eKhSACIR інституційному репозитарії Харківської державної академії культури
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Towards genome-wide association studies under abiotic stress in <em>Vitis vinifera</em>
No full textUMR AGAP - équipe DAAV - Diversité, adaptation et amélioration de la vigne ; équipe ID - Intégration de Données UMR AGAP - équipe DAAV - Diversité, adaptation et amélioration de la vigne ; équipe ID - Intégration de Données UMR AGAP - équipe DAAV - Diversité, adaptation et amélioration de la vigne ; équipe ID - Intégration de DonnéesInternational audienceGenome-wide association studies have proven their efficiency to decipher the genetic determinism of traits of agronomic interest in several plant species. In order to perform such studies in grapevine, we first designed an association panel of 279 V. vinifera cultivars from the French National Grapevine Germplasm Collection (Domaine de Vassal, INRA, France). It is composed of three subgroups of 93 cultivars representing the three main genetic pools, which differ in use and geographical origin: wine West, wine East, table East. This panel exhibited a good genetic and phenotypic representativeness of the whole collection. Linkage disequilibrium extent was quite small, 43 Kb for a corrected r2 predicted value of 0.2, emphasizing the need for several dozen thousands markers to achieve powerful genome wide association studies. The second step consisted in dense genotyping of this panel using a 18K SNP Infinium chip and genotyping by sequencing (GBS). While the first method provided useful genotypes at 12K SNPs, about 100K SNPs are expected using GBS with ApeKI. Data processing is in progress and this resource will be made available to the scientific community. The third step consists in phenotyping this panel for traits of interest. Vines were planted in a randomized block design at Le Chapitre Research Vineyard (Montpellier SupAgro, France). Traits related to yield (cluster and berry weights) and phenology (maturity date) were measured in three years within the DLVitis program. Then within the Innovine program, grass was used as a cover crop between rows in the whole trial and part of the design was irrigated to obtain two levels of water availability. In addition to yield and phenology traits, berry composition (sugars, acids, anthocyanins, tannins and aromas), pruning weight and adaptation to drought (delta C13) have been measured during two growing seasons under both water availability conditions. This association panel, together with the accumulated data, represent highly valuable resources for genetic studies in grapevine. We are calling for an international collaborative effort to use such a panel in field and greenhouse trials to address questions on adaptation to changing environments
Agriculture models at the crossroads of farming systems, food systems and territorial dynamics
No full textInternational audienceDifferent agriculture models can be developed to deal with sustainability issues. The objective of this paper is to present a new analytical framework allowing the identification of key agriculture models at the crossroads of farming systems, food systems and territorial (local) dynamics. The first dimension of this framework is based on the distinction between three key types of farming systems: synthetic inputs-based, biological inputs-based and biodiversity-based. They are more or less dependent on exogenous inputs and ecosystem services. The second dimension is based on the identification of how each of these three types of farming system interacts with global food systems and territorial dynamics i.e. circular economy, local food systems and integrated landscape approaches. Our framework makes it possible to specify agriculture models corresponding to a type of farming system and to the nature and level of its interactions with its socio-economic context. Finally, in considering six key agriculture models we sketch out key associated scientific issues
Microbiote intestinal chez le porc : paramètres génétiques de sa composition et liens avec des caractères immunitaires
No full textNational audienceOur objectives were to estimate genetic parameters of the gut microbiota composition in French Large White pigs, and to uncover co-variations between the abundances of microbial communities and immunity or growth parameters of the host. In the framework of the Sus-Flora project, we characterized the diversity of the faecal microbiota of 518 60 day-old piglets by sequencing a variable region of the ribosomal 16S gene. Our first results have shown that the genera Prevotella, followed by Oscillibacter, Dialister, Roseburia or Treponema are dominant in the porcine faecal microbiota. Heritability values ranging from 0.13 0.08 to 0.55 0.16 were estimated for the relative abundance of 19 of the most common bacterial genera, highlighting the contribution of the host genome to the shaping of the gut microbial ecosystem. Regularized canonical correlations and sparse Partial Least Squares analyses highlighted both positive and negative correlations between immunity traits (e.g. monocytes, eosinophils, platelets) and genera such as Prevotella, Roseburia and Dialister. The establishment of microbial diversity in the gut was assessed by following a subset of 31 piglets at 14, 36, 48, 60 and 70 days of age. We showed that the gut microbiota composition was stabilized after 36 days of age. In addition, a stratification of the 31 piglets in two groups was observed after weaning, suggesting the existence of enterotypes as observed in humans. These two enterotype-like clusters were primarily distinguished by the levels of unclassified Ruminococcaceae and Prevotella, respectively. These two enterotype-like clusters were also found in the cohort of 518 60 day-old piglets.L’objectif de cette étude est d’estimer les paramètres génétiques de la composition du microbiote intestinal chez le porc Large White et d’étudier les covariations entre cette composition et des paramètres immunitaires et de croissance. Dans le cadre du projet Sus-Flora, nous avons caractérisé la diversité du microbiote fécal pour 518 porcelets âgés de 60 jours, par séquençage d’une région variable du gène bactérien codant l’ARNr 16S. Nos premiers résultats ont mis en évidence une prédominance des genres bactériens Prevotella puis Oscillibacter, Dialister, Roseburia et Treponema. Des valeurs d’héritabilité comprises entre 0,13 0,08 et 0,55 0,16 ont été estimées pour l’abondance relative de 19 genres bactériens parmi les plus fréquents, démontrant ainsi une part génétique significative de la composition du microbiote intestinal chez le porc. Des corrélations génétiques positives et négatives sont identifiées entre abondances des taxons bactériens. Des covariations positives et négatives ont été trouvées entre des paramètres de formule sanguine (taux de monocytes, éosinophiles, plaquettes) et l’abondance des genres Prevotella, Roseburia, Dialister. Nous montrons également, pour un sous-groupe de 31 animaux, que la composition du microbiote intestinal se stabilise après 36 jours d’âge et que les animaux se séparent en deux groupes sur la base de la composition de leur microbiote intestinal, évoquant les entérotypes identifiés chez l’homme. Ces deux groupes, dominés par le genre Prevotella ou les Ruminococcaceae, sont retrouvés à 60 jours d’âge, avec la cohorte des 518 porcelets
Maternal exposure to diesel exhaust alters placental function and induces intergenerational effects in rabbits
No full textInternational audienceAirborne pollution is a rising concern in urban areas. Epidemiological studies in humans and animal experiments using rodent models indicate that gestational exposure to air- borne pollution, in particular diesel engine exhaust (DE), reduces birth weight. These effects depend on exposure duration, ges- tational window, and nanoparticle (NP) concentration. Our aim was to evaluate the effects of exposure to diluted DE on F0 on feto-placental development in a rabbit model in the F1 and F2 generations. Pregnant females were exposed to diluted (1 mg/m3), filtered DE (NP diameter ≈ 69 nm) or clean air (controls) for 2 h/day, 5 days/week by nose-only exposure (total exposure: 20 days in a 31-day gestation). DE exposure induced early signs of growth retarda- tion at mid gestation with decreased head length (p = 0.04) and umbilical pulse (p = 0.018). Near term, fetal head length (p = 0.029) and plasma insulin and IGF1 concentrations (p = 0.05 and p = 0.019) were reduced. Placental function was also affected, with reduced placental efficiency (fetal/placental weight) (p = 0.049), decreased placental blood flow (p = 0.009) and fetal vessel volume (p = 0.002). Non-aggregated and “fingerprint” NP were observed at various locations, in maternal blood space, in trophoblastic cells and in the fetal blood, demonstrating transplacental transfer. Adult female offspring were bred with control males. Although fetoplacental biometry was not affected near term, second generation fetal metabolism was modified by grand-dam exposure with decreased plasma cholesterol (p = 0.008) and increased triglyceride concentrations (p = 0.015). Repeated daily gestational exposure to DE at levels close to urban pollution can affect feto-placental development in the first and second generation
Improving the prediction of amino acid digestible in the intestine through meta-analysis
No full textSession 62 Theatre 9International audienceThe metabolisable protein (PDI) supplies were revised in the new INRA feeding system (2013). Consequently, the digestible amino acid (AA) supply in the intestine (AADI, in % of PDI) for cattle was to revise since it was developed in 1998. A meta-analysis was performed to estimate the AADI using a close approach to the past method. The new database is larger than the past one (30 publications and 133 diets from 1967 to 1992) since it includes 64 publications (from 1967 to 2013) on cattle and 243 dietary treatments mainly focussed on nitrogen supply (amount or quality). Each dietary AA supply in the duodenum (g/kg DM) was calculated using a linear combination of the rumen undegraded (RUP), the microbial and the endogenous protein flows in the intestine (PI) with the individual feed AA profiles and the two fixed microbial and endogenous profiles, respectively. It was then expressed in % of total AA (i.e. 16 AA). Each relationship between the measured and the calculated AA supply was analysed using a linear model of covariance with a fixed publication effect. The new vs the past models were for the 4 AA recommended in the INRA system: 0.80 + 0.90 × X (RMSE=0.29) vs 1.90 + 0.76 × X (RMSE=0.38) for Lys; 1.03 + 0.45 × X (RMSE=0.17) vs 0.32 + 0.73 × X (RMSE=0.26) for Met; 0.57 +0.79 × X (RMSE=0.24) vs 0.93 + 0.58 × X (RMSE=0.22) for His; 1.78 + 0.86 × X (RMSE=0.32) vs 2.55 + 0.76 × X (RMSE=0.45) for Leu, respectively. The new INRA PI estimations led to lower biases between the measured and the calculated AA supplies compared to the past models since lower RMSE were observed for 15 AA models in addition to a slope closer to one and an intercept closer to zero for 12 AA models. Further analyses will describe the interfering factors influencing the relationships observed for Met, Phe, Arg, Gly, and the RMSE for His. It will be possible to improve the AADI calculations by using these new models to estimate the AA in RUP and microbial PI and the digestibilities of RUP and microbial PI
Developmental and environmental causes for potential changes in odour perception in germ free rodents
No full textabsen
Cartographie par rad-sequencing de QTL à l'origine de neomales spontanés chez la truite arc-en-ciel
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Randomized blocked design applied for the multicriteria optimization of headspace trap extraction of furan and furfural from sponge cake
No full textFuran, a possibly carcinogenic compound to humans, and furfural, a naturally occurring aroma compound, can be produced in heat - processed foods [1,2]. Therefore, their simultaneous determination is important for food safety and quality purposes. Headspace techniques coupled to gas chromatography - mass spectro metr y (G C - M S ) are often used to analyze process - induced compounds. Although headspace trap (H S Trap) extraction has been recently used for furan quantitation in bread crust [3], this technique has not been used for the simultaneous determination of furan and furfural before. This work presents an optimal design of experiments ( O - D O E) approach using random blocks for the multicriteria optimization of H S Trap extraction of furan and furfural from sponge cake for their quantification by G C - M S . A bias related to sample preservation was observed during preliminary tests and eliminated in further assays by considering it as a blocking factor. A tailor - made experimental plan including four instrumental factors (i.e. thermostatting temperature and time, dry purge time, pressurization cycles) and two sample preparation variables (i.e. ratio of water and sample weight [dry basis] and total amount [dry basis]), considering the blocking factor was designed. Response surface models ( P - value <0.0001; R 2 0.974 for a ll mode ls) resulted in the identification o f most linear and so me quadratic terms and a few second order interactions as influencing the extraction of furan, furfural and their internal standards, d4 - furan and d4 - furfura l. Interestingly, one of the samp e preparation variables, namely the ratio of water and samp le weight (dry basis), showed no effect on furfural extraction, while different profiles for furan and d4 - furan were observed regarding this factor. A set of optimal conditions for a H S Trap extraction method was, for the first time, success fully defined by using the optima design of experiments methodology and a desirability function
LocaGIStics: design & evaluation of regional biomass delivery chains
No full textLocaGIStics: design & evaluation of regional biomass delivery chains. 24. European Biomass Conference and Exhibition - EUBCE 201
Sélection génomique chez les animaux domestiques : principes, applications et perspectives
No full textInternational audienceThe principles of genomic selection are described, with the main factors affecting its efficiency and the assumptions underlying the different models proposed. The reasons of its fast adoption in dairy cattle are explained and the conditions of its application to other species are discussed. Perspectives of development include: selection for new traits and new breeding objectives; adoption of more robust approaches based on information on causal variants; predictions of genotype × environment interactions.Cet article décrit les principes de la sélection génomique, avec les principaux facteurs de variation de son efficacité et les hypothèses sous-jacentes aux différents modèles proposés. Il présente ensuite les raisons de son adoption rapide en bovins laitiers et les conditions d’application aux autres espèces pour lesquelles la situation est moins favorable. Les principales perspectives de développement dans les prochaines années concernent la sélection de caractères nouveaux, l’adoption d’approches robustes utilisant l’information des mutations causales et la prédiction des interactions génotype × milieu