected genetic gain was calculated as the difference between the mean BV (or the mean TGV) of selected matings and the mean BV (or the mean TGV) of all possible matings. Results show that, for the analysed traits, mating allocation is a feasible and a potential strategy to improve the productive performance of the offspring (i.e. to improve their TGV) without compromising the additive genetic gain in this Landrace pig population.

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2018

An online phenotype database: first step towards breeding programs in local pig breeds

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Marie-José Mercat et al., 69th Annual Meeting of the European Federation of Animal Science (EAAP), Dubrovnik, Croatie, le 27-31 août 2018, visuels d'intervention

In order to further allow implementation of breeding programs in local pig breeds, with selection objectives defined for each local breed, we aimed at developing a standardised recording of carcass and meat quality traits. These data have to be connected with herdbooks to estimate genetic parameters of the traits (heritabilities and genetic correlations) which are necessary to define breeding objectives. Today the situation is very different from one local breed to another. No or very few phenotypes are recorded in some of them, while breeding programs already exist for a few breeds. To promote phenotyping, a dedicated database and a website were developed in the frame of the TREASURE project. First, the required variables have been collected for six local breeds: Basque (FR), Bísaro (PT), Crna slavonska (HR), Gascon (FR), Krškopoljski (SI) and Schwäbisch-Hällisches (DE). In total 74 variables have been identified dealing with animal herdbook information (10), rearing and growth (22), carcass (22) and meat quality (20) attributes. The database is compatible with the various identifiers used in the different countries: animal IDs, breed, farm… codifications. Major attention has been paid to the description of measurement methods of traits. Thus, each carcass and meat quality phenotype is associated to a method description representing 35 additional variables. The website can be easily translated into several languages. The website and database are currently on test until the end of the TREASURE project. All the breeds studied in TREASURE are free to use these tools. The database can be duplicated so that each partner can host its own data. Funded by European Union H2020 RIA program (grant agreement no. 634476).

PDF icon Marie-José Mercat et al., 69th EAAP, Dubrovnik, Croatie, le 27-31 août 2018
2018

Gut microbiota analyses for sustainable European local porcine breeds: A TREASURE pilot study

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J. Estellé et al., 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018

The study of gut microbiota and its effects on hosts has emerged as an essential component of host homeostasis and global efficiency. Besides host’s influence on gut microbiota, major quantitative and qualitative changes may occur in the composition of the intestinal microbiota due to the influence of diet and other environmental factors.
In accordance with the TREASURE project global aim of enhancing sustainability of production systems for local pig breeds, the objective of our task was to conduct a pilot characterisation of intestinal microbiota in order to test its usefulness to characterize several local European pig populations and their production systems. This approach has been applied to populations belonging to the following European traditional breeds: Gascon (France), Iberian (Spain), Krskopolje (Slovenia), Mangalitsa (Serbia), Moravka (Serbia) and Turopolje (Croatia). For each breed, faecal samples have been collected along different experiments performed in the TREASURE project targeting the comprehension of a particular traditional production system (e.g. open-air farming), management practice, or the comparison of breeds. In all experiments, the metagenomics technique employed is the re-sequencing of the bacterial 16S in an Illumina MiSeq system. Overall, the results have shown that the gut microbiota analysis is a promising approach for the characterisation of these local breeds, by allowing a deeper understanding of their production systems and potentially allowing the development of new certification approaches. Preliminary results will be summarized in this communication. Funded by European Union’s H2020 RIA program (Grant agreement no. 634476).

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2018

On the influence of host genetics on gut microbiota composition in pigs

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J. Estellé et al., 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018

