Loup Rimbaud
email: loup.rimbaud@csiro.au

Julien Papaix

Luke Barrett

Jeremy Burdon

Pete Thrall

Assessing the durability and efficiency of landscape-based strategies to deploy

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.

Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens

Loup Rimbaud, Julien Papaix, Luke G. Barrett, J.J. Burdon, Peter H. Thrall

To cite this version:

Loup Rimbaud, Julien Papaix, Luke G. Barrett, J.J. Genetically-controlled plant resistance can reduce the damage caused by pathogens. However, pathogens have the ability to evolve and overcome such resistance. This often occurs very quickly after resistance is deployed, resulting in significant crop losses and a continuing need to breed new resistant cultivars. To tackle this issue, several strategies have been proposed to constrain the evolutionary potential of pathogen populations and thus increase the durability of resistance deployment. These strategies mainly rely on using different combinations of resistance sources in time, space, or both. In time, such combination consists of crop rotations. In space, resistance sources can be deployed in the same cultivar (pyramiding), in different cultivars within the same field (cultivar mixtures) or in different fields (mosaics). However, experimental assessment of the efficiency (i.e. ability to reduce disease impact) and the durability (i.e. ability to limit pathogen evolution and delay resistance breakdown) of different deployment strategies presents a major challenge.

Therefore, we developed a spatially-explicit stochastic model to assess the epidemiological and evolutionary outcomes of the major deployment options described above, for both qualitative (major resistance genes) and quantitative resistance. In addition, we analysed the impact of landscape organisation (as defined by the proportion of fields cultivated with a resistant cultivar, and their spatial aggregation) and epidemiological or evolutionary parameters (e.g. dispersal abilities, mutation probability, cost of infectivity) through sensitivity analyses and polynomial regression.

The model has been parameterised for wheat resistance to rusts, caused by fungi of the genus Puccinia, but can be applied to many other pathosystems. Our results show that evolutionary and epidemiological control are not necessarily correlated, and that no deployment strategies is universally optimal.

Key words: deployment strategy, durable resistance, gene-for-gene resistance, plant disease, rust of wheat, spatially-explicit modelling


M Wilson

A J A Stewart

Jean-Claude Streito

S Seabra

Taxonomic difficulties among

  L'archive ouverte pluridisciplinaire

Seabra, Sofia G. 1 ; Neto, Ana Carina 2 ; Rodrigues, Ana Sofia B. 1 ; Streito, Jean-Claude 3 ; Genson, Guénaëlle 3 ; Pierre, Éric 3 ; Silva, Sara E. 1 ; Popova, Ganna 2 ; Marabuto, Eduardo 1 ; Figueiredo, Elisabete 4 ; Mateus, Célia 5 ; Wilson, Michael 6 ; Rei, Fernando T. 7 ; Quartau, José A. 1 ; Paulo, Octávio S. 1 ; Rebelo, Maria Teresa 2 1 cE3c -FCUL -Portugal; 2 CESAM -FCUL -Portugal; 3 CBGP -INRA -France; 4 LEAF -ISA -Portugal; 5 INIAV -Portugal; 6 National Museum Wales -UK; 7 ICAAM -UÉvora -Portugal.

Contact: sgseabra@fc.ul.pt; acneto@fc.ul.pt Morphological and genomic assessment of divergence between closely related species of the genus Philaenus (Hemiptera, Aphrophoridae) Philaenus spumarius is a widespread and polyphagous xylem-feeding insect. It is also the main vector of Xylella fastidiosa in Europe [1]. Philaenus. spumarius has a sister species, P. tesselatus, and they are differentiated on the male genitalia but not at karyological, mitochondrial DNA and some nuclear genes' levels [2,3,4]. Genome-wide markers revealed previously unreported genetic differentiation.

Here we aim at characterising morphological variation in the male genitalia in both species.

Integrating genomic data and more traditional approaches will allow to better define species and distribution boundaries, action-plans for the control of X. fastidiosa and conservation of natural ecosystems.

Both species occur in Iberian Peninsula

where P. spumarius is widespread but P. tesselatus seems to be restricted to the south where it is the dominant species.

