Virginia Garófano-Gómez

Dov Corenblit

Johannes Steiger

Bruno B Moulia

Stéphane S Ploquin

Patrice Chaleil

Olivier Forestier

André Evette

Eduardo Gonzalez

Borbála Hortobágyi

Response of black poplar (Populus nigra L.) to hydrogeomorphological constraints: a semi-controlled ex situ experiment

des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

I.S.RIVERS

Virginia Garófano-Gómez 1,2 ; Dov Corenblit 1,2 ; Johannes Steiger 1,2 ; Bruno Moulia 3 ; Stéphane Ploquin 3 ; Patrice Chaleil 3 ; Olivier Forestier 4 ; André Evette 5 ; Eduardo González 6,7 ; Borbála Hortobágyi 1,2 and Luc Lambs 6

1 Université Clermont Auvergne, UBP, MSH, Clermont-Ferrand, France (corresponding author: virginia.garofano_gomez@univ-bpclermont.fr). 2 CNRS, UMR 6042, GEOLAB -Laboratoire de géographie physique et environnementale, Clermont-Ferrand, France. The biogeomorphological life cycle of black poplar (Populus nigra L. )

• Black poplar is a keystone ecosystem engineer species. Specific ranges of hydrogeomorphological conditions control the successive phases of its entire life cycle. • Hypothesis: the impact of poplars on the landform structure modulates its own growth performance, biomass and architecture until it reaches sexual maturity. • The weight (T.1) will be modulated imitating the shape of an average hydrograph of a Spring flood in the Garonne River (where the clone Jean Pourtet comes from). • The burial (T.2) will be applied during the recession limb of the curve.

• 12 plants were destructively sampled to test the methodology of extraction, conservation and sub-sampling.

* Traits from winching test.

• The growth is optimum but some differences are evident depending on the original size of the cutting and the mother tree they come from.

The quantification of functional response traits of P. nigra will enhance our understanding of fundamental biogeomorphic interactions and its implication for the restoration of river systems.

2

• Analysis of root length confirms that roots could have different functions: anchorage (basal roots) and absorption (lateral roots).

• Hydrogeomorphological factors (topography, flow and sediment transport regimes) control vegetation dynamics in riparian ecosystems  but vegetation also has an impact on these factors, which in turn causes an effect on the plant phenotype.

  : To quantify key response functional traits (morphological and biomechanical) of Populus nigra L. cuttings to simulated hydrogeomorphological constraints (drag force and sediment burial) as well as to dissociate the specific responses to them.  3.2 Experimental design: 128 stem cuttings of P. nigra (variety Jean Pourtet) were measured, planted in permeable bags with an irrigation system attached and randomly assigned to one of the 4 treatments. Evolutionary feedback between woody riparian species and hydrogeomorphological constraints RESPONSE OF BLACK POPLAR (POPULUS NIGRA L.) TO HYDROGEOMORPHOLOGICAL CONSTRAINTS: A SEMI-CONTROLLED EX SITU EXPERIMENT Réponse du peuplier noir (Populus nigra L.) aux contraintes hydro-géomorphologiques : une expérimentation ex situ semi-contrôlée

•

  3 INRA Clermont Ferrand, UMRA547 Laboratoire de physique et physiologie intégrative de l'arbre fruitier et forestier, Site de Crouël, Clermont Ferrand, France. 4 Pépinière Forestière de l'Etat, DRAAF Pays-de-la-Loire, Guémené Penfao, France. 5 Irstea, UR EMGR, Saint-Martin-d'Hères, France. 6 Ecolab CNRS, Toulouse, France. 7 Department of Biological Sciences, University of Denver, Canada. PopTrait • At an evolutionary timescale, this reciprocal interaction has promoted the selection of certain plant traits to increase the persistence of woody riparian species within fluvial environments. • 3.2.1 Treatments: Gauge Sediment calibrated (grain size: 0-16 mm) Weight Sedimentation (grain size: 0-4 mm) T.1: Drag force T.2: Sediment burial T.3: Drag force + Burial T.4: Control T.1: Drag force T.2: Sediment burial • Temporal sequence of expected above-ground and below-ground plant development according to the application of treatments. (Experimentation from March to Sept. 2015)1 Concepts: 'ecosystems engineers' and 'positive niche construction'.

  Photo:G.Egger


Joannès Guillemot
email: joannes.guillemot@gmail.com

Nicolas K Martin-Stpaul

Eric Dufrêne

Christophe François

Kamel Soudani

Jean-Marc Ourcival

Paul Leadley

Nicolas Delpierre

The dynamics of annual carbon allocation to wood in European forests is consistent with a combined source-sink limitation of growth

à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Introduction

 The physiological processes underlying the limitation of forest growth are still under debate. A number of recent local investigations challenge the historical view of a strict carbon (C) limitation of growth that is the basis of the C allocation rules of most terrestrial biosphere models (TBMs).  The extent to which forest growth is under a C source-or a sink-control is of paramount importance to predict how trees will respond to global changes, especially with regards to the potential fertility effect of rising atmospheric CO 2 .

Objectives

 To evaluate the dynamics of annual C allocation to wood along regional gradients in 5 major European tree species (in relation to environment and C budget)  To implement the revealed C allocation rules within the CASTANEA TBM and evaluate the simulated wood productivity at regional scale  To evaluate the implications of our new allocation scheme for the productivity of French forests along the 21 st century

Results and Discussion

Material and Methods

Conclusion

 European forest growth is under a complex panel of source and sink limitations, related to ontogeny, direct effect of water shortage and lagged response to past condition.

 C supplygrowth homeostasis and sink controls should both be involved in growth modeling. This will strongly change our predictions regarding the future of forest growth. -C allocation to wood inferred from growth measurements (RENECOFOR permanent plots [A]) and simulated GPP and NPP.

-Assessment of inter-site and interyear drivers using a Random Forest machine learning.

-Performance evaluation was based on the French forest national inventory (5 years of stand biomass increments on >10000 sites).

-Parameters of the allocation scheme were adjusted using a Bayesian optimization (6 param.) and validated on an independent subsample.

-Projections were based on the IPCC AIB scenario [2].

-C allocation scheme in CASTANEA: 4 compartments in semi-competition for C supply ([B, 1]).

-Simulated growth results from both source-and sinklimitations (direct effects of water and temp. stresses on growth).

-GPPgrowth relationship is not consistent in temperate oak across France ([C]).

-Inter-site variability of C allocation to wood was mainly driven by an agerelated decline. -The direct control of temperature or water stress on sink activity exerted a strong influence on the annual wood growth ([D]).

-The lagged effect of the past environment conditions was a significant driver of the annual C allocation to wood ([D]).

-C supply strongly limited growth only in deciduous temperate species.

-The source-sink-C allocation scheme performed satisfactorily against observed forest productivity ([E]), unlike the CASTANEA standard version (data not shown).

-It is crucial to evaluate TBMs against productivity (flux) rather than against stand biomass (stock) to gain insight into the underlying processes of forest growth.

-The CASTANEA projections for the French forest productivity are strongly affected by the implementation of the sinklimitation of growth ([F]).

F

  The dynamic of annual carbon allocation to wood in european forests is consistent with a combined source-sink limitation of growth: Implications on growth simulations in a terrestrial biosphere model Joannès Guillemot, Nicolas Martin-StPaul, Eric Dufrene, Christophe François, Kamel Soudani, Jean-Marc Ourcival, Paul Leadley, Nicolas Delpierre To cite this version: Joannès Guillemot, Nicolas Martin-StPaul, Eric Dufrene, Christophe François, Kamel Soudani, et al.. The dynamic of annual carbon allocation to wood in european forests is consistent with a combined source-sink limitation of growth: Implications on growth simulations in a terrestrial biosphere model. EGU General Assembly 2015, European Geosciences Union, 2015, Bordeaux, United States. 2015, AGU Fall Meeting Abstracts. hal-02740605

  from sites representative of the main European biomes.

[ 1 ]

 1 Guillemot et al., 2014. Assessing the effects of management of forest growth across France, Annals of Botany 114:779,793. [2] Cheaib et al., 2014. Climate change impacts on tree ranges, Ecology Letters 15:533,544.


Virginia Garofano Gomez

D Corenblit

Bruno Moulia

J Steiger

M Abadi

Patrice Chaleil

Black poplar (Populus nigra L.) root response to hydrogeomorphological constraints: An experimental approach

de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Even though it is well recognised that black poplar pioneer trees are riparian ecosystem engineers which modify their fluvial habitat, e.g. by enhancing sediment accumulation, the below-ground responses of young poplars to hydrogeomorphological constraints are still poorly understood.

We performed a semi-controlled ex situ experiment to quantify key functional root traits of response of black poplar cuttings to simulated hydrogeomorphological constraints, i.e. drag force, sediment burial and their combination. The cuttings (n=128) were planted in woven polypropylene bags filled with sandy gravel and with an irrigation system attached, and assigned to one of the four possible treatments (1: drag force; 2: sediment burial; 3: drag force + sediment burial; 4: control). A completely randomized experimental design was employed with cuttings and treatments.

