The identification of small segments of chromosomes containing genes that control traits can improve the speed, efficiency and effectiveness of plant breeding. One method of identifying such segments is to look for correlations between DNA markers and traits. Typically, a marker is a short length of DNA with a known location on a chromosome. A strong correlation between marker and trait is an indication of a gene with an effect on the trait close to the marker. This process is typically carried out by searching for correlations among the progeny of a cross between two inbred parents. In such controlled crosses other factors affecting the genetic make-up of a population, such as migration, are eliminated. This minimises the occurrence of spurious correlations between markers and traits. This approach has two limitations. Firstly, marker-trait associations in bi-parental populations are not guaranteed to be important among the lines used by breeders. Secondly, correlations occur when marker and gene are quite a distance apart and these have little practical use. Ideally, the presence of a correlation should indicate that the marker is close to the gene. Plant breeders can then select for presence or absence of the marker, rather than selecting for the trait. This can be quicker and cheaper. Methods have been developed to overcome these limitations. One is to repeatedly cross individuals over successive generations before correlating markers and traits. These extra crosses cause thorough shuffling of genes coming from each of the parents, thereby improving the chance that marker-trait associations are only detected if the marker is very close to the gene. Such populations are called 'Advanced Intercrosses'. There is no requirement for an Advanced Intercross to have only two parents. Multiple parents can make the population more representative of the lines used by breeders. Multiparent Advanced Intercross (MAIC) populations take time to set up and more markers are required than usual. However, the cost of DNA markers is falling steadily. It is therefore important that MAIC populations are established now, to exploit cheaper marker systems as they become available. The work described in this proposal sets out to establish this resource for winter wheat. We shall set up two MAIC populations, one based on current elite lines and one based on older lines of historic importance. Within the time available, we shall also derive a set of inbred lines from the first generation of each population. These will be made available to all interested stakeholders. The use of these populations in very fine mapping is limited, but they will still allow location of genes with greater precision than possible with available alternatives. We have also identified two pre-existing highly outcrossed winter wheat populations. These have not been maintained under controlled conditions but are still likely to be of use as MAIC populations. We will generate 1000 lines from each of these populations to create a resource available immediately for very fine mapping. Although the theory behind the use of MAIC populations is understood, we need to confirm that it works in practice. For this purpose, we will use a system of cheap genetic markers called DArT (Digital Array Technology) to genotype (genetically fingerprint) samples of individuals and inbred lines. Using these data, we can check that the shuffling process occurs as expected and that the pre-existing populations can indeed be treated as if they were MAIC populations. Finally, we will use the DArT data to hunt for associations with the genes responsible for male sterility, present in the established outcrossing populations. The location of these genes in roughly known, but we shall refine it to provide a practical demonstration of the power of the MAIC. Locating this gene with greater precision will also help in the design and execution of future genetic experiments.

In the 20th century, agriculture has experienced major gains in productivity via homogenization and intensive use of input, two key components of the dominant model of agriculture in developed countries. This model is jeopardized by the awareness of rapid global change, increased environmental stochasticity and the need for greater sustainability of agriculture. A new paradigm is emerging, in which biodiversity and the mechanisms underlying its dynamics are considered assets for a sustainable agriculture relying more on ecological functions within agroecosystems. Crop genetic diversity should play an essential role in this context, as a key element contributing to agriculture multi-functionality and to the resilience of agroecosystems under rapid climate change and decreased chemical inputs. However, the use of genetic diversity within agroecosystems faces ecological, socio-economic, organizational and regulatory challenges. The main goal of the project is to better evaluate the possible roles of within-crop genetic diversity to reinforce the multi-functionality and resilience of cropping systems under global change. WHEATAMIX focuses on a major cereal, wheat, in a central area of production, the Paris basin. WHEATAMIX develops a highly multidisciplinary approach involving geneticists, agronomists, ecophysiologists, ecologists, economists, and management scientists, as well as key stakeholders (“Chambres d’Agriculture”, farmers). It is structured in four complementary work-packages: - WP1 will characterise key morphological/ecophysiological traits and genetic variability of wheat genotypes. We will examine the plastic response of these traits to plant-plant interactions and test how trait complementarity affects the performance of wheat genotypes in blends through experiments and modelling. - WP2 