The EU citrus industry is threatened by an emerging disease, the Huanglongbing (HLB) or citrus greening. It is considered as the most devastating disease in citrus due to its rapid spread, severity and the rapid progression of symptoms. The consequences are considerable losses in terms of fruit production and quality, costs and difficulty in preventing new infections, lack of resistant citrus varieties and economically viable treatments for infected trees, as well as the absence of sustainable control mechanisms. HLB is thus responsible for economic losses of several hundred million euros for the citrus industry worldwide. The objective of this ANR project is to help to set up a Horizon project that will continue the H2020 Pre-HLB project (2019-2023) in the framework of the HORIZON-CL6-2024-FARM2FORK-02-4 call for proposals. A strong European consortium involving Brazil is already established and involves a network of partners with multidisciplinary expertise. The research actions will be in continuity of those already initiated in the framework of pre-HLB and will aim to have the greatest possible impact preserving the Mediterranean citrus of HLB.

In Europe, rice (467 000 ha) is gown under permanently flooded (PF) conditions using irrigation waters of major rivers. Climate change, which has led to a greater fluctuation in river flows, is a major challenge to rice production systems, which depend on large and consistent water supplies. This challenge will become more acute in the future, with increased demands for rice both from within Europe (net deficit of 0.86 Mt) and from overseas. Rice yields under existing production practices are therefore threatened by scarcer water availability. In addition, PF rice fields emit greenhouse gases (GHG), such as methane (CH4), that have a strong global warming potential. Alternate wetting and drying (AWD) is a system in which irrigation is applied to obtain 2 to 5 cm of field water depth, and then turned off. After a short period (normally 2 to 7 days), when the field has dried out, water is re-applied. Preliminary studies suggest that AWD can reduce water use by up to 30 %, with no net loss in yield provided varieties well adapted to AWD are used, while CH4 emissions can be reduced by up to 48 %. However, uncertainties still remain as to the impacts of AWDS on GHG fluxes (e.g. CO2, N2O) and plant-mutualist and plant-pest interactions, which may influence the overall efficacy and viability of this new system. Thus, while AWD represents a potentially exciting alternative water management strategy for European rice production, a more complete agronomic, ecological and biogeochemical assessment of AWD is required to evaluate the benefits of the system. To close these critical knowledge gaps, GreenRice aims to test AWDS in Italy, Spain and France, in regions that are representative of the diversity of European rice growing areas, notably in deltaic areas where rice systems and natural protected wetlands are interdependent. We will evaluate the agronomic and environmental consequences of shifting from a PF to an AWD system, focusing on rice yields, water consumption, soil salinization, plant-soil-microbial interactions and GHG dynamics. We will identify varieties that maintain their productivity under AWDS through whole genome association mapping of a large panel of temperate varieties, using genomic selection to predict the values of additional breeding lines. We will investigate traits determining adaptation to AWDS, such as root development, AM colonisation, salt tolerance and resistance to nematodes; and the role of AM symbiosis in alleviating the impacts of biotic stress. An extensive gene expression study will identify the root types and genes important in transport process and the degree to which they are affected by AWDS. The role of plant functional traits and the soil microbial activity in modulating C, N and GHG fluxes will be investigated in both field-based and controlled environment studies. The results obtained will be disseminated to local stakeholders (primarily farmers and natural park authorities) and to the scientific community.