The treatments were applied according to the seasonal occurrence and average duration of floods in the region where the genotype came from. The drag force treatment consisted in the application of three different bending levels on the plant to simulate the drag force exerted during one single flood. A continuous sequence of three floods of one week each was simulated. The sediment burial treatment consisted in the application of a 15 cm-layer of sandy sediment around the main stem to simulate the deposited sediment after a flood event.

A destructive final harvest was performed at the end of one growing season. The below-ground morphology was characterised from manual measurements and image analysis using a traitbased approach. In order to test our hypothesis whether black poplar is able to modulate its phenotype when it is exposed to hydrogeomorphological constraints, we investigated the relationship between the different treatments and the morphology of the root system using directional and multivariate statistics. Our results show some differentiated trends and open up new perspectives for potential applications in bioengineering techniques and river restoration.

Keywords: Populus nigra L., root functional response traits, drag force, sediment burial

[P1.236] Black poplar (Populus nigra L.) root response to hydrogeomorphological constraints: An experimental

	approach , B. Moulia 1,2 1,2 , D. Corenblit V. Garófano-Gómez* 3 , J. Steiger Evette 5 , O. Forestier 6 , A. Garreau 1,2 , E. González 7,8 , B. Hortobágyi 1,2 , M. Abadi 4 , P. Chaleil 1,2 , F. Julien 7 , L. Lambs 3 , A. 7 , A. Masip 7 , S. Ploquin 3 , O. Voldoire 1,2 et al 1 Université Clermont Auvergne,, France, 2 CNRS, France, 3 INRA, France, 4 Véodis-3D, France, 5 Université Grenoble Alpes, IRSTEA, France, 6 Pépinière Forestière de l'Etat, DRAAF Pays-de-la-Loire, France, 7 Ecolab CNRS, France, 8 University of Denver, Canada


Fanny Calenge

Irène Gabriel

Sandrine Mignon-Grasteau

Jordi Estellé

Bertrand B Bed'hom

teaching and research institutions in France or abroad, or from public or private research centers.


Simon Rizzetto

Salim Belyazid

Jean-Claude Gégout

Manuel Nicolas

Didier Alard

Emmanuel Corcket

Noémie Gaudio

Harald Sverdrup

Anne Probst

Modelling the impact of climate change and atmospheric N deposition on french forests biodiversity

établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Modelling the impact of climate change and atmospheric N deposition on french forests biodiversity

Simon Rizzetto *(1,2) , Salim Belyazid (3) , Jean-Claude Gegout (4) , Manuel Nicolas (5) , Didier Alard (6) , Emmanuel Corcket (6) , Noémie Gaudio (1,2) , Harald Sverdrup (7) , Anne Probst (1,2)

Abstract

Since the 1980's, within the Geneva Convention on Long-Range Transboundary Air Pollution, European countries have joined their efforts to abate atmospheric acid pollution. Nevertheless, nitrogen emissions and depositions remain significant under ongoing climate change. Nitrogen atmospheric deposition is known to severely impact ecosystem functioning by influencing soil biogeochemistry, nutrients balance and, consequently, tree growth, forest health and biodiversity. The concept of "critical loads" was used and models were improved to mitigate the impacts of N deposition, by considering conjointly effects of climate change and N atmospheric deposition, to assess the evolution of forest ecosystem status over time.

The purpose of this study is to predict forest vegetation response to the combine effects of nitrogen atmospheric deposition and climate change by using a dynamic coupled biogeochemical-ecological model (ForSAFE-Veg). The Veg module is composed of 476 understory plant species representative of the main French forest ecosystems, and parameterized for a set of environmental factors based on expert advices. In this study, we propose a new parameterization for six main factors using statistical regressions models based on measured data for about 4000 forest sites. After validation using another independent set of vegetation relevés, the biogeochemical model ForSAFE-Veg was run using the most appropriate Veg module, on three forest sites from the french ICP Forest network. Changes in biodiversity were estimated by analysing the evolution of plants cover over 100 years, and considering the impacts of climate change and atmospheric nitrogen deposition scenarios separately and conjointly. The modelling outputs were considered at both species and ecological functional groups scales, to evaluate their relevance in characterizing nitrogen deposition influence on biodiversity. This will allow generalizing this approach to other species for which environmental factors are not easy to parameterize. * Corresponding author: simon.rizzetto@ensat.fr

International Congress Global Challenges of Air Pollution and Climate Change to Forests Programme and Abstracts

	1-5 June, 2015
	Hyatt Regency Palais de la Méditerranée
	Nice, France

Organized by

International Union of Forest Research Organizations -Research Group 7.01 COST Action FP1204 GreenInUrbs

  AgroParistech, Laboratoire d'Etude des Ressources Forêt-Bois (LERFoB), Nancy, France.(5) Office National des Forêts, Direction Forêts et Risques Naturels, Département Recherche et Développement, Fontainebleau, France. (6) UMR BioGeco INRA, Bordeaux, France.(6) Applied Systems Analysis and Dynamics Group, Chemical Engineering, Lund University, Lund, Sweden.

	(1) Université de Toulouse ; INP, UPS, EcoLab (Laboratoire Ecologie Fonctionnelle et
	Environnement); ENSAT, Avenue de l'Agrobiopole, Castanet-Tolosan, France. (2) CNRS; EcoLab ;
	Castanet-Tolosan, France. (3) Belyazid Consulting and Communication AB, Malmö, Sweden. (4)
	AgroParisTech, UMR 1092 INRA-


Marie Sauvadet

Matthieu Chauvat

Daniel Cluzeau

Pierre-Alain Maron

Cecile Villenave

Isabelle Bertrand

Soil micro-food web structure and functions exhibit contrasting dynamics according to litter quality

à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

-

  1 , M. Chauvat 2 , D. Cluzeau 3 , P-A. Maron 5 , C. Villenave 6 , I. Bertrand 7 Soil micro-food web structure and functions exhibit contrasting dynamics according to litter quality 1 INRA UMR FARE Reims; 2 ECODIV, University of Rouen,; 3 ECOBIO, University of Rennes; 4 INRA Agroecologie Dijon; 6 ELISOL Environnement; INRA UMR ECO&SOLS, Montpellier. Significant effects of litter quality on micro-food web structure and functions, but dependent of the stage of decomposition -Contrasting micro foodweb structurefunctions relationships according the litter degraded -Biotic interactions varied with litter quality and stage of decomposition, and were higher during the early stage of leaf decomposition

Acknowledgments

More informations: -Sauvadet et al. (2016) Soil

Biology&Biochemistry 95: 262-274

Projet SOFIA

Projet SOFIA (Soil Functional diversity as an indicator of sustainable management of Agroecosystems)


Bettina Bellocq

Cuq Bernard

Ruiz Thierry

Duri Agnès

Delaplace Guillaume

Ducept Fabrice

The specifications for the sustainable-design of thermo-hydro-mechanical paths for the elaboration processes of agglomerated products

Introduction & Objectives

Major aims of this work are: 1. To identify and model the structuration mechanisms developed under thermo-hydro-mechanical stresses. 2. To compare the energy consumption at the process level to the energy needs for local structuring mechanisms. 3. To represent the conceptualization process using dimensionless analysis.

1. Mechanistic approach 2. Twin product/process engineering approach

Knowledge integration approach

The main goal of the mechanistic approach is to determine the specific contribution of the powder reactivity during agglomeration processing. Durum wheat powders undergo reversible and irreversible physicochemical changes when submitted to thermo-hydro-mechanical stresses in relation with its composition.

This task leads to the establishment of specifications concerning the proteins in durum wheat. This approach will allow to identify the characteristics times and lengths, and estimate the energy requirements, for each physical and physicochemical mechanisms that are induced by the successive stages during processing. This approach, associated with experiments at different scales and with different pilot designs and combined with dimensional analysis, will conduct to generate specifications for the couscous process re-design.

Our objective is to specifically evaluate:

-The contribution of physical characteristics of particles to the agglomeration mechanisms.

-The contribution of proteins to the irreversible physicochemical mechanisms.

Our work is focused on morphogenesis and structuring mechanisms, using different technology modes and process conditions. In parallel, we realize measurements of the energy consumptions to estimate the energy cost of the processing of durum wheat semolina in couscous and the impact of the raw material diversity.

Knowledge integration approach, based on conceptualization approaches, allows the elaboration of functional diagrams using dimensionless criteria. Dimensional Analysis (DA) is a way to allow the decomposition of the whole couscous process in a "relevant number base" (dimensionless numbers), involving many complex mechanisms. We improve theoretical foundations to understand the uses of thermo-hydro-mechanical paths of powders reactivity during the process of durum wheat into agglomerated couscous grains. The current industrial process is poorly eco-efficient and energy consuming. There is a need for a multidisciplinary approach including cereal technology, product engineering, soft-matter science and granular matter physics.