-No differentiation between P. spumarius and P. tesselatus at mtDNA (same haplotypes in both).

-Clear differentiation between P. spumarius and P. tesselatus at genome-wide markers.

Results

Figure 1 -Sampling locations of P. spumarius and P. tesselatus for morphological analyses (N = 79). Four sampling points from Morocco not shown.

Philaenus tesselatus Philaenus spumarius

Introduction-

  No differentiation between P. spumarius and P. tesselatus in geometric morphometric analyses of habitus (data not shown). -Clear differentiation between species in aedeagus morphology in PC1. -Total length of aedeagus, mean lengths of lower and upper appendages are the best characters to discriminate species. Philaenus tesselatus tends to have larger values for these measurements. -Intra-specific morphological variation detected in PC2 and PC3 associated with mean curvature of upper appendages and mean length of middle appendages. -Philaenus tesselatus was only found in Portugal, Spain and Morocco in this study.

Figure 3 -

 3 Figure 3 -Principal component analysis (PCA) of morphometric measurements of aedeagus from P. spumarius and P. tesselatus.

Figure 4 -

 4 Figure 4 -Median-joining haplotype network based on mitochondrial gene cytochrome oxidase I sequences for P. spumarius. P. tesselatus haplotypes from Morocco are shown in red. Adapted from Rodrigues et al. [4].

Figure 5 -

 5 Figure 5 -Principal component analysis (PCA) of 2796 Single Nucleotide Polymorphisms for 133 individuals of P. spumarius (from several parts of Europe) and P. tesselatus (from Morocco, in red). Adapted from Seabra et al. (in prep).

Figure 2 -

 2 Figure 2 -Measurements on Philaenus aedeagus: TotLentotal length of aedeagus; LowLen -length of lower appendages; MidLen -length of middle appendages; UpLenlength of upper appendages; UpCur -curvature of upper appendages. Curvature determination based on Feduccia [5].

  The ability to correctly identify P. spumarius and P. tesselatus will allow a more comprehensive knowledge on their distribution, population dynamics and ecological requirements. These are known important drivers of X. fastidiosa spread by other vector species and are relevant for disease management.

  SNP markers will provide more accessible genotyping of specimens to discriminate these two closely related species (not distinguished by mtDNA).Total length of aedeagus and lower appendages provide the best morphological characters to distinguish P. spumarius from P. tesselatus.

Acknowledgements 1. Saponari et al. 2014. Infectivity and transmission of Xylella fastidiosa by Philaneus spumarius (Hemiptera: Aphrophoridae) in Apulia, Italy. Journal of Economic Entomology, 107, 1316-1319. 2. Drosopoulos & Quartau 2002. The spittle bug Philaenus tesselatus Melichar, 1899 (Hemiptera, Auchenorrhyncha, Cercopidae) is a distinct species. Zootaxa, 68, 1-8. 3. Maryańska-Nadachowska et al. 2012. Genetic diversity of Philaenus spumarius and P. tesselatus (Hemiptera, Aphrophoridae): implications for evolution and taxonomy. Systematic Entomology, 37, 55-64. 4. Rodrigues et al. 2014. New mitochondrial and nuclear evidences support recent demographic expansion and an atypical phylogeographic pattern in the spittlebug Philaenus spumarius (Hemiptera, Aphrophoridae). PLoS ONE, 9: e98375. 5. Feduccia 1993. Evidence from claw geometry indicating arboreal habits of Archaeopteryx. Science, 259: 790-793.

References


Cathleen Petit-Cailleux

Hendrik Davi

Sylvie Muratorio

Francois Lefèvre

Pieter Johannes Verkerk

Combined effects of climate and management on beech tree vulnerability and net ecosystem exchange across Europe

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


Keywords: Lolium perenne, Holcus Festuca rubra, Agrotis capillaris Dactylis glomerata, Arrhenaterum elatius Briza media, Brachypodium pinnatum Low SLA Low digestibility Manure, mineral fertiliser

How implementing a model with VenSim PLE ? example of the ModVege model .

