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.

Mobile DNA elements, referred to as Transposable Elements (TEs), are ubiquitous components of eukaryotic genomes. The earlier notion of TEs being junk DNA has been revolutionized by the discovery of their functional impacts, including their capacity to provide cis-regulatory elements (CREs) controlling the expression of nearby genes. While examples of such cases have been depicted, we still lack a complete understanding of the contribution of TEs to the evolution of biological functions, from conserved developmental functions to species-specific functions, including those underlying environmental response. In SATURN, we propose to determine the contribution of TEs to gene regulation across evolution using six plant species that diverged across a 20-200 My time scale and for which extensive genomic and functional data are available. Specifically, we aim to: (i) assess the contribution of TEs to CREs involved in developmental and stress-induced gene regulation, (ii) decipher how TEs contribute to conserved and species-specific expression regulation, and (iii) systematically test the role of TE-driven CREs in the regulation of gene expression. SATURN will decipher the contribution of recent and ancient TEs to functions that have shaped plant evolution and adaptation, using a highly interdisciplinary approach combining deep TE annotation, comparative genomics, innovative long-read-based epigenomics and transcriptomics developments, and in vivo functional validations. It will shed new light on the major TEs involved in species functional evolution, as well as on the type of functions that evolved due to TE insertions. Through the use of both model and crop species, it will bring fundamental knowledge on the molecular bases underlying the evolution of functional regulation, as well as valuable information for future breeding. The knowledge acquired by SATURN will be a cornerstone in the understanding of TEs’ functional contribution to species evolution.

Plant responses to biotic aggressions involve a great diversity of molecules including regulatory proteins and hormones. Among these actors, small secreted peptides, also named peptide phytohormones or phytocytokines, may directly interact with pathogens or act in signalling and cell-to-cell communication. They are produced from non-functional precursors through a maturation process, making characterization difficult only on the basis of their gene sequences. Only a small fraction of the genes liable to encode these secreted peptides has been described and their impact and diversity appears to be seriously underestimated. The main goal of STRESS-PEPT is to better understand the plant responses to biotic stress at the peptidome level and to characterize new molecular actors involved in defence mechanisms. Based on our experience and previous results, we plan to develop and apply a multidisciplinary genome-wide approach combining bioinformatics, differential transcriptomics and peptidomics to identify new secreted peptides in Arabidopsis and to describe their contribution to plant responses to different representative biotrophic and necrotrophic pathogens (oomycete, fungus and bacterial elicitor). The proposed methodology is organized in three complementary tasks: (i) An original bioinformatics pipeline will be used to screen the Arabidopsis thaliana genome in order to identify genes encoding precursors of secreted peptides, to cluster and classify them in gene families by homology and phylogenetic profiling and to predict the putative mature peptides through a sensitive conserved motif searching method ; these predictions will be integrated to RNAseq transcriptomics analyses applied on Arabidopsis in presence or absence of the different pathogens in order to tag the fraction of the secreted peptide precursor genes that are transcriptionally regulated by pathogen aggression(s). (ii) The same biological samples will be used to prepare extracts of peptides, from apoplastic fluids and total extracts, through an original protocol optimized for efficient mass spectrometry (MS) analysis: a LC-MS/MS based peptidomics approach will be applied on the different peptide extracts for the identification and the differential quantification of the secreted peptides and to characterize their post-translational modifications. (iii) A selection of promising peptides, based on transcriptomics and peptidomics data, will be made for functional analyses including assays on knock-out mutants and overexpressing transgenic lines. Synthetic peptide treatments will be performed in order to understand and validate their role in plant-pathogen interactions. The STRESS-PEPT consortium gathers bioinformaticians, molecular biologists, biochemists and plant pathologists expert of each studied pathosystem as well as a proteomics platform. The already established collaborations between these partners will ensure close cooperation and synergy throughout the 4 year project, and ensure obtaining results of high interest for the plant biology community. All the data generated will be stored and organized for efficient querying in a relational database publicly available at the end of the project. STRESS-PEPT will lead to significant advances in the discovery of new secreted peptides which are key players in danger sensing and the modulation of immune responses. According to their conservation among plant species, these peptides might be used in innovative strategies aiming at jointly optimizing plant quality and resistance, and should open new opportunities for sustainable crop management.