The approach is to initially list the influential variables to create a dimensional matrix. The dimensional matrix allows to express the process relationship linking the target parameter to the key process parameters. The target parameters are chosen from the physicochemical properties of the final agglomerated powder.

  The diagonalization of the matrix allows to define the coefficients of the dimensionless numbers and the final model. The target parameter values can be mathematically described by the product of exponential and powers laws. Acknowledgments: The authors would like to thank the Agence Nationale de la Recherche (ANR) for its financial support through the scientific program "Dur-Dur". Mixing Rolling Cooking Drying Technology modes are selected to generate different hydro-thermo-mechanical stresses during process: -Mechanical or pneumatic mixing process. -Rolling with inclined rotating cylinder. -Different cooking and drying technologies. Process conditions are selected by promoting the mechanisms as successive long-times stages or a simultaneous short-times stages and to investigate the impact of: -Shear -Water content -Times -Temperature Impact of the water content on the diameters of agglomerates (Hafsa I. et al., 2014) Impact of the rotation speed on the yield of different fractions of agglomerates Example of a dimensional matrix on an inclined rotating cylinder


Functional Genomics P3001-P3097

Chengyi Song (Yangzhou University) Ovulation rate is the first restrictive factor of litter size in pig. The difference in ovulation rate between breeds with high and low ovulation rate originate from the differences during mid-to later follicular phase in dynamics of follicular growth. In high ovulation rate sows, the follicle selection phase is prolonged and more preovulatory follicles emerge. The dynamic process involving selection and maturation of follicles is regulated and controled by a highly synchronized and exquisitely timed cascade of gene expression. Since miRNAs regulate gene expression extensively, and play an important role in the development of ovarian and female reproductive cells, the difference in ovulation rate between Chinese Meishan and Duroc sows maybe affected by the different expression of miRNAs in their ovarian follicles.Ovarian tissues of Meishan and Duroc at day 4 of follicular phase were collected, miRNA libraries were constructed and next-generation sequencing was conducted. In ovaries of Duroc and Meishan, a total of 272 and 275 pig miRNAs were detected, 125 and 155 predicted miRNAs sharing high homologies with known miRNA of other species were found, 49 and 57 novel miRNAs were detected, respectively. And some of the new miRNAs were verified.miRNA chips were used to screen the miRNAs differentially expressed in medium Follicles (with a diameter of diameter 5.0mm-6.9mm) between Meishan and Duroc sows. A total of 158 pig miRNAs were detected, and ssc-miR-30a, ssc-miR-708, ssc-miR-187, ssc-miR-486 shown significant difference in expression level between Meishan and Duroc, and 31 mammalian miRNAs unreported in pig shown significant difference as well. And the expression difference of some miRNAs were conformed. The expression profiles of several differentially expressed miRNAs in various tissues and follicles at different stages were investigated. The research provide an insight for better understanding the genetic basis and molecular mechanism of follicle development and high prolificacy affected by miRNAs in pigs.

P3090 Understanding the complex interaction between pseudorabies virus (PrV) and its natural host using RIP-Chip enrichment analysis.. Sophie Dhorne-Pollet, Jé rome Lecardonnel, Florence Jaffré zic, Marco Moroldo and Elisabetta Giuffra (Institut National de la Recherche Agronomique, AgroParisTech, UMR1313 Animal Genetics and Integrative Biology.)

MicroRNAs modulate cellular pathways by acting at the post-transcriptional level, through molecular interactions with target mRNAs via the RNA-induced silencing complex (RISC). During a viral infection, complex interactions take place between the virus and its host which involve, among other factors, microRNAs. Some host microRNAs are crucial for immune responses, and a few of them target viral mRNAs and inhibit viral replication. Moreover, microRNAs encoded by some viruses (mostly herpesviruses) can modulate the transition from latent to lytic replication and attenuate the host antiviral immune responses. An interesting model to study these complex interactions is the pseudorabies virus (an alpha-herpesvirus, PrV) responsible for Aujeszky's disease in pigs, its natural host. The intron of the large latency transcript of the PrV genome has been shown to encode a cluster of 11 microRNAs. To understand the biological role of viral microRNA during PrV infection, we previously compared a mutant PrV clone depleted of a cluster of microRNAs and a parental clone for their ability to establish latency in vivo in trigeminal ganglia.

Here we present a functional genomics approach based on the RIP-Chip assay to better understand the intricate interactions between the miRNAs found expressed by PrV during latency and the host mRNAs. We first optimized the experimental procedures in terms of cell lines,


SANTA CRUZ • CHILE

ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Exploration of constitutive and induced markers of disease severity caused by Botrytis cinerea in the primary metabolome of tomato

Constitutive markers of plant defense are required to provide solutions for plant protection by the control of its environment. While dozens of plant secondary metabolites have been identified as putative markers of defense against necrotrophic fungi, few where robustly related to disease intensity. In this work, we explored the potential of primary metabolites as predictors of disease severity. Plant soluble sugars, as main components of primary metabolism, are thought to be implicated in defense against pathogenic fungi. However, the function of sucrose and hexoses remains unclear. A different role for glucose and fructose in tomato defense against Botrytis cinerea was hypothesized. We examined tissue contents in primary metabolites at the time of inoculation with B. cinerea for tomato plants subjected to a range of abiotic environments created by various nitrogen and water supplies. Sugar contents and defense hormonal markers were then quantified during the infection process. In a first step, we assessed multiple combinations of primary metabolites as possible constitutive markers of disease intensity. In a second step, we checked for the kinetics of the selected markers during the infection process. Ratios of soluble sugars, rather than those of organic or amino-acids where identified during the first step as best correlators of disease intensity. Soluble sugar contents of tissues surrounding infection sites evolved differently after inoculation. The fructose content never decreased after inoculation with B. cinerea, while that of glucose and sucrose showed either positive or negative variation, depending on the abiotic environment. Increase in relative fructose content (defined as the proportion of fructose in the soluble sugar pool), was observed in absence of glucose accumulation, and was associated with lower disease intensity. A lower expression of the salicylic acid marker PR1a, and a lower repression of a jasmonate marker COI1 was associated with higher relative fructose contents. We concluded that fructose relative content was both a constitutive and induced marker of symptoms in a range of environments. Small variations of fructose content among the sugar pool are unlikely to affect pathogen growth by itself. Our data strongly suggest that the adjustment of relative fructose content is required for enhanced defense against B. cinerea.

01594722 XVII International Botrytis Symposium Santa Cruz -Chile, 2016. O.5b.3: EXPLORATION OF CONSTITUTIVE AND INDUCED MARKERS OF DISEASE SEVERITY CAUSED BY Botrytis cinerea IN THE PRIMARY METABOLOME OF TOMATO François Lecompte 1 *, Philippe C. Nicot 2 , Julie Ripoll 1 , Manzoor A. Abro 2 , Astrid K. Raimbault 3 , Félicie Lopez-Lauri 3 and Nadia Bertin 1

	1 PSH unit, INRA, F-84914, Avignon, France;

François Lecompte, Philippe C. Nicot, Julie Ripoll, Manzoor Ali Abro, Astrid K. Raimbault, Félicie Lopez-Lauri, Nadia Bertin To cite this version: François Lecompte, Philippe C. Nicot, Julie Ripoll, Manzoor Ali Abro, Astrid K. Raimbault, et al.. Exploration of constitutive and induced markers of disease severity caused by Botrytis cinerea in the primary metabolome of tomato. 17. International Botrytis Symposium, Université du Chili. CHL., Oct 2016, Santa Cruz, Chile. hal-2 Plant pathology unit, INRA, F-84140, Montfavet, France; 3 UMR Qualisud,-Université d'Avignon et des Pays du Vaucluse, F-84916, France. francois.lecompte.2@inra.fr


Duri Agnès
email: agnes.duri@supagro.inra.fr

Mandato Sandra

Cuq Bernard

Ruiz Thierry

Powder properties influence on the local stress profile in a granular column

In a wet agglomeration process, inside a low shear mixer, the blade displacement allows for homogenizing the pulverized liquid on the powder surface and promoting the growth mechanisms of agglomerates. This mechanical action is efficient if the blade can apply an adapted stress field in the granular media. Low shear mixers with a vertical arm can cyclically mix the grain bed by alternating dynamic states of the particles close to the blade and static states beyond the influence length of the mobile. As a consequence, the blade displacement alternately disturbs the mechanical profile at equilibrium inside the powder bed which strongly affects the flowing powder properties once the powder is in movement. Until recently, the qualification of the static state of a granular media was described by Janssen's model, which under some hypotheses, allows calculating the stress at the bottom of powder column. Recent stress measurements, conducted by some of us, showed that Janssen's profile is different from the local stress profile. The objective of this work is to experimentally measure the local stress profile inside a semiconfined granular bed with a force sensor immersed in the powder bed. Several reactive powders issued from durum wheat were selected to estimate the physical characteristic impact of the particles (size, angle of rest…). The results show that the shape of the local stress profiles is similar whatever the powder characteristics. The construction of the local profile is discussed according to a structuration of three layers in the powder bed, which seem to be separated by two characteristic lengths.