The modelling approach : 4 steps

•••

  Scales & level of detail of the model • Modelling method Adapted from Coquillard & Hill, 1997and Hirooka, 2010 Conception • Formalisation (equations) • Implementation (code) • Verification • Parameterisation/Calibration • Robustness and software reliability • Comparison of observed vs simulated values • Use of criteria of evaluation Evaluation Exploitation Responses to the questions adressed • Understanding of the simulated processes to simulate the dynamics of the biomass production, structure and forage quality in response to management and climate, in case of permanent pastures and temperate regions  Operational objective • to use this model in a whole farm simulator to represent each grassland field  has to be simple ! (not to model each species separately …)  outputs = inputs for an intake and production model composition = association (in constant %) of functional groups of species with similar functional traits (Cruz et al., 2002) : functional approach ! 2. Sward heterogeneity = the relative abundance of 4 structural plant components 3. Growth, senescence & abscission = continuous flows 4. Seasonal pattern of shoot growth = functional trait 5. Quality (digestibility) of green compartments, senescence and abscission are affected by compartment ageing 6. During harvest, 10% of the harvestable biomass is lost effects of variables on flows During the reproductive growth, growth is distributed between GV & GR = Reproductive function (REP) OMD of dead compartments is constant  OMD of green compartments •  linearly with AGE from a maximum (at AGE=0) to a minimum (at maximum AGE) • The maximum AGE corresponds to: • leaf life span (LLS) for GV • duration of the reproductive period (ST2-ST1) for GR OMD DV Seasonal pattern of storage/mobilisation of reserves • Empirical function (SEA)  ST < 200°C d (winter) = minimum (minSEA)  ST1-200 < ST < ST1-100 (growth) :  to a maximum (maxSEA)  ST1-100 < ST < ST2 (summer) :   ST > ST2 (after the end of reproductive growth) = minSEA Residual biomass after cutting The pasture is considered to be cut 5 cm above ground level  Harvested biomass in each structural component hBM GV = BM GV -resBM GV and similarly for compartments GR, DV, DR  Total harvested biomass hBM = hBM GV + hBM GR + hBM DV + hBM DR

Growth (GRO) Senescence (SEN)

Calculation of the age

Coupling with a ruminant livestock model (Jouven et al., 2007)


domain: sdv shs

text:
Mathilde Belluz
email: belluz.mathilde@wanadoo.fr

Florence Hellec
email: florence.hellec@inra.fr

Rearing calves with nurse cows: experiences of French organic dairy farmers

Wri en by Mathilde Belluz and Florence Hellec, october 2018

Improving animal welfare on farms is currently a major issue, in response to expecta ons of ci zens and consumers. In organic farming, reflec ons are con nuing on how to change livestock produc on prac ces to allow animals to express their natural behaviour most fully. Calf rearing in dairy systems is a focus of a en on. At the moment, separa ng calves from their mothers remains the most common prac ce, but new techniques that favour the maternal bond are appearing. Understanding these prac ces be er to iden fy condi ons under which they can be adopted by more farmers was the goal of a survey conducted in spring 2018 of organic dairy farmers who rear calves with adult cows. This work has been made under the GrazyDaiSy project, funded by the European Union program Core organic.

A socio-technical survey

The first step consisted of iden fying farmers following this prac ce, using informa on from advisors and technicians of organic agriculture organisa ons, as well as veterinarians. The surveys were socio-technical, that is, focused on the farmers' calf-rearing prac ces, their view of this form of livestock produc on, and its advantages and disadvantages.

Ul mately, 20 dairy farmers were surveyed: 5 in the Lorraine region and 15 in western France. Farmers were younger and more highly educated than the average French organic farmer and most of them par cipated in exchange networks with other colleagues. In their regional contexts, their farms are representa ve of organic dairy farms. Fine-scale analysis dis nguished three types of dairy farmers: organic pioneers (converted long ago, with low-yielding herds: 4500 L/cow), those with small extensive farms (small, low-yielding herds: 44 cows at 5400 L/cow), and those with new intensive organic farms (recently converted, with large, highyielding herds: 75 cows at 6000 L/cow).

