In the context of climate change and increased perturbations caused by human activities, understanding the evolvability and resilience of populations colonizing new areas is of critical importance. Although reproduction is the most influential trait governing evolutionary responses to environmental changes, little attention has been paid to the influence of partial clonality on the genetic sustainability in invading populations. As shown in our previously funded project Clonix, even moderate rates of clonality can profoudnly affect the evolutionary trajectory of isolated populations. Clonix2D will extend our understanding of the evolutionary consequences of partial clonality on genetic diversity and structure during colonization events. We will use a multidisciplinary approach involving mathematical modelling, simulations, and population genomics using various model species across the eurkaryotic domain. The proposed consortium has the necessary expertise for all aspects of the project. Clonix2D is subdivided into three tasks: Task1 will formalize the theoretical consequences of increasing rates of clonality using simulations and mathematics of stochastic processes on 1a) dispersal modes, 1b) partial and complete geographical isolation, and 1c) the effect of repeated bottlenecks and sequential founder events on genetic diversity and structure. Task2 will concentrate on empirically inferring the evolutionary histories of partially clonal populations that have colonized new areas by 2a) formalizing coalescent-based and forward inference methods, 2b) studying their compared accuracies in identifying known demographic scenarios (including clonal rate), and 2c) using real datasets obtained by the different partners to infer demographic parameters on a range of organisms with contrasted ecology and colonization history to test for robustness of the method. Task3 will focus on discriminating the signatures of demographical events (e.g., founder effects, demographic expansion) from selective pressures by 3a) identifying typical genome-wide signatures of soft and hard selection in partial clonality, and 3b) by quantitatively delimiting when those signatures can be identified from typical signatures studied in Task1. This last task is obviously the most challenging as clonal reproduction generates strong linkage across genome that impedes the detection of loci under selection. Here, we hypothesize that uncoupling the effects of selection from demographic histories and reproductive modes on a population of genomes can be achieved using temporal data and adapted methods to correct for demographic scenarios with identifiable signals. This project relies on a strong body of theoretical developments. In this respect, three out of five partners have a longstanding collaboration in software development from source code to the release of user proved program. Risks are, thus, under control and manageable. In particular, a strong methodological strength of this project is the complementarity of the two modeling approaches retained for simulations of population genetics datasets: a forward algorithm based on genotype matrix transition and a reverse coalescent based program. This complementarity will be useful both for exploring theoretical questions but also in particular for a cross validation of inference methods. Another strength and originality of the project is to consider mixed reproductive modes and variable rates of clonality which will increase matching between modelling and biological data analysis. Clonix2D brings together researchers and technical staff that have long been studying convergent issues on population genetics and ecology of partially clonal invading species. We have complementary expertise covering the full spectrum needed to tackle the objectives of this project. As such, we have already authored flagship papers on some of these themes, and developed synergistic and innovative research.

Extreme and variable climate conditions are expected to become more frequent worldwide with projected climate change. European agriculture is facing the crucial challenge of adapting crop productivity to climate change and will need the development of crops with increased resilience to abiotic stress factors triggered by climate change. Crop yield stability is dependent on the response of key developmental and growth processes to stress conditions. Delayed or accelerated flowering time, alteration of root architecture and growth, and disruption of pod-shattering are common responses displayed by crops exposed to high temperature or drought conditions associated to climate change. SYBRACLIM will evaluate the impact of these environmental factors on developmental and physiological processes directly influencing the yield of oilseed rape, Europe’s premium oilseed crop. We will also shed light on the genetic and molecular bases of the tolerance of different rapeseed varieties to increasing temperature and drought stress. The SYBRACLIM consortium is multidisciplinary and includes both commercial breeding companies and leading research groups with high complementarities that cover the fields of genetics, genomics, physiology, breeding and agronomy in Brassica crops along with modeling of crop performance under climate change. Rapeseed is one of the world’s most important sources of high-quality vegetable oils for human nutrition and biofuels, and particularly in Europe is also a major contributor to vegetable protein diets for ruminant livestock. SYBRACLIM will implement a multidisciplinary and innovative approach to characterize the phenotypic changes related to flowering time, root development and pod shattering in response to increased temperature and drought, and to analyse the productivity (yield, oil and protein content) in rapeseed varieties. We will also use genomics-assisted selection of stress-tolerance traits in controlled environments and field trials. The relationship between performance and variability of the studied developmental processes will allow us to identify new genetic traits associated with adaptation and use them to design stress tolerant rapeseed crops by complementary plant breeding and biotechnology strategies. Finally, we will integrate all these environmental, phenotypic and productivity data in models that will assess the performance of rapeseed varieties across different climate conditions. These models will be applied to simulate expected performance of rapeseed traits under projected climate change scenarios. Because breeders need decades to develop new varieties, this approach will enable anticipatory breeding for early development of germplasm carrying the necessary genetic variation to cope with climatic changes. SYBRACLIM will provide tools to allow the farmers to design better strategies for adapting cropping systems to climate change, contributing to secure yield of Brassica crops in Europe.