Drought is the main problem of agriculture worldwide and the situation is expected to get worse with climate change. Agriculture in the Mediterranean area could be particularly damaged and one of the primary menaces is agro-diversity depletion. Maize is one of the most important crops worldwide and is a model crop in plant breeding; however, it is especially vulnerable to abiotic stresses (heat and drought) encountered in a scenario of climate change. The objectives of DROMAMED are to: 1) assemble germplasm collections of maize adapted to Mediterranean dry areas, pooling and evaluating stress-resistant varieties from the national collections, 2) support innovative farming systems by promoting quality and sustainability of agricultural models based on organic and family agriculture, 3) study genetic factors involved in maize adaptation to drought and heat stress, 4) investigate the physiological and morphological mechanisms involved in maize responses to stresses, 5) establish predictive models and selection criteria for breeding programs focusing on tolerance to stress (phenotypic, marker assisted and genomic selection models will be designed to improve tolerance to individual and combined stresses), and 6) release new stress tolerant varieties and knowledge for being used by stakeholders; all these achievements will contribute to the sustainability of production and mitigation of the effects of stress in present and future climate scenarios. DROMAMED intends to 1) valorize the germplasm collections maintained in Mediterranean countries, with entries that have been selected for adaptation to a large diversity of stressful environments, 2) promote innovative crop management practices to increase quality and sustainability of organic and family agricultural systems, 3) capitalize current and new knowledge about mechanisms of tolerance to abiotic stresses, and 4) develop selection methods that will increase our ability to improve breeding approaches enhancing maize tolerance to abiotic stresses. DROMAMED will contribute to the progress of knowledge beyond the state of the art by dissecting the genetic, biochemical, morphological and physiological mechanisms underlying stress tolerance, providing useful tools and materials to capitalize the diversity of maize for cultivation under low inputs in the Mediterranean area and thus leading to rescue germplasm for future agriculture. The social impact will be encouraged in DROMAMED reling on close contacts between associations that represent the needs of producers and researchers to gather precise information on demands of stakeholders, try to fulfil as much as possible those demands, and transfer to growers technical knowledge to facilitate cultivation of the released drought tolerant populations. These associations are the Spanish Society for Organic Agriculture (SEAE), the Italian Maize Growers Association (AMI), the Italian Confederation Agricultural Producers (COPAGRI), the Breeding Cattle Associations of Antalya Province of Turkey (BCAAT), and the Organic Agriculture Association of Turkey (ETO).

The interaction between transposable elements (TEs) and their hosts is one of the most intricate co-evolutionary processes found in nature. Quantifying how TEs impact their host’s fitness has practical relevance in relation to real-world applications, such as understanding the molecular bases of selected phenotypes, or assessing mutational load in crops (so-called “cost of domestication”). The following project will focus on the impact of TEs on the host’s fitness, using the date palm (Phoenix dactylifera) as a model. This crop is of major economic and social importance in the Middle East and Northern Africa, and its consumption keeps rising every year. However, it is also threatened by more frequent droughts and increasing salinity due to climate change. A precise characterization of its genetic diversity is therefore essential to understand the adaptability of this species to growing environmental pressures. The project will use genomic data to examine the role of polymorphic TEs in selection and differentiation of date palm varieties across the species range. It will revolve around two questions: What is the distribution of TEs fitness effects in date palms? Can this distribution be predicted from functional genomic features such as gene regulatory networks? We will develop and apply new methods in population genomics to estimate the fraction of advantageous and harmful polymorphic TEs. We will compare results with de novo functional annotations of chromatin organization and regulatory networks to draw a comprehensive view of TEs’ impact on a keystone perennial species of agronomic interest for both developed and developing countries.