Calves nursed by nurse cows

Sixteen dairy farmers used "nurse cows" to feed their calves. The prac ce consists of leaving 2-3 calves with a cow, separated from the dairy herd, un l weaning (an average of 6 months). Usually female calves iden fied as future replacement heifers are reared in this way, but some mes male calves are, too. The early life of calves can be managed in three ways, as illustrated below.

Which cows are selected as nurse cows?

Each farmer carefully decides which cows will become nurse cows, a choice that provides flexibility in management of the dairy herd. Farmers tend to choose "problem" cows: older cows with lowerquality milk (high soma c cell counts) or those difficult to milk. A er the nursing period, nurse cows can return to the dairy herd, be culled (for incurable problems), or con nue serving as nurse cows.

How is the group of nurse cows managed?

Of the 16 farmers surveyed, 14 put the group of nurse cows and their calves to pasture a er 15 days. There is no need for a specific type of fence, but one needs to accept that the calves will walk under the wires at first. Since their "milk pail" is inside the field, though, they will return as soon as they are hungry. The "organic pioneers", who have more experience with the prac ce, indicate that the calves are wilder at first; they must be visited regularly to keep them from becoming "wild deer". A er weaning, they become used to humans and more docile. The farmers did not no ce any problems with these animals once they became dairy cows in the milking parlour.

What are the adop on techniques?

This key period determines the success or failure of this type of nursing. Adop on requires surveillance and par cular a en on for 1-2 weeks, when the calves and nurse cow are placed in a stall away from the dairy herd. If the cow resists, certain farmers use restraining techniques. Only farmers who perform "group adop ons", in which a calf has access to several nurse cows, men on failure. Adop on thus seems easier when a nurse cow/calf pair is created.

When and how to separate the calf?

All of the farmers surveyed perform late weaning at 4 -9 months of age. They have different reasons for doing so, such as calf health, acquisi on of a stronger immune system, and learning of social rules, but also for prac cal reasons, usually separa ng calves and nurse cows when they go to the rearing house for wintering. Only one farmer performs progressive separa on, gradually decreasing the contact me between calves and nurse cows. Two farmers use homeopathy to calm both calves and nurse cows. Weaning causes animals to moo for several days, but otherwise it is not generally considered a difficult phase.

How do farmers feel about the experience? Increased growth allows for earlier calving

All of the farmers highlight increased growth, and 11 of them want to increase produc vity by decreasing the age at first calving from 36 to 24 months. They thus decrease the number of non-produc ve animals on the farm and consequently forage requirements, while producing more milk during a cow's produc ve life with the same replacement rate.

Healthier herds

External factors that favour infec ous diseases and diges ve problems (nipple, milk temperature and milk amount) are be er controlled. Early grazing of calves with the cows increases calf immunity, which is why the farmers state that their calves are generally in good health. No treatment is given to prevent cases of diarrhoea or the development of parasites. There are thus fewer sick calves and thus lower veterinary bills.

Work that restores meaning to the profession of a dairy farmer

The search for economic performance

Feeding milk to calves (in pails, feeders, etc.) is considered difficult, demanding, and o en called a "chore". The group of calves and nurse cows needs only daily surveillance. Farmers consider it more pleasant and interes ng. Some decided to place (or place once again) observa on at the heart of their profession. In this way, they detect the signs that indicate the health and welfare of their animals more rapidly.

Descrip ons of the prac ce's advantages for economic performance vary among the types of farmer. Whether to decrease produc on costs of the milk-feeding phase, maximise produc on capacity, decrease demanding work, or maximise the use of herbage, rearing calves with nurse cows provides answers for improving each of these aspects.

Group of nurse cows and their calves grazing in the experimental farm of INRA-Mirecourt, eastern France source: Mathilde Belluz)

Among interviewed farmers, 4 leave calves with their biological mother for a short period (15-45 days) before switching them to ar ficial feeding (no nurse cows). They follow this prac ce to ensure the health and welfare of the animals or decrease work demands. To avoid decreasing milk produc on, the calf is separated from its mother before weaning. It may then refuse to feed for at most one day before accep ng another feeding system.

These farmers consider the use of nurse cows too constraining and think that they do not have the area, buildings, or animals necessary to set up this prac ce.