Unlike multicellular eukaryotic hosts that evolved diverse cell-types to achieve distinct biological functions and promote tasks division, unicellular organisms rely on metabolic exchange with their surrounding biotic environment. Metabolic interdependencies and cross feeding exchanges can occur and explain co-existence within complex bacterial communities. However, a key question is whether populations of genetically identical bacteria can minimize energetically costly processes by executing different metabolic tasks at the subpopulation level. DIVIDE will explore the division of labour between bacterial subpopulations of a core member of A. thaliana root microbiota – Pseudomonas brassicacearum R401 (PsR401) – a robust root colonizer that also modulates microbiota composition at the root interface. Three complementary guiding principles regarding the division of labour in PsR401 population will be explored in the DIVIDE project : (1) a transcriptional differentiation among bacterial cells rising from genetic changes within the population to promote population growth (2) a 'noisy regulation' of metabolism mediated by heterogeneous transcriptional reprogramming in bacterial cells within a clonal population (i.e. not all bacteria within the population would adjust their genome expression to the environmental constraints) (3) a division of labour in the context of the synthesis of three energetically costly metabolic compounds (iron chelators, antimicrobials, and phytotoxins) as a key mechanism to promote PsR401 persistence and competitiveness at roots. By combining a library of transposon mutants, transcriptional reporter lines, novel single cell transcriptomic approaches and microbiota reconstitution experiments in gnotobiotic plant systems, DIVIDE aims to provide a novel understanding of whether metabolic ‘coordination’ within a bacterial population is key for bacterial establishment in the root environment.

Meiotic recombination is a fundamental process for all sexual eukaryotes; it is required to produce balanced gametes and therefore is essential to the fertility of species. Furthermore, meiotic recombination is also crucial for plant breeding because it allows, through the formation of crossovers (COs), to reshuffle genetic material between individuals and between species. Major international efforts have been made to identify the genes that are involved in meiotic recombination in plants, primarily using diploid Arabidopsis thaliana as model system. Therefore much of this work has disregarded the consequences of polyploidy, one of the key features of crop plant genomes, on meiotic recombination. Essential questions thus remain unsolved: How is meiotic recombination regulated in polyploid (crop) species? Why and how does polyploidy increase the rate of meiotic recombination? How can such improved knowledge on recombination be exploited for crop improvement? This project will address these questions specifically, using two complementary polyploid crop species: oilseed rape (Brassica napus; AACC; 2n=38) and bread wheat (Triticum aestivum; AABBDD; 2n=42). We will set up a complete set of integrated analyses to explore many inter-related aspects of CO regulation in polyploid crops. Task 1 aims at characterizing the molecular underpinnings of CO suppression between homeologous chromosomes in wheat and oilseed rape. We will proceed with positional cloning of the PrBn (in oilseed rape) and Ph2 (in wheat) loci. For this latter case, particular emphasis will be placed on evaluating TaMSH7, the most promising candidate for Ph2. CROC will thus advance understanding of the mechanisms that hamper the incorporation of beneficial traits from wild relatives into crop plants by promoting a diploid-like meiosis in allopolyploids; overcoming this specific stumbling block would open the road to the creation of new crop varieties resistant to diseases and more efficient in nitrogen use (to name only these). Task 2 will advance understanding on the cause of the striking CO rate increase we have discovered in Brassica digenomic triploid AAC hybrid and its possible application to wheat. We will determine whether these extra COs i) arise from one or the other CO pathways and ii) can be combined with those resulting from the mutation of an anti-recombination meiotic protein. We will unravel the individual and interaction effects of three C chromosomes on the rate and distribution of COs between homologues and test whether wheat pentaploid AABBD hybrids have the same boosting effect on CO frequencies as Brassica AAC triploid hybrids. The expected outcomes will pave the way to broaden the genetic variation that is available to plant breeders. CROC is a timely project that is shaped to address fundamental questions with practical objectives; it is directly upstream of research on innovative plant breeding technologies contributing to the competitiveness of French/European Agriculture and thus completely relevant to this call. CROC combines a group of researchers with a comprehensive and complementary expertise and set of facilities. Its strong translational emphasis ensures that the results obtained will have general significance that extends beyond oilseed rape and bread wheat. Our work will thus shed new light on the pending cause of CO variation in polyploid plant species, a critical issue for genetics, evolution and plant breeding.

Small (s)RNA-directed RNA interference (RNAi) plays an important role in epigenetic regulation of gene expression, antiviral defence and cross-talk between eukaryotic organisms. In this project we will dissect the biogenesis and function of sRNAs in 3-way plant-virus-insect vector interactions and exploit trans-kingdom RNAi mediated by mobile sRNAs to investigate molecular mechanisms underlying virus transmission by vectors and to interfere with the transmission process. To this end we will use two related legume viruses of family Nanoviridae and aphid vectors causing economically-important diseases worldwide. Based on available evidence and preliminary data described below, we hypothesize that mobile viral sRNAs, generated by plant RNAi and ingested by phloem sap-feeding aphids, penetrate into aphid cells and target genes, thereby regulating gene expression to facilitate the passage of viral particles throughout aphid body and inoculation of a new host plant. Likewise, virus-induced mobile plant sRNAs may regulate aphid gene expression in favour of virus transmission. Finally, the plant genes presumably targeted by viral or virus-induced plant sRNAs, or mobile aphid sRNAs may also have impact on virus acquisition by aphids and hence transmission. To test these hypotheses we will profile sRNA-ome, transcriptome and RNA degradome of plants and aphids fed on virus-infected and control legume plants. We will then use virus-induced gene silencing (VIGS) and exogenous RNAi approaches to (i) validate the role of virus-regulated and sRNA-targeted genes in virus acquisition and transmission by aphids and (ii) investigate molecular mechanisms underlying the circulation and persistence of viral particles in the aphid body. Our results would ultimately contribute to designing RNAi-based tools and other novel approaches to control aphid-borne diseases not only by killing insect vectors but also by interfering with virus transmission without impacts on vector viability/fitness that may force selection for insect resistance.