Gut microbial population acts in complement with its host through nutrient digestion and health of the gastrointestinal tract. Changes in microbiota composition may then lead to changes in nutrient digestibility. The present study aimed at determining the effects of dietary fibre content on gut microbiota composition and apparent faecal nutrient digestibility in pigs. Furthermore, the relationships between microbiota and digestibility coefficients were investigated. Growing-finishing pigs (from 35 to 74 kg mean body weight) were fed alternatively a low-fibre (LF) and a high-fibre (HF) diet during 4 successive 3-week periods. Data collection for digestibility measurements was achieved during the last week of each period and faecal microbiota was collected at the end of each period for 16S rRNA gene sequencing. The two diets fed by the pigs could be discriminated using 31 predicting OTUs in a sparse partial least square discriminant analysis (mean classification error-rate 3.9%). Furthermore, microbiota was resilient to diet effect. Pearson correlations between microbiota composition and apparent digestibility coefficients of energy, protein, cellulose and hemicellulose emphasized the fact that in LF group, Clostridiaceae and Turicibacter were negatively correlated with protein and energy digestibility coefficients whereas Lactobacillus was positively correlated. In addition, Lachnospiraceae and Prevotella were negatively correlated with cell wall components digestibility. In HF diet, no significant correlation between microbiota and digestibility was found. The present study demonstrates that 3 weeks of adaptation to a new diet seem to be sufficient to observe resilience in growing pigs gut microbiota. In addition, faecal microbiota can be used to classify pigs according to their diet. Because some bacterial family and genera are favourable to digestibility, this study suggests that manipulations of bacterial populations can improve digestibility and feed efficiency. This study is part of the Feed-a-Gene Project, funded from the European Union’s H2020 Programme under grant agreement no. 633531.

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2018

Integrating blood transcriptome and immunity traits to identify markers of immune capacity in pigs

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T. Maroilley et al., 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018

Understanding individual variability of immune capacity in livestock has become a priority to improve sustainability, with the aim to increase disease resistance and resilience in breeding programs. In this study, 550 60-day-old French Large White pigs vaccinated against Mycoplasma hyopneumoniae (M hyo) were monitored for 55 immunity traits (ITs) measured from blood samples (SUS_FLORA ANR funded project). The ITs included two types of parameters. First, parameters directly measured from blood: complete blood counts, counts of various cell subsets by flow cytometry, serum dosage of anti-M hyo IgG and haptoblobin. Second, parameters measured after in vitro stimulation of total blood: phagocytosis, production of cytokines (IL-1&”6;, IL-8, IL-10, IL-17, TNF&”5;, IFN&”7;) after stimulation by LPS or mitogenic agents. All animals were genotyped with 60K Illumina SNP chips. A subset of 243 piglets was chosen for blood transcriptome analysis using Agilent microarrays. We explored covariations between blood expression profiles and IT levels, and could draw lists of the most correlated genes with each IT. Each list represented candidate blood biomarkers potentially predictive of IT variations. As an example, we found 134 genes associated with phagocytosis capacity and we identified a subset of genes that could significantly predict levels of eight ITs related to phagocytosis by a sPLS approach. This gene subset included CXCR1, CCR1 and TLR2. Few candidate biomarkers were previously shown to be genetically controlled for their transcription in blood by eGWAS. Thus, our results provide new data to decipher the genetic architecture of IT variations. A next step will be to understand how IT variations could reflect individual robustness while facing pathogens, and how blood biomarkers could be used as predictors of immune capacity.

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2018

Impact of weaning age on gut microbiota composition in piglets

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F.R. Massacci et al., 69th Annual meeting of the european federation of animal science (EAAP), Dubrovnik, Croatie, 27-31 août 2018

Weaning is a crucial period of pigs, accompanied by nutritional, environmental and social stresses. Studies comparing different ages at weaning have shown that increasing weaning age improves wean-to-finish growth performances and reduces mortality. However, the impact of weaning age on the early-life establishment of the gut microbiota remains under-investigated in pigs. Our objective was to compare the gut microbiota composition of piglets weaned at different ages. 48 piglets were divided in 4 groups of 12 animals weaned at either 14, 21, 28 or 42 days-of-age.
Faecal samples were collected at 3 different time points: day of weaning, 7 days after weaning and at 60 days of age. Faecal DNA bacterial composition was assessed by sequencing the V3-V4 regions of the 16S rRNA gene.
Bioinformatic and biostatistical analysis showed that each weaned group had significant differences between the sample points through weaning transition, confirming that the gut microbiota changes before and after weaning. In addition, microbiota diversity increased according to weaning age, with piglets weaned at 42 days-of-age having a highest alpha diversity and richness. Interestingly, piglets weaned at 42-days maintained a more stable diversity until day 60. We show that late weaning leads to a higher diversity of potentially beneficial microbes prior to the crucial challenge of weaning and might thus provide a competitive advantage to piglets.

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2018

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