Data comparison between EC method (field scale) and SF 6 method (animal scale)

• In 2010, the pasture was a potential sink with net fixation of 559 g CO 2 eq m -2 .

• When considering CH 4 fluxes, the sink of GHG was reduced by 310 g CO 2 eq m -2 , leading to a net sink of 249 g CO 2 m -2 .

• By using Giger et al. methodology, CH 4 emission would represent 80% instead of 55% of the potential annual carbon dioxide sink, which underlines the need for direct field measurement. • EC method: heifers emission rate varied with distance between fenced area and EC mast.

• Uncorrected EC fluxes were on average 85% lower than those calculated with SF 6 method (164 (± 8) g day -1 head -1 ).

• The correction with a two-dimensional footprint function [7], allowed to compensate for the dilution effect on measured CH 4 flux.

• Corrected EC fluxes were in average 28% lower than SF 6 method.

INRA UR0874,Grassland Ecosystem Research,5,Ch de Beaulieu,France. Authors adress: tiphaine.tallec@cesbio.cnes.fr, katja.klumpp@clermont.inra.fr • CH 4 emissions from 5 heifers were simultaneously measured by EC and SF 6 tracer techniques during 4 days.

• Heifers were confined in the prevailing wind direction to ensure their presence in the footprint area.

•Two distances were tested (10 and 30m) • Optimization of both integrated plumes allowed to calculate a CH 4 emission of 280 (± 18) g day -1 head -1 .

(1) The accuracy of the EC method varied depending on distance between animals and EC mast and on animal grazing activity (moving in and out the footprint area), indicating the limits of the systems and necessity to animal tracking or filling source homogeneity distribution condition. (2) However, considering the whole grazing season, CH 4 budget estimations were close to results based on theoretical calculation methods.

(3) EC method and associated detailed measurements offer original research opportunities to study in situ effects of management and vegetation structure at field and animal scales on adjacent paddocks, and may contribute to the development of more adapted mitigation options.

  Methane emissions represent 8% of EU15-GHG emissions, where 50% originate from livestock. Despite numerous measurements of enteric CH 4 emissions have been carried out in artificial conditions [1], an extrapolation of those measurements to field scale and grazing animals, often hampers precision due to spatial and temporal variation in feed intake quality and quantity. Accurate measurements from ruminating herds are, thus, required to improve emission coefficients. Measurements were carried out at the French semi-natural upland grassland site Laqueuille. Site is continuously grazed from May to October. Live weights of animals and livestock rate have been taken every two weeks. The reliability of EC technique was tested by comparing field scale measurements with Gaussian plume model simulation [2], animal scale measurement (SF 6 tracer technique) [3], and theoretical calculation method based on factor emission use [4] [5] [6].

  The EC-system comprises a 3D sonic anemometer, a fast closedpath CH 4 analyzer (FMA) and an open path CO 2 -H 2 O analyser (LI-7500) installed at a height of 2m. Measured methane concentrations (i.e. from herd and artificial source) along the plume transect were compared with output of the multiple gauss plume model [2].

  close to results from theoretical calculations (i.e. based on ingested biomass and animal weight) of the averaged modelled and measured CH 4 plumes were close along the transect.


Marie-Helene Desmonts
email: mh.desmonts@aerial-crt.com

Marie Thiollet-Scholtus

Ewann Hamon

Adeline Rapin

Sophie Gavignet

Lionel Ley

Aude Lagenfeld

Najat Nassr

Marie-Hélène Desmonts

Erwann Hamon

Aude Langenfeld

An innovative soil management

come   L'archive ouverte pluridisciplinaire

INTRODUCTION

Sustainable grape production entails the implementation of management practices that permit low pesticides inputs, maintain grapevine performance, and conserve soil quality. The nutrition of the vine is one of the major parameters influencing the nature and the content of the secondary metabolites produced by the vine. These metabolites have a direct impact on the organoleptic quality of the wine. The present work investigates the quality of production of two varieties of grape (Riesling and Pinot Gris), in different combinations of locations (in Alsace, France), vintages and vineyards managements.

Work supported by French Ministry and Europe (FEDER)

• The sensory visual and aromatic attributes of harvest berries enabled to distinguish the six sites-systems and the two studied year, but not the organic systems from the integrated ones.

• The chromametric measurements were correlated to the expert color ratings in relation to the grape variety.

• The sensory profile of the wine was linked to berry quality at harvest. • There is no significant impact on consumer preferences of the wines.

• It would be interesting to continue describing the sites-systems with the production practices and others studied years.

 Wines with variable sensory qualities

 berries chromametric measurements correlated with expert color ratings

RESULTS

Sensory profiles of berries not dependant from the system type The oenologists (Fig. 5) and the consumers (data not showed) made no significant differences (at 5%) between the 2 Pinot Gris 2014 wines for quality sensory attributes. The 3 Riesling wines differed qualitatively on all criteria except for the typicality: the RibeauPI and RibeauAB wines were significantly more appreciated (at 5%) than the wine IngerAB with a strong aromatic potential and a stronger Terroir influence.

  Fig 3. Descriptive sensory profiles of the 4 Riesling IngerAB, ChâtenAB, RibeauAB and RibeauPI, berries 2014 (A)

Fig 4 .

 4 Fig 4. 6 berries Riesling and Pinot Gris

Fig 5 .

 5 Fig 5. Hedonic sensory judgements of the 3 Riesling IngerAB, RibeauAB and RibeauPI and 2 Pinot Gris, RouffPI

Fig. 1 :

 1 Fig. 1 : Espace de couleur CIE L* a* b

  Fig. 2: Sensory laboratory room of 13 independent boxes


Anne-Lise Jacquot

Catherine Disenhaus

Yannick Le Cozler

published or not. The documents may come     What do young French people think about livestock productions in 2014 ?

What do young French people think about livestock productions in 2014?

Jacquot AL 1,2 , Disenhaus C 1,2 , Le Cozler Y The gap between LP chain's reality and citizen's expectations is increasing

• A lack of data about feelings and knowledge about LP of young people, as future citizens and consumers

Material & Methods

• Surveys all over France from 13 th to 24 th

What are their perceptions about livestock farming systems?

-Two third of SSP considered that being a farmer is a good job obtained by superior studies … but unprofitable, especially considering working time -Animal welfare is their first concern (80%) even though mainly well regulated by law … with only herbivorous animal having good welfare conditions -LFS has negative effects on environment (54%) on water (72 %) & air quality (57 %), … BUT positive impacts on tourism (38 %) & landscape (37 %) -LFS can be responsible of appearance of new diseases in human (for 47 % of them)

What kind of consumer are they?

-Eating meat is important and regular (94 %). For 66 % of SSP, a meal without meat, fish or egg is not a real meal

Why is it important for SSP to maintain livestock production in France ?

  January 2014 carried out by 35 Master 2 students • A closed-questionnaire (49 questions) full-filled by French secondary school pupils (SSP) who get their "baccalauréat" (GCE A-levels) in June 2014 ( 17/18 years of age) Animal welfare is their main concerns (80 %) more than environment protection (54 %) and food production (48 %) Finally, 96 % of them estimated that keeping livestock production is of great importance in France Similar studies carried out in other European countries could be useful to prepare some of expected changes in the coming years Authors wish to thank all participants who kindly answered their questions A need to better understand this sub-population by conducting surveys 28 different high-schools (general, farming & technical) 1083 SSP 1. What do they know about livestock farming systems? -On a scale from 0 to 10, 70% consider their knowledge under 5, even though 78 % of them visited at least once a livestock farm -Knowledge on LFS originated from media (25%), family or neighbourhood (23 %) or school (18 %)

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  To preserve heritage (food, animal) & landscapes -To reduce environmental impacts -To provide food with high quality standard of production -To maintain economic life on rural territories


