Hybridization between plants with different ploidy often encounter post-zygotic reproductive barriers in the seed, which are mediated by transposon-derived small RNAs that disrupt genomic imprinting. Strikingly, this is highly reminiscent of hybrid dysgenesis in Drosophila, suggesting that plants and animals utilize similar small RNA guides to control transposon activity and dosage in hybrid genomes. EpiHYBRIDS aims to provide mechanistic insight into the origins and function of small RNAs responsible for hybrid seed collapse in Arabidopsis, by performing 1) large-scale small RNA depletion and 2) targeted epimutagenesis at imprinted loci with single-cell resolution. The overall goal of this project is to elucidate the epigenetic basis of genome dosage responses in interploidy crosses, but the results may provide valuable insight on additional small RNA-related phenotypes that are highly relevant for modern agriculture and food production, such as heterosis and apomixis.

The main goal of this project is to understand the regulatory logic underlying the control of leaf shape in plant focussing on a set of key regulators, the CUCs transcription factors. The diversity of shape seen in the plant kingdom is astonishing. How from small groups of cells encompassed in a primordium such variety of shape can be generated? The answer is maybe lying in the intricate regulatory network controlling cell fate and boundaries. It is believed indeed that changes in gene regulatory network (GRN) grandly contribute to morphological changes and therefore represent large evolutionary targets potentially producing important effects with limited pleiotropy (Doebley JF et al., 2006; Carroll SB, 2008; Arnaud et al., 2011). The proposed project is an opportunity to understand the regulatory logic of transcription factors, the combinatorial regulatory code governing a developmental process. To understand how genes control shape - a question relevant to all aspect of developmental biology and with important implications on crop improvement - we propose to focus on one of the simplest plant structure, the leaf. Grasping the mechanisms regulating leaf development will require the understanding of the regulatory logic of CUP-SHAPED COTYLEDON (CUCs), which are master regulators of leaf shape. This fundamental research project will use a highly integrative approach combining molecular, genetic and computational approaches to gather information relative to GRN controlling leaf serration. Such a multi-disciplinary approach will allow us to define the GRN controlling leaf margins at the molecular level, and use these data to generate a high-resolution model of the GRN that control leaf morphology. The identification of new components in the leaf shape GRN and the generation of computational model of the regulatory interactions will strengthen current knowledge on leaf development and widen the perspective for crop improvement, having therefore a high impact in the area of growth and development.

Seed structure is central to modern agricultural production because it influences yield and nutrient composition. Flowering plants evolved a large spectrum of seed architectures through natural and human selection. Three major types of seed architectures have been characterized according to the volume ratios of embryo, endosperm, and the nucellus maternal tissue. Whereas the roles of endosperm and embryo have been partially elucidated, less is known about nucellus development which accumulates most of the nutrients in perispermic seeds. Economical interest in perispermic pseudocereals is growing exponentially with Amaranthus being considered the grain of the twenty-first century. The project aims at deciphering the molecular mechanisms underlying tissue and nutrient partitioning in Amaranthus perispermic seeds.

The plasma membrane (PM) and the plant cell wall (CW) form together an exocellular continuum that acts as a dynamic barrier against environmental threats. The properties of the PM and the plant CW have been studied independently for several decades but increasing evidence indicates that a continuous dialogue between the PM and the CW takes place with the intracellular machinery playing the role of conciliator. LOOPIN is a multidisciplinary project combining genetics, molecular biology, cell biology and glycochemistry that will answer the pending key research question: What molecular negotiations underlie the reciprocal regulation between the PM and the CW? The original strategy of LOOPIN is based on my recent breakthrough results which suggest that (i) it exists an amazing diversity of PM-derived oligosaccharides (OS-like) and CW-derived oligosaccharides (OS) (ii) and that OS and OS-like may act as sugar-encoded messengers allowing the CW and PM external leaflet to communicate and adjust the plant cell response according to the environmental conditions. The challenge is to crack the sugar code involved in regulating CW/PM integrities and to understand how it controls the development. The objectives are (i) Set up biochemical and cell biology approaches to investigate the role of OS and OS-like in the CW/PM interplay, (ii) Identify biological active OS and OS-like involved in the CW/PM interplay and (iii) Decrypt the signalling pathways they trigger by selected OS- and OS-like. The approach of LOOPIN is unprecedented and should revolutionize our vision of how plant cells regulate the dynamics of the exocellular continuum.

