Behavioural epidemiology studies the interaction between human behaviour and the spread of infectious diseases. Plant pathogens and their insect vectors are among the main threats to global food security. The methods used to control plant pathogens and their vectors must be ecologically-friendly and sustainable. To date, the few models that couple grower behaviour with plant disease epidemics do not address pathogen evolution. However, grower decisions impose new selection pressures on pathogens, which evolve and adapt to control methods. Grower decisions may concern several control methods including the use of disease-resistant varieties, roguing (i.e., removing) infected hosts, and the use of biocontrol agents against pathogens or their insect vectors. Our biological models include the Citrus greening disease (caused by vector-borne bacteria), and nematodes of potato and tomato. The objective of this project is to develop a theory of behavioural epidemiology specific to plant health, with an evolutionary perspective. More specifically, we will explore the key mechanisms allowing the adoption (or not) of control methods in sufficient proportion to maintain disease incidence under an acceptable level, taking pathogen evolution into account. Such control methods are often expensive, and we aim at assessing to what extent subsidising them would stabilise their use in order to maximise plant health in the long-run. The consortium gathered around this project brings together expertise in plant disease epidemiology, mathematics, computer sciences, and economics. The interdisciplinary nature of the project will lead to original research in the field of plant disease epidemiology and evolution. From an applied perspective, this project will help design policies to control plant diseases that consider the dynamic behaviour of growers as well as pathogen evolution. This research aims to develop plant protection methods respectful of people and their environment.

With the shift towards a reduced reliance on external inputs in agriculture, identifying management options that enhance the provision of ecosystem services has become a critical issue. Pest control resulting from the activity of naturally present predators and parasitoids is frequently cited as an important service that could reduce pesticide use as targeted by the French 2018 Ecophyto governmental action. However, the link between management options, pest control level and ultimately crop yield is poorly understood. The PEERLESS project aims to identify alternative management strategies that enhance the crop protection service provided by functional biodiversity and ultimately to optimize agricultural systems, at local and landscape scales, for economic viability and sustainability. PEERLESS brings together six partners organisations with extensive expertise in agronomy, spatial ecology, ecology of interactions and public economy. The project combines: (i) an empirical assessment of naturally occurring crop protection from weed and insects pests in annual (wheat-oilseed rape rotations) and perennial (apple orchards) systems across a broad range of landscape and agronomic situations; (ii) ecological engineering with an assessment of alternative plant protection system to improve crop protection at the local scale; (iii) an in-depth study of the structure of trophic networks; and, (iv) population dynamics of key pests and their regulators in case study areas. These components will support the parametrisation of spatially-explicit, predictive models to (v) test the effect of landscape patterns of alternative local and landscape management strategies on pesticide use, pest control, crop yield and farmer income and (vi) identify landscape scale viable management strategies to control insect and weed pests.

The BRING IT ON project aims at bringing a new solution to breed oilseed rape (Brassica napus) for resistance to one of its major insect pests, the pollen beetle (Brassicogethes aeneus). Thus, it is targeted to the “Conception of more resilient systems to bio-aggressors” principal theme, with a varietal resistance to the pest that could be used in different crop management approaches. Our results show that such resistance exists in the close relative Sinapis alba and we have identified and confirmed contrasted accessions in both field and controlled conditions. With no other option for resistance breeding in oilseed rape, our solution is currently at TRL4. However, to reach TRL5, we need to ensure the ability to transfer efficiently the resistance to oilseed rape. Understanding the genetic and chemical determinants will give tools to achieve this transfer and accelerate resistant oilseed rape breeding by many years. Indeed, oilseed rape is heading for a dead end as a crop if solutions to escape the dependency to insecticides are not found. Finally, although specific to the resistance to pollen beetle, our project will generate resources that could be used for other oilseed rape insect pests and methods for other crop/insect interactions. BRING IT ON aims at making use of the diversity of resistance present in S. alba to identify the genetic determinants of this resistance and identify the chemicals compounds produced by S. alba resistant accessions to provide a solution for oilseed rape resistance breeding. Genetic and genomic resources in S. alba will be constructed from three different sources of resistance and QTL analyses will be performed to identify genomic regions involved in resistance. In parallel, previous results have shown that the resistance is expressed after contacts between the pests and the plant, thus, identifying chemical compounds produced by the plant that deter the pollen beetle will point towards biosynthetic pathways to improve by breeding. The combination of the two approaches will help prioritizing regions to target for validation and then use in breeding. Thus, the main user for this solution will be breeding companies that will be able to take up the solution quickly to generate resistant varieties. From the expected outcomes of BRING IT ON, marker assisted selection from the QTL regions or candidate genes will be used to generate new varieties in less than 10 years. In line with the Ecophyto plan, our solution will help decrease insecticide treatments. Thus, it will be beneficial to growers from both an economic and health perspectives. Reducing pesticide treatments in the spring at flowering time, a crucial period for pollinators, will also impact populations of beneficials insects, whether bees or biocontrol agents for other insect pests. According to a survey conducted in 2020 by Terres Inovia, resistant varieties, coupled with crop management strategies could help avoiding an average of 1.2 insecticide application per year. BRING IT ON has built a complementary consortium from 1) a private company (INNOLEA, Partner1) dedicated to the identification and understanding of beneficial alleles for oilseed crop breeding, in line with 3 major plant breeding companies in France (Lidea, Limagrain and RAGT) and bringing a strong genetic expertise, 2) a public institute (IGEPP, Partner2) specialized in developing innovative and sustainable solutions for plant production and protection and bringing a strong chemical ecology expertise and 3) an applied research institute (Terres Inovia, Partner3) for oil and protein crops and hemp with an objective to help growers in the diversification and sustainability of their production, with a strong expertise in field evaluation.