Fernando Andrés

Maida Romera-Branchat

Rafael Martínez-Gallegos

Vipul Patel

Korbinian Schneeberger

George Coupland

Repression of the FT-signaling pathway mediated by organ patterning genes

Floral organs are produced in response to environmental and endogenous cues from populations of cells that are allocated on the flanks of the shoot apical meristem (SAM). These environmental

cues are integrated into flowering signaling networks by the thermosensory, vernalization/autonomous and photoperiodic genetic pathways. FLOWERING LOCUS T (FT) is a key component of the photoperiodic pathway. In Arabidopsis thaliana, FT mRNA is expressed specifically in the companion cells of the phloem and its protein systemically moves to the shoot apex to activate flowering. FT is unloaded into the shoot meristem, and physically interacts with a bZIP transcription factor called FD, which is expressed in the meristem. FD is required for FT function, and the FT-FD complex is believed to activate the transcription of several floweringpromoter genes. Primary transcriptional targets of FD are the floral identity genes APETALA1 (AP1) and LEAFY (LFY), whose expression in lateral organ primordia confers floral fate. Therefore, FT-FD complex is predicted to be active in the incipient floral primordia in order to induce the expression of AP1 and LFY and promote floral meristem identity. BEL1-like homeodomain (BELL) transcription factors play important roles in SAM function. PENNYWISE (PNY) is a BELL protein which is involved in lateral organ patterning and the acquisition of competence to respond to floral inductive signals. Interestingly, simultaneous mutations in PNY and its paralog POUND-FOOLISH (PNF) block the ability of FT to activate flowering. However, how organ patterning genes can affect the FT-signaling pathway remains unclear. We performed a sensitized screen for Arabidopsis mutants and identified a set of mutations that reduce the capacity of FT to promote early flowering. By employing Next Generation Sequencing we identified a new mutant allele of PENNYWISE (PNY) (called pny-58) which strongly suppresses the flowering function of FT. We made use of this new allele to unravel the genetic and molecular connections between the FT-signaling pathway and organ patterning genes. Remarkably, we found that PNY binds to the promoter and regulates the expression of BLADE-ON-PETIOLE1 (BOP1) and BOP2 genes, two BTB-ankryin transcriptional coactivators. BOP1/2 are normally expressed in a few cells at the base of the developing leaves and incipient leaf primordia. However, we observed that in the absence of functional PNY, the patterns of expression of BOP1/2 mRNA become broader in the SAM. This indicates that an important function of PNY is to limit the BOP1/2 mRNA at specific locations. Surprisingly, our genetic and molecular studies show that this broader expression of BOP1/2 delays flowering by repressing the expression of FD in the SAM. In addition, we show that FD expression is reduced at the flanks of the SAM in the pny-58 mutant as a consequence of the ectopic expression of BOP1/2 genes. Therefore, AP1 and LFY cannot be properly activated by the FT-FD module and the floral transition is delayed. These results together shed light on the interaction between organ patterning genes and the FT-signaling pathway during flowering in Arabidopsis.


J Soulat

S Léger

B Picard

V Monteils

IMPROVING BEEF SENSORY QUALITY THROUGH BREEDING PRACTICES MANAGEMENT

Keywords: breed types, fattening period, young bull I

To identify the benefic effects of breeding practices, for the fattening period, on the Longissimus Thoracis sensory properties, a dataset obtained from 329 young bulls (2 breed types: beef and hardy) was analyzed. Animals were classified in 2 clusters: high and low sensory quality of beef meat. Different breeding practices combinations driven to high sensory quality were highlighted with decision trees, according to breed types. A higher beef quality is possible with a forage intake ≥ 1.95 kg DM/d in the fattening diet and a fattening period duration < 178 d for young beef breed bulls. The slaughter age of young bulls had a positive impact on beef quality of hardy breeds (≥ 17.2 mo) and beef breeds (between 15.4 and 16.8 mo) if it was combined with a longer fattening period duration and a higher average daily gain, for beef breeds and in addition with a heavier weight for hardy breeds.

INTRODUCTION

In France, bovine breeds were selected according to production system. Three breed types are identified: dairy, beef and hardy breeds. Besides the breed, the bovine production used diversified breeding practices (animal type, gender, age, diet, etc.) which influence the quality of beef meat [START_REF] Oury | Mode de conduite en élevage et tendreté de la viande bovine[END_REF]. Furthermore, the principal valuable quality trait for consumers is tenderness [START_REF] Geay | Effect of nutritional factors on biochemical, structural and metabolic characteristics of muscles in ruminants, consequences on dietetic value and sensorial qualities of meat[END_REF]. The aim of this study was to determine which breeding practices had a positive impact on the sensory quality of beef meat. This study was carried out during the fattening period of young bulls according two breed types (beef and hardy).

II. MATERIALS AND METHODS

Dataset

This study was realized on the individual data of 329 young bulls. For each young bull, breeding practices for the fattening period and Longissimus Thoracis (LT) sensory properties were available.

Sensory analysis

LT samples taken 24h post-mortem were maturated during 14 d at 4°C. The samples were grilled (55-60°C), tenderness, flavor and juiciness were scored between 0 and 10 by trained taste panels (Table 1) [START_REF] Dransfield | Meat quality and composition of three muscles from French cull cows and young bulls[END_REF].

Statistical analysis

All statistical analyses were realized with R 3.1.1 [START_REF] Core | R. A language and environment for statistical computing[END_REF]. Decision trees enabled to determine breeding practices combinations to obtain a higher beef meat quality. For sensory data from the 329 young bulls, a cluster analysis with kmeans method, was performed with linear model residuals of sensory data (tenderness, juiciness and flavor). Working with residuals allowed to take off effects of evaluation variability between sensory panels. Residual sensory data were clustered into 2 classes. Student test were realized to compare significance and breeds, breed types and projects repartition between the 2 classes. Then, the 13 breeding practices variables, for each "Beef" and "Hardy" breed types, were used to establish decision trees with the package rpart [START_REF] Therneau | rpart: Recursive partitioning and regression trees[END_REF] in R logical witch use CART method. To evaluate decision tree, a classification error was calculated. The decision tree, obtained on all BB young bulls (n = 215), retained 5 breeding practices variables: fattening period duration, forage quantities intake, ADG, slaughter age and net energy intake (Fig. 1) to allocate young bulls in 8 terminal sheets divided into 3 HSQ and 5 LSQ. The classification error of this tree was 30.2%. Three breeding practices combinations drive to a high sensory quality:

1: A fattening period duration < 178 d and a forage intake ≥ 1.95 kg DM/d. When the fattening period duration was shorter, the forage intake had a positive impact on the beef meat quality.

The decision tree obtained on all HB young bulls (n = 114), retained 5 breeding practices variables: final live weight before animal quit farm, ADG, fattening period duration, beginning live weight and slaughter age (Fig. 2) to allocate young bulls in 6 terminal sheets divided into 3 HSQ and 3 LSQ. The classification error of this tree was 42.5%.Three breeding practices combinations drive to a high sensory quality: Despite, relatively high classification errors of trees, the percentage of good animals classified in the terminal HSQ sheets was high. Data highlight different breeding practices combinations to manage meat quality of young bulls. Some practices were common among these combinations for both breed types (fattening period duration, ADG, slaughter age) but with different levels of intervention within the decision trees. Other practices impact only one breed type (forage intake and net energy for BB, and live weights at the beginning and the end of the fattening period for HB). The implication of some dietary variables in the BB decision tree can be explained by more variability among the diets for the BB than the HB. In the literature, few studies, concerning the breeding practices of young bulls, showed a link with the sensory properties of LT [START_REF] Oury | Mode de conduite en élevage et tendreté de la viande bovine[END_REF].

IV. CONCLUSION

The breeding practices combinations to manage the sensory quality of beef meat need to be adapted according to the breed types. The HB young bulls can be slaughtered older than the BB, if they had a final weight ≥ 570 kg, an ADG ≥ 1.3 kg/d and a fattening period ≥ 161 d. Further studies with numerous animals must be conducted to confirm the identified combinations.

Table 1

 1 Dataset description

			Breed types
			Beef	Hardy
			(n = 215)	(n = 114)
		Mean ± sd	Mean ± sd
	Breeding practices
	Slaughter age (mo)	16.6 ± 2,6	17.5 ± 2.7
	Beginning live weight (kg)	400 ± 63	386 ± 35
	Final live weight (kg)	668 ± 107	659 ± 128
	Slaughter live weight (kg)	650 ± 103	645 ± 127
	Fattening period duration (d)	166 ± 63	163 ± 25
	Forage intake (kg DM/d)	4.3 ± 3.1	5.7 ± 1.6
	Concentrate intake (kg DM/d)	4.5 ± 2.7	2.5 ± 1.1
	Dry matter intake (kg DM/d)	8.9 ± 1.2	8.2 ± 0.9
	% Forage (% of the DMI)	47.4 ± 32.6	68.5 ± 14.8
	% Concentrate (% of the DMI)	52.6 ± 32.6	31.5 ± 14.8
	Energy intake (Mcal/d)	14.1 ± 2.3	15.0 ± 3.3
	Average daily gain (kg/d)	1.7 ± 0.8	1.8 ± 1.0
	Efficiency (kg/kg DM)	0.2 ± 0.1	0.2 ± 0.1
	LT sensory analysis (scale: 1-10)
	Tenderness	5.4 ± 1.2	5.7 ± 1.1
	Juiciness	5.3 ± 1.0	5.3 ± 1.0
	Flavor		5.1 ± 1.1	5.3 ± 0.9
	sd: standard deviation, LT: Longissimus Thoracis,
	n: number of animals
	III.	RESULTS AND DISCUSSION
	Sensory data were classified in 2 clusters "high
	sensory quality" (HSQ) and "low sensory quality"
	(LSQ) of respectively 163 and 166 young bulls.
	The 2 clusters were significantly different (p <

Table 2 )

 2 . Each breed and project were represented in each cluster. The HSQ cluster contained 102 BB and 61 HB young bulls. The LSQ cluster contained 113 BB and 53 HB young bulls.

