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.

ROTATES aims to sustainably enhance agrobiodiversity and ecosystem services by introducing and promoting minor starchy root and tuber crops (MRT) sweet potato, yams, cassava and taro, considered minor crops and currently underutilized in Europe, in both conventional and organic farming systems. These crops have substantial growth potential in temperate regions to meet the increasing demand in Europe, which has tripled over the last decade. The inclusion of MRT crops will complement the cohort of minor crops introduced into European agrosystems by the previously funded projects. Employing a multidisciplinary and multi-actor approach, ROTATES will (i) identify levers for MRT crop adoption along the value chain, through a comprehensive diagnosis of constraints and opportunities for MRT crop adoption, agronomic practices to inform farm typology analysis, genetic material assessment, and disease pressure evaluation, (ii) deploy MRT crops by developing agroecological management practices, including crop rotation and intercropping, to leverage the benefits on provisioning and regulating ecosystem services, establishing breeding hubs to deliver varieties adapted to the agroecological systems, and creating a clean seed system relying on a policy framework for phytosanitary certification to support sustainable production and material exchange, (iii) unlock the value of MRT crops by establishing sustainable and innovative healthy and traditional food and feed transformation processes, integrating livestock to recycle unused plant by-products and provide crop amendments - gluten-low-to-free pasta, bread, and plant-based ice cream and feed for ruminants and monogastrics- (iv) promote adoption along the value chain, targeting primarily farmers and growers, through marketing avenues and capacity-building efforts. ROTATES will contribute to improving producers’ income, enhancing product value, increasing agrobiodiversity, and reducing Europe's import dependence.

Citrus huanglongbing (HLB), or greening, is the most destructive citrus disease worldwide, and threatens the sustainability of the industry, affecting tree development, production, and fruit quality. All Asian citrus species, including all commercial varieties, are susceptible to HLB; however, tolerance and resistance have been described in some citrus relatives belonging to the Oceanian genera Microcitrus and Eremocitrus. Species of these genera are sexually compatible with Citrus spp.. CIRAD has generated a unique diversity panel of diploid intergeneric-hybrids (Citrus sp. x Microcitrus sp.) over several generations. FUNDECITRUS, whilst, has generated several biparental populations of intergeneric-hybrids (Citrus sp. x Microcitrus sp.) from first and second generation issued from controlled crosses. Such wide crosses may result in non-Mendelian inheritance of phenotypic traits due to the reformatting of the epigenetic landscape. The overall objective of the EpiHLB project is to identify genes and genomic regions associated with HLB resistance and to determine how their expression is controlled. A core collection of intergeneric-hybrids will be selected from the CIRAD and FUNDECITRUS populations, and their response to infection will be studied under HLB challenge inoculation stress. The project will focus on the role of genetic and epigenetic factors in the regulation of gene expression linked to HLB resistance by developing a multi-omic quantitative approach that combines multiple layers of association studies. The strategy is to join genomic (GBS and WGS), transcriptomic (RNA-seq and small RNAseq), and epigenetic (methylome) studies to the phenotype in order to develop models of omics-association. In the framework of the implementation of sustainable integrated pest management, the results of this project will contribute to the development of innovative strategies to create cultivars and rootstocks resistant to this disease, severely affecting a socioeconomically important crop worldwide.

Floods are responsible for around 60% of all agricultural damage and crop loss (FAO, 2015). The perspective of global climate warming will affect cultivated areas and crop growing conditions, impacting the future of food security in the world. The identification of genes controlling flooding tolerance is one of the keys to the development of submergence-tolerant varieties in cereals, a problem that affects an increasing number of cultivated areas worldwide. Rice has aerenchyma, which are air-filled cavities that connect the aerial parts and roots, allowing them to maintain their respiration and growth under submerged conditions. Aerenchyma formation is an adaptive response to submergence in rice but the gene network controlling aerenchyma and cortex formation is still unknown. The main objective of the project is to identify and characterize transcription factors involved in cortex and aerenchyma tissue differentiation in rice using a systems biology approach. This work will help to identify key genes behind aerenchyma and flooding tolerance in rice. These genes will be future candidates for breeding better-flooding tolerance cultivars in rice but also in cereals.

There is an increasing demand for cereal varieties capable to maintain their yield under limited soil resources (e.g. water, nitrate) both in developed and developing countries. In 2012 breeding companies have released maize lines marketed for drought resistance which occupied in 2014 more than 10% of the maize planted surface in the USA. Most of these varieties are improved for global water use efficiency and osmoprotection mechanisms. However, many traits contribute to drought tolerance but none is effective in all contexts and some can reduce yield under well-watered conditions. Thus there is an increasing interest to breed for root architectures allowing plants to better exploit the water and mineral resources of the soil. This has been largely underexploited up to now most likely because the root system is not easily observable. The root system of cereals is mainly composed of shoot borne crown roots. Their number is an important component of the root ideotypes that have been proposed to adapt plants to water and/or mineral nutrient deficiencies. Mutations in the rice transcription factor CROWNROOTLESS 1 (CRL1) and in its ortholog ROOTLESS CONCERNING CROWN AND SEMINAL ROOTS (RTCS) in maize lead to the impossibility to initiate crown roots. To identify new master regulatory genes involved in crown root development, we are developing a systems biology approach to determine the gene regulatory network (GRN) involved in crown root formation in rice. The GRN modelling is based on spatial and kinetic transcriptome data obtained using an original crown root inducible system byCRL1 transcription factor that we engineered in rice, and TDCor, an algorithm using time delay analysis of gene expression kinetics to infer the regulatory relationship between genes, without a priori on the function of the genes. This approach will allow us to identify new master regulator genes of crown root formation that escaped the classical genetic investigations due to the high functional redundancy observed in the genome of cultivated cereals. Five master rice regulatory genes corresponding to major hubs of the GRN will be selected prior to the start of the project, their orthologs identified and expressed in maize under the control of a constitutive or drought inducible promoters. Maize T0 plants are thus expected at the early beginning of the project. In addition, we propose to identify the direct targets of CRL1 by chromatin immunoprecipitation sequencing experiments, to validate in vivo the regulatory interaction of major hubs of the network, to refine GRN inference and to select 2 new candidate genes. The function of the selected genes (5+2) will be then studied by inactivating them via CRISPR-Cas9 in rice, or expressing them constitutively or in a drought inducible manner in rice and maize. Those lines will be phenotyped using dedicated platforms available in our consortium or onto specialized platforms. The most promising genes modifying the root system architecture and plant drought tolerance will be patented. The corresponding maize lines will be used to generate hybrids that will be challenged in field for their capacity to maintain yield under drought conditions. To reach this objective our public-private-partnership joins together two academic teams with a private company. The “cereal root system” team from UMR DIADE (IRD-UM) has expertise in cereal root development, system biology and applied mathematics. The “Adaptive Development of Rice” team from UMR AGAP (CIRAD) has a strong background in rice functional genomics including rice transformation. The private company Biogemma has expertise in maize transformation, phenotyping and field experimentation. We expect that this three years project will lead to the identification of new genes allowing suitable modification of rice and/or maize root architecture, drought tolerance and yield under water deficit condition.