The ECLODERA project is an answer to the theme “Development of alternatives for managing bio-aggressors” for a situation that has become orphaned since the withdrawal of the 1,3-dichloropropene (in 2018). It will allow the maturation (TRL 4 to TRL 6-7) of two complementary solutions to control the carrot cyst nematode Heterodera carotae: the use of molecules from root exudates to induce the hatching of larvae in the absence of the plant (suicide hatching) and the use of a resistant variety as a service plant. The locks that will be addressed relate to i) the identification of the molecules responsible for the hatching, ii) the durability of the solutions, alone and combined, and (iii) their positioning in the farming system, considering potential variations in efficiency due to the composition of the soil microbiota selected by the crop succession. A non-target metabolomic approach (GC-MS and LC-MS) will first identify the active molecule(s) and then formulate them as a biocontrol product causing the hatching of H. carotae. An experimental evolution approach will evaluate the durability of the two solutions (biocontrol and resistant variety), used alone or in combination. And combined approach of metagenomics and experiments under controlled conditions will investigate the effect of soil microbiota on the effectiveness of the biocontrol solution in order to optimize and test in field trials the positioning of both solutions in the agronomic system. ECLODERA builds on solid results from previous scientific works that have shown the effectiveness and potential of these solutions to replace the use of chemical nematicide while preserving the environment and health of users. The adoption by carrot producers of these solutions, which are easily integrated into the current system, will be encouraged by regular exchanges with the different players in the sector (dedicated WP). The consortium brings together a research institute (INRAE-IGEPP), an agro-supply industrial (CMI-Roullier), a seed company (Vilmorin-Mikado) and a technical institute (SILEBAN). By bringing together industrialists with R&D, production and distribution tools with researchers from the academic world and representatives from the sector, this partnership enables rapid dissemination to producers, first recipients and future users of these new solutions.

Adaptation of organisms to contrasting environmental conditions is a major driver of species diversification. However we know very little on the genetic basis underlying ecologically-relevant traits, and on how and at what speed adaptive divergence leads to genetic differentiation. Here, we will use the pea aphid, a well-suited system for adaptive genomics, which conveniently shows a complex of plant-specialized biotypes, ranging from sympatric host races to incipient species, and resulting from a recent adaptive radiation. By combining novel phylogenetic and population genetic analyses of massive genomic dataset, innovative tools for functional analysis and unique biological resources, we will 1) reconstruct the evolutionary history of plant specialization and biotype formation, 2) identify genomic regions under divergent selection and characterize the genomic architecture underlying plant-based differentiation, and 3) identify genes and functions involved in plant specialization in the pea aphid complex. This project relies on a consortium of 3 French partners and 2 associate partners from other European countries who will bring complementary skills and know-how for the development of multidisciplinary approaches and combination of methods needed to reach project's objectives. This project will allow testing whether multiple independent events of adaptation to different environments involve the same genomic regions and the same set of genes and how genetic divergence accumulates along the genome through time in reproductive isolation. It will also increase knowledge on how insects overcome plant defenses and acquire new hosts on which they may become adapted, paving the way for the development of sustainable control strategies against aphids as important crop pests, based on enhanced plant defenses.