Table 2

 2 Sensory clusters description on all animals

		Sensory quality
		High	Low
		(n = 163)	(n = 166)
		Mean ± sd	Mean ± sd
	Sensory (scale: 1-10)
	Tenderness	6.1 a ± 1.0	4.9 b ± 0.9
	Juiciness	5.7 a ± 1.0	4.9 b ± 0.8
	Flavor	5.4 a ± 1.1	5.0 b ± 1.0
	n: number of animals, a,b (p < 0.001)

  61 st International Congress of Meat Science and Technology, 23-28 th August 2015, Clermont-Ferrand, France 1: A final live weight before transportation for slaughterhouse ≥ 570 kg and an ADG < 1.3 kg/d.

						Fattening period
	2: A final live weight before transportation for	duration
	slaughterhouse ≥ 570 kg, ADG ≥ 1.3 kg/d, a
	< 178 days fattening period duration < 161 d and a start live			≥ 178 days
	fattening weight < 379 kg.
	Forage intake 3: A final live weight before transportation for slaughterhouse ≥ 570 kg, an ADG ≥ 1.3 kg/d, a			Average daily gain
	fattening period duration ≥ 161 d and a slaughter
	< 1.95 kg DM/day age ≥ 17.2 mo.		≥ 1.95 kg DM/day	< 1.2 kg/day	≥ 1.2 kg/day
		Average daily gain						Slaughter age
	< 1.4 kg/day		≥ 1.4 kg/day					< 15.4 mo	15.4 mo ≤ Age < 16.8 mo	≥ 16.8 mo
			Net energy
			intake
		< 13.9 Mcal/day	≥ 13.9 Mcal/day
	LSQ	HSQ	LSQ		HSQ		LSQ	LSQ	HSQ	LSQ
	(n = 28 ; 75 %)	(n = 11 ; 81.8 %)	(n = 23 ; 60.9 %)	(n = 92 ; 63 %)	(n = 15 ; 100 %)	(n = 16 ; 87.5 %)	(n = 8 ; 87.5 %)	(n = 22 ; 54.5 %)
			Final live weight
			(before quit farm)
	< 570 kg		≥ 570 kg
				Average daily
					gain
			< 1.3 kg/day				≥ 1.3 kg/day
								Fattening period
								duration
						< 161 days		≥ 161 days
						Beginning live weight		Slaughter age
					< 379 kg		≥ 379 kg	< 17.2 mo	≥ 17.2 mo
	LSQ	HSQ		HSQ		LSQ	LSQ	HSQ
	(n = 33 ; 64 %)	(n = 28 ; 78 %)	(n = 12 ; 91.7 %)		(n = 21 ; 52.4 %)	(n = 13 ; 84.6 %)	(n = 7 ; 57.1 %)

61 st International Congress of Meat Science and Technology, 23-28 th August 2015, Clermont-Ferrand, France

Figure 1. Decision tree for Beef Breeds n: number of animal in the terminal sheet, %: animal percentage in the good cluster, HSQ: high sensory quality, LSQ: low sensory quality Figure 2. Decision tree for Hardy Breeds n: number of animal in the terminal sheet, %: animal percentage in the good cluster, HSQ: high sensory quality, LSQ: low sensory quality

st International Congress of Meat Science and Technology, 23-28 th August 2015, Clermont-Ferrand, France

ACKNOWLEDGEMENTS

Authors thank all research project responsible (Jacques Agabriel, Yves Geay, Jean-François Hocquette, Didier Micol, Gilles Renand & Bernard Sepchat) to make available the data used for this study and the different person involved in the data base management in the INRA herbivores research joint unit.


Jordi Estellé

Núria Mach

Yuliaxis Ramayo-Caldas

Florence Levenez

Gaëtan Lemonnier

Catherine Denis

Joël Doré

Yvon Billon

Marie-José Mercat

Catherine Larzul

Patricia Lepage

Claire Rogel-Gaillard

Gut microbiota composition in swine: genetic parameters and links with immunity traits

IFIP-BIOPORC, Pôle génétique, La Motte au Vicomte, France

The intestinal microbiome plays a major role in host's physiology and homeostasis. It participates in the immunological barrier against infections, helps to develop and mature the immune system, and contributes to extract nutrients and energy from food. Despite large scale studies in human, little is known on gut microbiota composition and potential associations with individual traits in livestock species. The objective of this study was to estimate the genetic parameters of the gut microbiota composition and analyze its links with immunity traits in French Large White pigs. A cohort of 60 days old piglets was assessed for fecal microbiota composition by pyrosequencing the 16S rRNA gene. First results on 299 piglets showed a predominance of Prevotella followed by Oscillibacter, Dialister, Roseburia and Treponema. Among a set of 63 genera, 7 had low (0.1<h2<0.2), 15 medium (0.2<h2<0.4) and 8 high (h2>0.4) heritabilities for abundance variations. At the genetic level, the relative abundance of Prevotella, Oribacterium, Selenomonas, Dialister and Megasphaera were found positively correlated with each other and tended to be negatively correlated to other genera. Finally, regularized canonical correlations (rCCA) and sparse Partial Least Squares (sPLS) analyzes highlighted both positive and negative correlations between various immunity traits (e.g. monocytes, eosinophils, platelets) and genera such as Prevotella, Roseburia and Dialister. In this report we demonstrate for the first time that the gut microbiota composition in swine is influenced by the genetics of the host. In addition, we have found covariations between microbiota composition and immunity traits. These results pave the way for studying the microbiota as a new component of phenotype construction in pigs. Microbiota parameters together with zootechnical and immunity traits will help to better decipher the driving forces that shape animal performances and robustness. Keywords: pig; gut microbiota; immunity, genetic parameters


domain: sdv sde shs sdv.bv

text:
Pierre Chopin
email: pierre.chopin@antilles.inra.fr

Jean-Marc Blazy

Loïc Guindé

Jacques Wery

Thierry Doré

A MODELING FRAMEWORK FOR DESIGNING AND ASSESSING MULTI-FUNCTIONAL AGRICULTURAL LANDSCAPES WITH SCENARIO ANALYSIS

ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

A modeling framework for designing and assessing multi-functional agricultural landscapes with scenario analysis

Pierre Chopin, Jean-Marc Blazy, Loic Guinde, Jacques Wéry, Thierry Doré

To cite this version:

Pierre Chopin, Jean-Marc Blazy, Loic Guinde, Jacques Wéry, Thierry Doré. A modeling framework for designing and assessing multi-functional agricultural landscapes with scenario analysis. 5. International Symposium for Farming Systems Design (AGRO2015), Sep 2015, Montpellier, France. 553 p., 2015, Proceedings of the 5th International Symposium for farming systems design "Multi-functionnal farming systems in a changing world". hal-02740901

Introduction

In order to insure the provision of food and services by agriculture while limiting its negative impacts, innovative agricultural systems have to be designed. The design of such systems has shown some limits in addressing regional and global issues. For instance, at the field scale, some cropping systems may fail to reach the objectives defined at the regional scale due to the low scaling integration and the spatial heterogeneity in the region. Model-based prototyping of agricultural landscapes can allow the impact assessment at regional level of drivers that act at field, farm and regional levels. In order to ascertain whether a combination of levers can drive agriculture towards sustainability, we designed a modeling framework, to exp lore successive steps of scenario development and assessment with indicators . To this end we introduce an approach based on several types of scenarios.

Materials and Methods

The method is built to i) understand the potential levels of sustainability that can be reached by the cropping system mosaics and ii) gain knowledge on the potential levers of change of the cropping system mosaics (Fig. 1). The framework guides the assessment of the consequences of several types of scenario , with a regional bioeconomic model, on the organization of cropping systems . Indicators are used to assess the cropping systems externalities at regional scale. An iterative approach is presented to guide the use of the model with different phases (Fig. 1): s cenarios are built in a pre-modeling phase; they are implemented in a modeling phase for visualizing their consequences on the cropping system mosaics; the post-modeling phase assesses the contribution of the cropping system mosaics to sustainable development.

Fig.1. The modelling framework for buil ding sustainable agricultural l andscapes

We built our framework around the MOSAICA regional bioeconomic model (Chopin et al., submitted). MOSAICA optimizes the overall farmer's utilities by allocating cropping systems to their spatially located plots. The allocation process of cropping systems to plots, recorded in a geographical database, is driven by several types of constraints or objectives imp lemented at different spatial scales among which biophysical, economic, structure constraints at field, farm, sub-regional or regional scales. The optimization of farmer's utilit ies or other variables of the system produce new agricultural landscapes that are assessed with a set of sustainability indicators.

In our framework, the MOSAICA model is used with four different types of scenario for prototyping agricultural landscapes for one specific goal (such as energy self-sufficiency). First, short-term optimized scenario provides a target value by optimizing one given sustainability indicator (e.g. the production of bio mass for electricity). Secondly, an exploratory scenario combines several types of levers (economic, agronomic...) to reach the target value defined before (the overall farmer's revenue is maximized). Third ly, normat ive scenario is introduced to assess whether or not the target can be reached with the levers fro m the explo ratory scenario. Fourthly, a long-term optimized scenario is parameterized to assess the relevance of levers to imp rove the long-term potential of the system (by optimizing the production of biomass with the levers selected). The levers that improve the state of the system for each objective, (increase food production, employ ment...) are selected and combined in a last exploratory scenario called " Go sustainable" scenario to improve the overall response of agricultural landscapes to sustainable development.

