The current global warming scenario predicts an increase of geographic expansion of pathogen distribution and epidemics. These future outbreaks represent a major threat to crops and are likely to cause significant yield losses. In this context, a major challenge is to identify the bases of resistance mechanisms allowing plants to cope with future epidemics and to develop, for instance new products for plant protection. Indeed, in the field, to grow and reproduce, plants have to face and simultaneously adapt to multiple stresses including abiotic (drought, salinity, temperature) and biotic (bacteria, fungi, viruses, insects). Often concomitant in natural conditions, these adverse abiotic and biotic constraints affect plant growth and ultimately productivity worldwide. While some genetic components of plant responses to environmental constraints were identified and characterized in the recent decades, our knowledge on the strategies developed by plants in response to combined stresses (biotic and abiotic) remain fragmented. More particularly, environmental changes such as a subtle but permanent increase in temperature (3-5°C), inhibits the major defense mechanisms against pathogen attack. Thus, the understanding and the identification of molecular components integrating environmental stimuli and controlling plant responses are of major interest for sustainable agriculture and global food security in the near future. This project will explore the contribution of calcium signaling modules in plants interacting simultaneously with biotic and abiotic factors. It is now well documented that most of the external stimuli induce a rapid increase in free calcium levels within plant cells and that these calcium variations are essential to coordinate the adaptive responses. To be informative, calcium increases need to be decoded and relayed by calcium-binding proteins also referred as calcium sensors to carry-out the appropriate responses. Although calcium signals are involved in most stress-signaling pathways, their direct manipulation in a targeted way (i.e. enhanced stress tolerance) would be tedious due to the diversity of actors participating in shaping these signals. One alternative would be to manipulate the function of the calcium-sensor proteins and/or of their targets involved in decoding the calcium signals. The originality of the project is to focus on the plant specific family of CalModulin-Like calcium sensor proteins (CMLs) due to their important role in both biotic and abiotic responses. The biological relevance of these calcium sensors, specific to plants, constitutes an emerging field in plant signaling research area and our goal is to demonstrate, using reverse genetic tools, that CMLs are central integrators of biotic and abiotic stresses responses. The project will be developed on two models plants: Arabidopsis thaliana and Tomato (Solanum lycopersicum) and will mainly consider the impact of temperature increases on the interaction of both Arabidopsis and Tomato with two of the most destructive plant pathogenic bacteria worldwide, Ralstonia solanacearum (Rs) and Pseudomonas syringae pv. Tomato (Pst). Tomato was selected because it is not only a widely cultivated species highly sensitive to Rs but also an excellent model in plant-pathogens interaction studies. The functional characterization of some selected CMLs, associated to environmental stresses, will be performed in response to Rs and Pst infections in conditions of a weak and permanent increase of temperature (3 to 5°C) and a particular attention will be dedicated to the molecular processes controlled by these CMLs through the identification of their downstream targets.

In agriculture, abiotic stresses are major causes of yield loss. In the context of global warming, it is predicted that heat stresses will decrease crop yields by 3 to 7.4% for each degree Celsius increase. One of the urgent challenges for the seed industry is to improve the resilience of crop species to heat stress. Farmers are waiting for resilient varieties to guarantee the level of production in quantity and quality under a wider range of temperatures. Tomato is one of the main agricultural products of the European Union. Cultivated throughout Europe in the open field, under cover and in greenhouses, it is a model crop from a biological and agronomic point of view. Abiotic stresses are major problems for tomato producers and solutions are needed to stabilize yields. Despite its ability to grow in variable climates, tomato production is highly impacted by heat stress, among other abiotic stresses. In particular, heat stress affects the reproductive system, root development and seedling growth. Heat shock proteins represent a widely conserved class of proteins involved in stress response and plant growth and development. Although they were first discovered in the context of the heat shock response, most biotic and abiotic stress responses require the concerted action of heat shock proteins to regulate stress response and acclimation. Elucidation of the molecular mechanisms responsible for the regulation of heat shock proteins is essential to improve the tolerance of crop plants to biotic and abiotic stresses. The FloCad team and Gautier Semences have conducted several studies that have identified regulators of heat shock protein expression as targets for improving crops under abiotic stresses. The association of the two entities proposes the creation of the joint laboratory BioAdapt which aims to use these regulatory genes as breeding targets to improve the resilience of tomato to heat stress.