Combine several innova ve prac ces

Alterna ve feeding prac ces are only one ac on among others that dairy farmers use to increase the autonomy of their livestock systems. Consequently, these prac ces are o en combined with other innova ons such as crossbreeding, once-a-day milking, reflec on about calving periods, dynamic rota onal grazing, etc. Farmers can combine these structural components of farms to create consistent and logical configura ons that to help them a ain their objec ves.

Word cloud: wild, reproduc on, economic, observa on, network, health, growth, farmer, docility, easy, exchange, herbage, animal welfare, system, autonomy, calf, produc on, work, grazing, nurse cow, once-a-day milking, cross-breeding

Toward wider diffusion of the prac ce

The accounts of the dairy farmers are in line with results obtained by the organic experimental sta on of INRA at Mirecourt, France. A group of 9 calves fed by 3 nurse cows gained 238 g more per day per calf than a group fed by ar ficial feeding. This encouraging growth rate allowed the calves, once they became heifers, to be inseminated at 15 months rather than 27 months, thus gaining one year of produc on. In GrazyDaiSy project, subsequent to this first field-study, parasite monitoring (blood sampling, scatology, weighing) will be performed on about 15 farms that combine feeding of dairy calves with nurse cows and grazing.

Other studies will begin soon in France, especially at the INRA site at Marcenat, which works to produce technical and economic reference data for cow-calf rearing. Given the posi ve effects on calf rearing and the general sa sfac on of dairy farmers in following this prac ce, nurse cows surely have more to reveal…

For more informa on: Belluz M., 2018, L'élevage des veaux lai ers par des vaches adultes, une technique innovante en élevage biologique, 40 pp., Master's thesis, VetAgro-Sup, Campus Agronomique de Clermont-Ferrand.

   No. of dairy cows = 70  Milk prod./cow/yr = 5873 L  % grassland = 84%  MWU = 2.5 15 farmers in western France:  UAA = 119 ha  No. of dairy cows = 62  Milk prod./cow/yr = 5463 L  % grassland = 88%  MWU = 2.7 Calf and their mother grazing in eastern France (source: Mathilde Belluz)Archived at http://orgprints.org/34000

Acknowledgements: Thanks go to the dairy farmers, veterinarians, and agricultural professionals who contributed to the steady progress of this study.


domain: sdv sde sdv.bv shs

text:
Jean-Marc Blazy

Solene Guillot

Loic Guinde

Régis Tournebize

Matthieu Duval

Jorge Sierra

François Causeret

Gaël Nicolas

Justin Claude-Maurice

Stan Shimrith

Selbonne

Integrated modeling of transition scenarios towards climate-smart agriculture based on agro-ecology and territorial bio-economy

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

The emerging concept of climate-smart agriculture aims to provide an integrated approach of agriculture to address the triple challenge of food security, adaptation of agricultural systems and climate change mitigation [START_REF] Lipper | Climate-smart agriculture for food security[END_REF]. If agro-ecology and territorial bioeconomy are levers advocated to achieve these objectives, the transition to such systems is hampered by socio-economic barriers to their adoption, which express at the farm and territory levels. Most of the research on climate change mitigation via soils has often focused on field-scale actions, without considering possible synergies and antagonisms with other farm and regional-scale issues. Few agricultural systems design methods are available to develop transition scenarios that explicitly consider interactions between spatial scales. To develop scenarios combining agronomic innovations at the field scale and economic levers at the regional scale, we propose an approach combining prototyping and regional bioeconomic modeling. In this paper, we present this approach and its application to the design of climate-smart market gardening in Guadeloupe.