Nitrate (NO3-) is the main source of Nitrogen (N) for herbaceous plants. It also acts as a signal molecule regulating the expression of hundreds of genes, including actors of NO3- acquisition and primary metabolism pathways. This Primary Nitrate Response (PNR) has mainly been studied in Arabidopsis (Arabidopsis thaliana), leading to the identification of the transcription factors AtNLP6 (NIN-LIKE PROTEIN 6) and AtNLP7 as major regulators (Castaings et al., 2009; Konishi and Yanagisawa, 2013). The overexpression of AtNLP7 triggers an increased plant growth, via a stimulation of N and carbon assimilation (Yu et al., 2016), identifying the NLP family and the PNR as levers to improve the plant Nitrogen Use Efficiency (NUE) to obtain high crop yields under low N fertilization. The PNR mechanism appears partially conserved in other species, despite the identification of cereal specificities (He et al., 2015). Our preliminary results show a role of NLPs in regulating the PNR in Pooideaes, a monocotyledon subfamily that includes wheat (Triticum aestivum), barley (Hordeum vulgare) and Brachypodium (Brachypodium distachyon). We propose to decipher the PNR in Pooideae, using NLPs as entry point. Based on a comparative functional genomic study, we aim at acquiring fundamental knowledge on the regulatory mechanism. Precisely, we intend to identify regulated genes and pathways at a large scale, to pinpoint the role of NLP transcription factors in Pooideae and to dissect the molecular mechanistic of NLP functions. By comparing our data to knowledge obtained on Arabidopsis, we will gain insight into the conservation/divergence of the mechanism between species. We selected Brachypodium and barley as model species due to their sequenced diploid genomes and to the increasing amount of methods and resources available. European Union is the first producer of barley grains (40% of the world production), with France and Germany as leading countries (each representing 18% of the EU production), validating the choice of this crop. The choice of the non-domesticated species Brachypodium is instrumental to gain insight into the evolution between monocots and dicots and into the domestication of cereals. This reference species will also enable state-of-the-art molecular technics that would be hampered in other Pooideaes, and will speed-up the discovery process due to its short life cycle and its small stature. Orthologs of AtNLP6/7 were identified in barley and Brachypodium (HvNLP1, BdNLP6 and BdNLP7, respectively). We experimentally found that BdNLP6 and BdNLP7 are encoding 2 transcripts each, due to an alternative splicing event that has also been observed for ZmNLP6 (Burdo et al., 2014) and is predicted for HvNLP1. The alternative splicing leads to the truncation of PB1, a putative protein-protein interaction domain conserved in all plant NLPs. Theses alternative proteins suggests a specificity in cereals of the NLP-dependent mechanism. The PNR will be characterized using a comparative transcriptomic approach between our 3 species of interest, producing to our knowledge the first transcriptomic dataset on PNR in Pooideae. The conservation of function between our NLPs of interest will be deeply assessed by mutant analysis and inter-species complementation. Subsequently, the post-translational regulation of Pooideae NLPs, their target genes and the role of the alternative splicing will be identified. As far as we know we are the first group to undertake an extensive study of PNR and NLPs in Pooideaes. This starter project will be instrumental in stably establishing the young scientific coordinator as a leader in the field of NO3--response in cereals, and will stimulate international collaborations for subsequent projects. The fundamental knowledge produced in this study will be valuable for subsequent applied purposes.