3 Results -Discussion We here present some results from the use of the framework in Guadeloupe, a French archipelago in the Caribbean for the energy self-sufficiency objective (Chopin et al., to be submitted). The levers tested are the decrease of subsidies for sugar, the setting up of a biomass industry for electricity production and the addition of a crop energy activity for farmers. The response to the sustainability objective increases with levers (Table 1) that help achieve the objective of producing 56MW.yr -1 and also improve the potential of response of the landscape in long-term scenario to 93MW.yr -1 .

Fig. 2. Evolution of responses to sustainable issues compared to the initial situation

The "Go sustainable scenario" which combines all the relevant levers selected for each of the five objectives improves the system by increasing its contribution to each objective selected (Fig. 2). Fo r instance, the response of the food selfsufficiency objective increased by 150% and the overall agricultural value double d compared to the initial landscape due to the development of crop-gardening, in the south of Guadeloupe, and energy crops within the entire region.

Conclusions

The modeling framework guides the use of the regional model could be used in other regions to help identify the most appropriate levers to increase the response of agriculture to sustainable development. This holistic approach provides analysis of changes that occur at the regional, the farm and the field scale, and can highlight the evolution of externalities of cropping system mosaics in a quantitative and spatially exp licit way.

Chopin, P., Blazy, J;-M., Guindé, Loïc., Doré, T . MOSAICA: a multi-scale bioeconomic model for the design and ex ante assessment of cropping system mosaics. Submitted to Agricultural Systems. Chopin, P., Blazy, J;-M., Guindé, Loïc., Wery, J., Doré, T . Designing multi-functional landscapes in agricultural regions: Application to the Guadeloupe Island. To be submitted to Global Environmental Change.

Table 1 .

 1 Results for the energy self-sufficiency objective with the different type of scenario

	Type of scenarios


Amadou Ndiaye

Franck Taillander

Nadine Leconte

Fabienne Lambrouin

Alicja Sobantka

Christophe Fernandez

Geneviève Gésan-Guiziou

F Garnier-Lambrouin

A Sobańtka

Knowledge book on milk microfiltration : an INRA project to identify key actions in research on proteins fractionation

à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

The expertise of both industry and research institutes has created an important collection of knowledge on food processes, which is the result of scientific and technological research and experimental knowhow. However, despite a great number of results published in the form of "peer" reviewed papers and patents, it has been failed to formalize, organize and complete the acquired knowledge. The need for a sustained capitalization is crucial in view of: i) preventing the loss of knowledge due to the departure of employees over the years; ii) avoiding the dispersal of existing experimental data; iii) and finally, allowing optimal exploitation of data and knowledge. The objective of this work is to address these challenges by developing an electronic knowledge book (kBook) of one specific food process, the microfiltration of skimmed milk. Microfiltration of skimmed milk is widely used in the dairy industry to separate casein micelles from soluble protein aiming at producing a retentate used in cheese making and a permeate containing whey proteins with valuable nutritional and functional properties. Due to the increasingly use of this operation at industrial scale, there is a need to collect and correlate the existing knowledge in a structured way and to gain a better insight of the overall process. The knowledge was first elicited through semi-structured interviews with a group of experts on dairy filtration. Concomitantly, data and knowledge from patents and literature was collated. In a next step, a kBook was established, whose pages were formatted in concept maps (cmap) and technical sheets that are connected by hypertext links. A cmap is a semantic graph where nodes represent concepts that are connected by arcs expressing the relationships between them. A formatted cmap answers a specific question about one central concept. The hyperlinks between cmaps, technical sheets and cmaps and technical sheets form a network of knowledge which can be browsed by the user to find relevant answers to its questions. Several knowledge areas have been identified so far including milk pretreatment, microbiological stabilization, microfiltration and analytical methods for the characterization of fractions. A global representation of the overall process from raw milk to fractions of proteins, based on the individual cmaps has been built. The practical structuration of the knowledge and the original version of the kBook will be disclosed at the congress. The development and use of this new approach for the representation of a food processe will be discussed.

Highlight 1: An electronic knowledge book (kBook) on milk microfiltration has been established Highlight 2: A kBook facilitates the diffusion, re-use, review, reassessment and update of new findings Highlight 3: A kBook minimizes the user disorientation while supporting its acquisition of knowledge


domain: sdv info

text:
est destinée au dépôt

  Effect of cold incubation temperature and cold ambient temperature at start on performances, body temperature and health criteria in fast-growing broiler chickens Dzidzo Nyuiadzi, A. Travel, Bertrand Méda, Cécile Berri, L. Bignon, Christine Leterrier, Laurence L.A. Guilloteau, Vincent Coustham, L. Dusard, Frederic Mercerand, et al. To cite this version: Dzidzo Nyuiadzi, A. Travel, Bertrand Méda, Cécile Berri, L. Bignon, et al.. Effect of cold incubation temperature and cold ambient temperature at start on performances, body temperature and health criteria in fast-growing broiler chickens. Incubation and Fertility Research Group (IFRG) Meeting the 2015 IFRG meeting and 7th combined workshop on fundamental physiology and perinatal development in poultry, Sep 2015, Berlin, Germany. hal-02740929


est destinée au dépôt


Bellocchi Gianni

Ehrhardt Fiona

Conant Rich

Fitton Nuala

Harrison Matthew

Lieffering Mark

Minet Julien

Martin Raphaël

Moore Andrew

Myrgiotis Vasileios

Rolinski Susanne

Ruget Françoise

Wang Hong

Wu Lianhai

Ruane Alex

Soussana Jean-François

Methodology -An exercise adapted from C3MP (Coordinated Climate-Crop

Keywords: Yields, GPP, NPP, net above-ground primary production, net herbage accumulation, SOC stock, SON stock, N2O emissions

Modeling Project), AgMIP

• 16 contrasted grassland sites were used covering a large climate gradient over 3 continents (mean annual temperature T from 7 to 14°C; mean annual precipitation P from 380 to 1380 mm) • Model simulations of grassland systems using 99 combinations of climate drivers {Temperature, Precipitation, CO 2 } to explore yield and GHG responses to climate change. • Calibrated models on specific sites & global models on a set of common sites.

• Grassland management considered for simulation: no N-limitation, no irrigation, cutting events.

Context -A study for temperate grassland systems

The development of climate adaptation services requires an improved accuracy in model projections for climate change impacts on pastures. Moreover, changes in grassland management need to be tested in terms of their adaptation and mitigation potential. Within AgMIP (Agricultural Model Intercomparison and Improvement Project), based on the C3MP protocol for crops, we explore climate change impacts on grassland production, future greenhouse gas emissions and removals in temperate grassland systems. Key words: Climate change, Pasture, Carbon, Greenhouse gas, Soil, Livestock. Site specific emulator calculated with 99 scenarios. Temperature changes from -1°C to +8°C, precipitation changes from -50% to +50%, CO 2 concentration from 380 ppm to 900 ppm.

Each dot represents an individual run. The mesh curve was fitted with the emulator calculated as described (n=99 ; r 2 =0.995, P<0.001).

  Session: L3.1 Climate adaptation and mitigation servicesResults -Site specific sensitivity of grasslands annual production to climatic drivers (Illustrative example for site Ellinbank Dairy research institute, Australia, DairyMod).

  *CO 2 *Yield ; local mean T (°C) Extension to global maps for grassland systems Relative changes in grassland production and N 2 O emissions under future climatic scenarios (2050s RCP 4.5, 2050s RCP 8.5) compared to current climate were projected from the emulator for all sites. Results show that without N limitation, production and N 2 O emissions mostly increases by the 2050's. Elevated CO 2 (ca. 600 ppm in both RCPs) plays a large role in this increase and this questions the extent to which models may overestimate this CO 2 effect (e.g. for P limited grasslands). The use of an emulator provides a fast-track to upscale simulations for global grasslands and test a large range of climate scenarios, as well as adaptation and mitigation options. By extending the methodology to tropical grassland systems and rangelands, global maps for the variation of production, carrying capacity and GHG emissions could be generated for the grassland biome.Sensitivity of temperate grasslands production & N 2 O emissions to climatic drivers from an ensemble of models

  Fig.c


Caroline Teyssier

Alexandre Morel

Jean-François Trontin

Francoise Corbineau

Anne-Marie Lomenech

Martine Beaufour

Isabelle Reymond

Claire Le Mette

Kévin Ader

Luc Harvengt

Are cotyledonary somatic embryos of Pinus pinaster Ait. equivalent to the zygotic counterpart ?

