BrasExplor - Wide exploration of genetic diversity in Brassica species for sustainable crop production

The main problem in the context of climatic changes is to develop varieties adapted to the future variations of climate in the different countries of the Mediterranean basin. The project relies on the hypothesis that environmental conditions have driven the genetic diversity of both wild and cultivated populations. From an unexplored diversity of both species economically important, cabbages and turnips, we propose to look for correlations between environmental variation and plant morphological, physiological, developmental and molecular diversity. From these data, we will try to identify traits underlying adaptation and to characterize the genetic architecture of adaptation to climate and soil variation (both edaphic and biotic variations), urgently needed to develop plant species breeds more adapted to fluctuating environments. We propose to use different high throughput technologies for sequencing and phenotyping. The partner skills will allow investigation of the physiological response of B. rapa and B. oleracea to warm and cold temperatures and to water stress under controlled at different developmental stages which will be compared to results obtained under field conditions. Results from such analyses will be interpreted in regards to the geographic origin of the populations. An original feature of our project is the multi-disciplinary approach we propose to apply. Indeed, to tackle our objectives, the proposed project will combine botanical and biogeographical approaches, agronomy, population and quantitative genetics as well as genomic approaches, ecology and physiology. In addition, several partners will work in close interaction with farmers and stakeholders during the project. This should facilitate the promotion of local varieties and the development of prebreeding populations from the new adaptive diversity identified in the frame of BrasExplor. The proposed project is also an opportunity to preserve new genetic resources and to open the European market to original morphotypes of local landraces, which start to disappear in several countries.

WP1: Collects ~100 populations of wild populations and local landraces per species with precise descriptors for each population, along the climatic gradient in the different countries from North of France to Saharan regions. Climate variables for each location will be extracted from the public databases WorldClim (https://www.worldclim.org/) allowing description of contemporary climatic conditions. In order to remove maternal effect among the Brassica populations, wild populations and local landraces will be propagated in the same location and under homogenous conditions before sending seeds to all partners. WP2: DNA of each population will be sequenced (x10) from a bulk of 30 plants/populations. After alignment of DNA sequence on reference genome for each species, SNP (Single Nucleotide Polymorphism) will be identified for population structuration, identification of core collection for each species and Genome-environment association (GEA) analyses for identifying significant associations between genetic polymorphisms and environmental variables WP3: On all the populations propagated, we will assess germination under stress conditions, analysis of plants growth under cold temperature, plant growth under field experiment, with microbiota analysis in relation with plant diversity. On core collections, we will analyze plant growth under warm temperature with deep phenotyping of root architecture and of flowering parameters, self-incompatibility and morphological and eco-physiological traits under field conditions in the different countries. WP4: We will experiment local varieties in the different countries for characterization and demonstration to farmers and consumers and build by crosses prebreeding populations WP5: Organization of interplays between partners, of sharing documents, protocols, data and metadata through Virtual Environment for Research (VER), of interplays between partners and Ministry in charge of material diffusion, of communication on the project (web site, communications…) and of student or scientist formation.

The major impact of the project will be the preservation of natural and local resources and optimization of the use of this diversity in the context of global change for Brassica vegetables. The detailed assessment of local landraces will allow (i) the preservation of endangered varieties, (ii) the development of niche market appropriate to small-scale farming systems from well-adapted varieties corresponding to local uses. It is expected that this collaborative work will highlight the interest for specific varieties that are associated with the Mediterranean diet. They will be presented to farmers and consumers with publication of adapted cooking recipes book. They will be deposited in Genetic Resource Centers (BrACySol in France, KIS in Slovenia) following the international protocols. From the data obtained, we will build core-collections for both species maximizing allelic and adaptive diversity. These collections will be tested in the different countries offering the opportunity to identify the most relevant diversity in each environment for further uses. The identification of soil microbiota-plant interaction genetic bases will allow in perspective studies to: i) select for microbial communities protecting Brassica species to environmental fluctuations or extreme conditions, ii) breed new varieties with the ability to select for beneficial bacterial responsible for the uptake of key-nutrients and helping plants to adapt to climate change. Sequencing of each population and identification of genomic regions involved in the response to different abiotic stresses will open the avenue for new breeding strategies through marker-assisted selection. Communication (website, twitter, meetings…) of the results will be presented to the different actors, breeders, farmers, consumers in addition to the scientific community. Academic formation will be proposed to students.