-Materials and methods

The methodological framework follows the one proposed by [START_REF] Blazy | Integrating field, farm and territory scales in the design of agricultural systems[END_REF] and is made of three steps (Fig. 1). First the territorial diagnosis consists in a farm survey and a census of residual biomasses available within the territory. The farmers were interviewed to characterize their current crop management systems and technical and economic performance (step 1). The analysis of the residual biomasses available serves to define several agro-ecological prototypes of innovative crop management systems based on organic inputs obtained from biomasses recycling. In the second step, we experimented prototypes mixing tomatoes and lettuce based on agro-ecological principles: use of local species, minimum tillage, biocontrol, use of organic inputs like mulch, composts and biopesticides. Their experimentation in station made it possible to identify the best combinations of practices and to evaluate their technico-economic performances (step 2). To evaluate the adoption potential of the best prototypes and transition scenarios at regional scale, we used the MOSAICA bioeconomic model [START_REF] Chopin | MOSAICA: A multi-scale bioeconomic model for the design and ex ante assessment of cropping system mosaics[END_REF] and the results of steps 1 and 2 to calculate technico-economic coefficients to parameterize the model. Then we simulated transition scenarios including socio-economic levers such as the technical improvement of cropping systems, the training of farmers, the creation of eco-markets, and the redesign of public policies (step 3).

-Results -Discussion

The experiment evaluated the agronomic and economic performance of 24 prototypes and statistical analysis identified the factors with most significant effects (Table 1). For both crops, mulching with bagasse allows for better yields. For tomatoes, all composts can improve yield. However, yields and economic results obtained for best performing prototypes remain lower than those of conventional systems do. This can be explained by low availability of nutriments and motivate the need for transition levers. 1. Summary of significant results (P<5%) on yield of tomato and lettuce compared to the reference (no mulching, no compost, no irrigation). NS: not significant; WPC: wood paletts chips; Biogwa, FertigwaF and Vegegwa are three industrial composts of Guadeloupe.

Creating organic inputs rich in bioavailable nutrients from the residual biomass of the territory should be a priority area of research. The most promising results are obtained by combining the use of mulches and composts with an advantage for bagasse mulching and Biogwa and FertigwaB composts. We have not demonstrated a significant effect of irrigation, which can be explained by the beneficial effect of mulching, and confirms the interest of this practice in terms of adaptation to climate change in dry areas. The configuration of the plot in permanent cropping planks makes the work and the circulation easy and practical, however the time of work for the spreading of the biomasses, which has been realized manually, is high. Mechanizing these operations could significantly increase the profitability of the innovative systems. The association with lettuce is

Territorial diagnosis:

-Farm survey -Identification of residual biomass

Prototyping:

-Redesign of crop management systems -Field assessment 3. Regional modelling:

-test of economic levers -scenarios of transition promising to compensate for the inferiority of the yields obtained on tomato. The experimental results were used as the basis for the construction of territory-wide transition scenarios that were evaluated with the MOSAICA model. The best scenario combines 5 levers: 1) the best prototype of cropping system, 2) a mechanization of the spreading operations that allows to reduce by 10% the time of work, 3) an ecolabel that allows an increase in the price of sale of 50% in the market, 4) an agro-environmental and climate subsidy of 2600 €/ha/year, 5) a technical training of farmers which reduces by 20% their risk aversion. This scenario lead to substantial modifications in the agricultural landscape, with a doubling of market gardening areas, which would be fully converted into climatesmart systems. In terms of contribution of this scenario to the sustainable development of the territory, this scenario contributes to reducing the average GHG emissions of the agricultural sector by 26%, increasing farmers' incomes by 19% and decreasing by 10% the uses of pesticides and 9% the amount of mineral nitrogen used. These results make it possible to argue the positive impacts of such systems at the scale of the territory and thus justify a remuneration for the ecosystem services they provide.

-Conclusions

Through an integrated approach of farming system design, we developed prototypes of market gardening systems and identified scenarios to promote their adoption across the territory. The coherent arrangement of levers that relate to the technical improvement of cropping systems, the training of farmers, the creation of eco-markets, and the redesign of public policies, may be relevant for the transition to climate-smart systems based on agro-ecology and bioeconomy. To go further, we will continue to improve the prototypes and experiment on more sites and seasons, as well as co-build transition scenarios with stakeholders. The research priorities in this science front are scaling up agronomic innovations, taking into account spatial heterogeneity, systemic experimentation and the coupling of biotechnical and economic models operating at different spatial scales.

Figure 1 .

 1 Figure 1. The three steps of the method for integrated design of agricultural systems.