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Magdalena Kristiawan
email: magdalena.kristiawan@nantes.inra.fr

Della Guy

Kamal Valle

Laurent Kansou

Amadou Chaunier

Bruno Ndiaye

Chantal Vergnes

David

G Della Valle

K Kansou

L Chaunier

A Ndiaye

B Vergnes

C David

A phenomenological model of starchy materials expansion by extrusion

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During extrusion of starchy products, the molten material is forced through a die so that the sudden pressure drop causes part of the water to vaporize, giving an expanded cellular structure. The moisture is lost due to evaporation and heat transfer, as the material cools down. Thus, the material crosses glass transition Tg and becomes solid. No simple deterministic model is available to describe satisfactory dynamic, multiphysic and multiphase phenomena during expansion. Current models are too complex to be coupled with simple mechanistic model of corotating twin-screw extrusion process, in order to predict the cellular structure of starchy foams.

Our objective is to elaborate a phenomenological model of expansion, simple enough to be coupled with Ludovic ® , a simulation software of twin screw extrusion process. From experimental results that cover a wide range of thermomechanical conditions, a concept map of influence relationships between input and output variables is built. It takes into account the phenomena of bubbles nucleation, growth, coalescence, shrinkage and setting, in a viscoelastic medium. The input variables are the moisture content MC, melt temperature Tp, specific mechanical energy SME, shear viscosity η at the die exit, computed by Ludovic ® , and the melt storage modulus E'(Tp>Tg). The latter represents the elongational viscosity, and takes into account the influence of starch amylose content. The outputs of the model are the macrostructure (expansion indices and anisotropy factor), and cellular structure (fineness) of solid foams, determined by X-ray tomography. Then a general model is suggested: VEI=α(η/η0) n in which VEI is the volumetric expansion index. The model parameters, α and n depend on Tp, MC, SME and E'. The link between macroscopic anisotropy and fineness is also established, allowing the prediction of cellular structure. Finally, the model is validated using experimental data of wheat flour extrusion from literature.


text:
Carole R Moreno

Romieux Moreno

Philippe P Jacquiet

Frédéric F Bouvier

Jacques J Cortet

Alexandra Blanchard-Letort

Fabrice Guégnard

Dominique Francois

Yves Bourdillon

Christelle C Grisez

Françoise Prevot Prévot

Frederic Bouvier

Françoise Prevot

Audrey Averadère

Julie Demars

Julien Sarry

Alessandra Stella

Florent Woloszyn

Kamila Canale-Tabet

Jacques Cabaret

Gwenola Tosser-Klopp

Guillaume Salle

Validation of QTL affecting resistance to nematodes in Sheep identified in a Back-Cross design in a pure breed population

Keywords: Nematode, Resistance, Sheep, SNP

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Introduction

Gastrointestinal nematodes constitute a major cause of production losses and mortality in grazing ruminants (Mandonnet et al. (2005); Davies et al. (2006)). Anthelminthic drenching has been the main control strategy for the last 50 years. However, the ecotoxicology of some drugs has been clearly demonstrated and several parasite populations throughout the world have developed resistance to one or several classes of anthelmintic. Thus, selection of animals naturally resistant to intestinal nematodes appears as a complementary control strategy for nematode fight.

Resistance is classically measured by faecal egg count (FEC), an indirect measure of worm population and in relation to the ability of the host to regulate establishment, development, fecundity and survival of worms. However, FEC-based genetic selection requires selection candidates to be challenged. Moreover, FEC is time consuming and expensive because of the large number of coprological examinations required. Classical or genomic selection based on FEC is therefore difficult to implement on a large scale. Selecting for resistance would be substantially simplified if genes determining resistance and susceptibility were known, making it possible to select animals on their genotype.

QTL having an effect on resistance to internal parasites in sheep have been accumulated since 10 years. In the 3SR EU project, the main QTL regions were detected on chromosomes 4, 5, 7, 12, 13, 14 and 21 (Sallé et al. (2012); Riggio et al. (2013)). These regions were used to design a dedicated 1000-SNP assay.

Since 4 of these 8 QTL were detected by Sallé et al. (2012) in a back-cross Black Belly*Romane protocol, the idea of the present paper is to check the existence of these QTL in the commercial French Romane breed.

Materials and Methods

Population. The Romane (ex-INRA 401 line, cross Romanov x Berrichon) lambs were produced at the INRA experimental farm "La Sapinière" (Osmoy, Cher, France). 26 males and 179 females were used to procreate 148 male and 129 female Romane lambs. Lambs were kept inside to overcome possible nematode infections.

Genotyping. A 1000-SNP assay was designed to validate the QTL detected on chromosomes 3, 4, 5, 7, 12, 13, 14 and 21 in previous studies performed in frame of the 3SR EU project. Approximately 110 SNP within 5 centimorgans (cM) were chosen by QTL region, using SNP existing in 50K and 800 K SNP chips by mapping them to Oar-v3.1 by BLAST using flanking sequences provided by Illumina and ISGC. Two exceptions were made: on chromosome 12, 262 markers were chosen on 10 cM because the confidential interval was large and on chromosome 21 where 10 SNP were chosen in a region of an obvious candidate gene: pepsinogen. Genotyping was performed using the KASP™ (Kompetitive Alelle Specific PCR) technology ((LGC, Teddington, UK).

Data. The six-month-old sheep were orally infected twice with 10,000 H. contortus infective larvae, the two experimental challenges lasting four weeks and being terminated by an oral drench of ivermectin (Oramec ® , Merial, 0.2 mg/kg BW). The second infection took place after a two-month washout period. Faecal samples were taken directly from the rectum on day 24 and day 35 post each infection (FEC1, FEC2, FEC3 and FEC4). FEC were determined using the modified MacMaster technique (Raynaud (1970)) in saturated salt solution with a lower limit of detection of about 30 eggs per gram of faeces. The mean of day 24 and day 35 FEC in first or second challenge were also considered (denoted FEC12 and FEC34 respectively) for further analyses.

Statistical analyses. Individual FECs were fourthroot transformed and averaged within each challenge to create variables FEC1t, FEC2t, FEC3t, FEC4t, FEC12t and FEC34t. A GLM analysis was performed to identify significant environmental effects: sex, litter size, artificial versus natural suckling, management group and all interactions between these effects. Then, SNP effect was tested following the EMMAX association analysis method (Kang et al. ( 2010)). This model simultaneously estimates the SNP effect while correcting for the fixed environmental effects and fitting a genomic relationship matrix to account for existing kinship. The SNP-based relationship matrix was estimated following the method of VanRaden et al. ( 2008) using every other SNP not located on the chromosome of interest. Because of the close location of SNP in each tested QTL regions, we considered a complete LD between SNP within the tested QTL regions. Consequently, the genomewide thresholds were obtained by applying the Bonferroni correction P genome-wide =1-(1-P SNP ) n , where n is the number of chromosomes.

Results and Discussion

Phenotype analysis. Means of FEC measured in the second infection were significantly reduced compared to the first infection. It is classically observed in this type of experimental infection (Sallé et al. (2012)). The dynamics and the intensity of FEC were different between the two infections. The main significant fixed effect was the sex: males were more infected than females which is classical [START_REF] Zuk | [END_REF]).

QTL validation. 6 out of the 8 tested QTL regions in the present study showed significant effect in the considered Romane population. Among the four main QTL detected by Sallé et al (2012), the QTL located on chromosomes 5, 12 and 13 were confirmed as affecting the first infection FEC (Table 1). However, the effects of the QTL located on OAR12 and 13 on FEC at second infection were not confirmed. The significant markers positions were located at 1 or 2 cM from the maximum likelihood signal found by Sallé et al. (2012). The other tested QTL regions on chromosomes 3, 4 and 7 were chosen because they were identified in other naturally infected populations of the 3SR project (a back cross between Lacaune and Sarda Breeds and a Scottish Blackface population) (Riggio et al. (2014)). Interestingly, significant markers of chromosomes 3, 4 and 7 affect mainly resistance during the second infection which mimics naturally repeated infections (Table 1). None of SNP closed to pepsinogen affects significantly FEC traits, but blood concentration of pepsinogen will be soon available.

Table 1. Genome-wide P-values of significant markers for the first and/or the second experimental infection by H. contortus.

Conclusion

The effects of three out of the four main QTL detected in a previous back cross between Black Belly and Romane breeds (Sallé et al. (2012)) were confirmed in a pure Romane breed population. Some other regions detected previously in two additional naturally infected populations also seem to exert significant effect on H. contortus infection. Haplotype-based analyses will be performed to confirm the similarity with the regions previously identified in the BC population.

Literature Cited

Davies, G., Stear, M.J., Benothman, M., et al., (2006)

Acknowledgments

The authors are greatly indebted to the INRA Experimental farm "La Sapinière" for the production of the resource population, the management of the flock, the sampling of lambs and for their participation to egg counts. We also would like to thank the Toulouse Midi-Pyrénées bioinformatics platform that partly supported computations and the ISGC consortium for providing SNP informations for this study. This study was funded by the French Region Centre "BIOVIPAR" project and the "3SR" project, www.3srbreeding.eu).