EVENTS aims to investigate both the positive and negative impacts of endogenous viral elements (EVEs) on plant metabolism. EVEs are viral sequences that are integrated in the genomes of their hosts. In plants, most characterized EVEs originate from viruses in the families Caulimoviridae and Geminiviridae, which have DNA genomes, following passive horizontal gene transfer (HGT). Members of the project team recently showed that DNA from ancestral viruses in the family Caulimoviridae were captured within the genomes of a wide range of angiosperms, including economically important crops (rice, sorghum, citrus, grape, apple, pear, strawberry, eucalyptus, poplar, tomato, potato, cucumber, cotton). A new genus, tentatively named Florendovirus, was proposed to accommodate these viruses. Several endogenous florendoviruses could potentially be replication competent and, therefore, infective, although this hypothesis has not yet been tested. Different members of the project team have also discovered new geminivirus-like elements (EGVs) in the genome of yams and demonstrated that these EGVs represent transcriptionally active endogenous geminiviral sequences that may be functionally expressed in their respective host plants. Building on this pioneering work, EVENTS focuses on the role of caulimovirid and geminivirid EVEs in virus evolution and their functions in plants. EVENTS will create automated computational tools to search for these EVEs in plant genomes and will implement these tools in a large-scale plant EVE discovery program, providing access to viral sequences that were integrated millions to tens of millions of years ago. These EVEs will be used to reconstruct accurate time-scaled evolutionary histories of entire viral lineages across unprecedented time-spans, helping to refine predictive models of viral emergence. EVENTS will investigate the contributions of caulimovirid and geminivirid EVEs to viral diversity. A range of antigenic and molecular detection tools will be created and used to screen germplasm collections and collected samples for viral particles and infective genomes of as yet undescribed geminiviruses and florendoviruses with EVE counterparts. Graft experiments will be carried out to confirm infective status. The project will also explore synergistic interactions between endogenous viruses and exogenous viruses encoding suppressors of silencing, in order to investigate the role of silencing in the regulation of EVE gene expression in plants. The contribution of caulimovirid and geminivirid EVEs to genetic and epigenetic regulation of plant gene expression will be investigated in silico through the systematic search for fused (viral/plant) open reading frames, alternative promoters, intron splicing sites and premature terminations of transcription. Immunological and molecular approaches will be designed and used to search for and characterize EVE-derived proteins and/or RNAs expressed in host plants. Experimental approaches using recombinant infective viral clones expressing EVE sequences will be designed and implemented to evaluate potential antiviral resistance in plants conferred by EVEs acting as natural viral transgenes. By developing novel integrated and multidisciplinary approaches to illuminate the diversity of EVEs in plant genomes, their roles in viral evolution, their functions and potentially beneficial roles within their host plants, EVENTS stands at the forefront of an emerging research field. We anticipate that the project will contribute significantly to societal issues such as the control of viral diseases and the advancement of plant biotechnology. EVENTS brings together leading groups with complementary expertise in virology, bioinformatics and molecular systematics working in France, South Africa and Australia. Partners have a proven record of collaboration and joint publications that demonstrate their ability to meet project goals and deliver results in ground-breaking research domains.

The ability for a population to adapt to environmental changes depends on several factors such as its size, genetic diversity, or mating patterns, in particular selfing rates. In flowering plants, mating patterns are highly variable from strict outcrossing to predominant selfing and almost a half self-fertilize at various rates. Nevertheless, random mating is a classic assumption and the effect of selfing on adaptation remains largely unresolved: on the one hand, the young age of selfing lineages suggests that selfing species lose the ability to adapt to changing environments; on the other hand, the large proportion of selfers in crops suggests that selfing could facilitate adaptation to human use. Selfing can indeed have multiple and complex effects. It shapes the genetic variance of a population, but also the interaction between selection and drift or migration. Selfing is also likely to alter population’s demography, because inbreeding and outbreeding depressions affect the vital rates of individuals. Both these genetic and demographic impacts bear upon the probability of adaptation to environmental variation, which depends on a race between the speed of the adaptive process and the speed of population decline. A refined understanding of these impacts is therefore essential to predict the fate of selfing species in the current context of global change and to improve conservation and management strategies of both natural and cultivated populations. In this project, we propose to tackle three main issues regarding the effect of selfing on adaptive processes, through a combination of theoretical developments and fine scale analyses of three species. Our study systems include two predominantly selfing and one partially selfing species, all undergoing adaptation to environmental changes related to human activities. First, we propose to focus on the response to selection within population, by developing models explicitly taking into account the complex genetic architecture of traits and specific selection regimes. This modelling approach will be combined with the temporal monitoring of experimental or natural populations under selection. Secondly, we will examine how selfing affects local adaptation in populations connected by gene flow. To achieve this, we will analyse the interplay between selection, drift and gene flow under partial selfing to predict the rate of phenotypic divergence and to quantify local adaptation to heterogeneous environments. Thirdly, we will investigate how temporal variations in selfing rates modify the dynamics of adaptation, while explicitly taking into account demographic effects (especially inbreeding depression and reproductive assurance). This proposal unites research groups that have long been addressing related questions and have complementary expertise (e.g. ecology, demography, population and quantitative genetics, evolutionary theory, crop science).