Structural variation is a major driver of genetic diversity and an important substrate for species adaptation and selection. Understanding the relationships between structural variants and functional innovations thus represents a major issue to be addressed. In allopolyploid species, which are common in angiosperms and particularly widespread in crops, exchanges between homeologous chromosomes (i.e. between constituent subgenomes), called HEs for homoeologous exchanges, represent a major source of structural variants. However, we still know little about the genome-wide distribution and resulting functional diversity generated by these variants even though they may have played a prominant role in the evolutionary success of allopolyploidy in plants. In the EDIn project, we will develop an integrated set of analyses to advance knowledge on the causes and consequences of HEs, from the mechanisms responsible for their formation to their effects on gene and genome expression, on chromatin dynamics and plant phenotypic variation in oilseed rape, Brassica napus. Based on highly original plant material specifically designed to promote HE, combined with state-of-the-art multi-omics approaches, our project will address fundamental questions in the context of the allotetraploidy of the B. napus crop genome. EDIn is composed of three main workpackages. WP1 aims to profile the products of inter-homoeologue recombination at very high resolution and build a predictive model of their occurrence, which would be useful in breeding for managing introgressions in crop x wild relative hybrids. WP2 aims to evaluate the global consequences of HEs on gene expression at genome-scale but also at population level. In particular, it will make it possible to characterise the impact of HE on gene regulation networks, which would represent the first in-depth analysis for an allopolyploid crop. WP3 aims to establish the causality of specific HEs by developing an original genetic association study, and to characterize their impact on the reorganisation of the genomic and epigenomic landscapes. In a highly original manner, WP3 will study the changes in the epigenome and the reorganisation of chromatin that introgression of alien chromatin originating from a HE can cause. Our results should therefore prove fruitful in developing useful knowledge and operational strategies for the improvement and diversification of allopolyploid crops, in particular for the management of their genetic diversity or associated genetic resources. This research will be conducted by a consortium of renowned scientists who bring highly complementary expertise, know-how and/or facilities, allowing a more complete understanding of the impact of HEs on the functioning of the allopolyploid genome. One original aspects of this consortium is its direct link to higher education, which represents an excellent opportunity to teach students about the socio-economic impact of public research and train future researchers in the field of recombination, genomics, epigenetics, chromatin organisation and dynamics, for plant breeding.

Seeds are at the core of agriculture, constituting a major source of food for humans and animals. Climate change is expected to have a dramatic impact on seed germination and seedling emergence as they are tightly controlled by environmental cues. In particular, the temperature regime that prevails during seed formation on the mother plant directly impacts dormancy depth at harvest, which can directly influence population dynamics and productivity of all agrosystems. RNASEED project associates the 3 following partners: Institute of Biology Paris-Seine, Sorbonne Université (P1), Institute of Plant Science Paris Saclay (P2), Jean Pierre Bourgin Institute (P3). We will investigate the effect of temperature regime during Arabidopsis seed development, mostly perceived through the plant hormone abscisic acid (ABA) metabolism and signaling, on resulting seed dormancy. The objective of RNASEED is to determine whether the temperature effect on seed dormancy can be modulated by an under-explored component of the transcriptome, the non-coding RNA (ncRNA)-mediated regulation of gene expression. RNASEED will first take advantage of the numerous preliminary transcriptomic data, available at P1 and P3, obtained within the EU project ECOSEED, that suggest a role for small and antisense RNAs in dormancy regulation. Then we will set-up genetic tools, transcriptomic and translatomic analyses to gain fundamental insights into the mechanisms controlling seed dormancy to uncover a novel molecular network of dormancy regulation integrating small RNA and antisense RNA action. In addition to genetic and reverse-genetic approaches for modulation of regulatory RNAs in transcriptional networks, we will also develop nanoparticle technologies for delivering regulatory RNAs to seeds with the ultimate objective to modulate seed dormancy using new RNA-based tools identified in the study. RNAseed is divided into 4 work-package (WP) combining data mining, experimental approaches and transfer of knowledge to practice. We will decipher the small RNA network that controls responses of developing seeds to temperature by combining data mining of ECOSEED datasets and preparation of small RNA libraries (WP1). The analysis of the designed network will allow identification of candidate small RNAs, antisense RNAs or targets showing potential function in controlling temperature perception by developing seeds (WP2). Candidate regulatory RNAs which will be further validated using CRIPR-cas9 or overexpression and subsequent seed germination phenotyping (WP3). In addition we will also investigate their role in the selective translation that governs seed germination (WP3). Lastly RNASEED also aims to transfer the acquired knowledge to practice and we will try to modulate seed dormancy through the use of nanoparticle, either provided by seed coating or by priming, that will deliver regulator RNAs to the seed. Thus, we expect that RNASEED will make a leap forward in the understanding of the role of non-coding RNA in seed biology and that it will provide novel technological tools to modulate dormancy at the time of sowing

The maintenance of genome integrity is essential in meristems that generate new organs and tissues throughout the life of the plant. Several transcription factors controlling the DNA damage response (DDR) have been identified. However, how and in what order they act to induce different responses in different cell types remains an open question. The coordinated activation of successive levels of response, and the differential control of cell division and cell death in different cell types, are essential to preserve meristematic function in response to DNA damage. In this project, we propose to spatially and temporally resolve the regulatory network associated with DDR in the root meristem. The root meristem is generally the first to be exposed to potential toxic substances in the environment, and is also essential for root growth, and thus for the whole plant. By combining the most recent genomic techniques (snRNAseq and snATACseq), cell biology (live-imaging) and biochemistry (proximity labelling), we will reconstruct the regulatory networks involved in the DDR in a cell-specific manner. This model will be validated by reverse genetics and molecular biology (ChIP) approaches. Beyond the spatio-temporal resolution of the DDR, which is essential to understand how meristematic function is preserved in response to stress, the implementation of these integrative approaches will pave the way for similar studies applied to other physiological contexts such as heat stress or drought, thus addressing the major challenges associated with plant growth in the context of climate change.