will quantify multiple ecosystem services provided by variety diversity within wheat fields: yield (including grain quality) and its stability, regulation of foliar diseases, insect pest and weed biocontrol, maintenance of soil fertility, along with biodiversity conservation. We will analyse trade-offs and synergies among ecosystem services, as well as links between particular baskets of services and bundles of traits of varieties. - WP3 will study the techno-economic interest of blends and associated baskets of services for -and their acceptability by- key stakeholders. We will explore the organisational and economic bases of blend choice by the wheat chain (from seed companies to millers), with a focus on the Paris basin. Existing lock-in to the use of associations of wheat varieties will be analysed. These 3 WPs will use common, complementary experimental approaches: i) individual plant phenotyping to characterize traits and their plasticity for 50 wheat varieties; ii) a main diversity experiment (65 100m2 wheat plots with 1, 2, 4 or 8 varieties, under low input) to quantify variety diversity effect on ecosystem services; iii) replicates of the same diversity experiment in 5 sites across France using smaller (7m2) plots, under low and high inputs, to test the robustness of wheat diversity under a wide range of environmental conditions; iv) a network of 50 farms, encompassing agro-climatic variability in the Paris basin, to compare the ecological and techno-economic performance of blends with that of monocultures, in direct link with key stakeholders. - WP4 will combine results from WP1-3 and mobilize key stakeholders to build scenarios of the development of wheat variety blends in the Paris Basin considering various future climatic and economic contexts. Opportunities offered by and impacts of the introduction of wheat variety blends in the Paris production basin will be assessed on the basis of these scenarios. A strategy for the dissemination of project results will also be implemented.

Global change has a critical effect on biological and socio-cultural diversity leading to a strong demand for the development of sustainable food-agro-ecosystem. In this context, a better understanding of these diversities in the bakery food chain would facilitate development of more sustenance in this food chain. Hence, the objectives of BAKERY are to provide a detailed description of biological and socio-cultural diversity to enable a better understanding of the interactions and services in an organic or low input “Wheat/Human/Sourdough” food-agro-ecosystem. The aim is to develop a pluridisciplinary and participatory research project aiming at (i) describing socio-cultural diversity of bakers’ practices and consumers’ representations, (ii) studying the effects of wheat varieties, terroir and bakers’ practices on the diversity of sourdough microbiome, sensorial and nutritional bread quality as well as consumers preferences, (iii) analyzing the nature of the sourdough microbial interaction (complementation or selection) and their consequence on the sourdough fermentation and bread quality, (iv) integrating all the data to find determinants of the biological and socio-cultural diversity in the bakery chain, and (v) propose strategies for the conservation of biological and socio-cultural diversity in bakery. We will survey 30 French bakers and farmers/bakers who make sourdough breads, using flours resulting from agro ecological practices and distribute their production locally. Information on bakers’ practices as well as wheat seeds’ origin (for baker/farmers), flour, sourdough and bread samples will be collected. In addition we will interview thoroughly a total of thirty consumers of some of the surveyed bakers. The wheat seeds, flour and sourdough microbiome will be analyzed using metagenomic pyrosequencing and phylogeny analysis of rDNA loci. Biochemical characterization as well as sensorial analysis will be performed for sourdoughs and breads. This will delineate sourdough biodiversity, bread quality, and also the diversity of baker practices and consumer representation and implementing an integrated database. Simultaneaously taking advantage of previous works of the project partners on participative wheat breeding, we will use control experiments for analyzing the effect of terroir, of bread wheat varieties (ancient vs modern) and bakers’ practices on the sourdough microbiome and bread quality. Furthermore, we will study the sourdough microbial interaction by analyzing fermentation and population dynamic in reconstituted communities composed of lactic acid bacteria and yeast species. This approach will allow the characterization of the nature of the microbial species interaction (ecological facilitation or selection) and their consequences on the sourdoughs services (dough characteristics and bread quality). Thus, the analysis of these controlled experiments will provide candidate determinants of the diversity in “Wheat/Human/Sourdough” food-agro-ecosystem. The BAKERY project will allow us: (i) to increase our knowledge on the diversity of bakers’ and farmers/bakers’ practices and consumer representation of sourdough breads, (ii) to characterize and to conserve the microbial diversity of French sourdoughs, (iii) to better understand the impact of different determinants on the biodiversity and functioning of the “wheat/Human/Sourdough” food-agro-ecosystems, (iv) to think about the complementarity of ex situ and in situ conservation of wheat and microbial genetic resources and (v) to identify action promoting sustainable bread making practices. This ambitious project is based on the integration of innovative approaches and advanced tools (participatory research, pluridisciplinary interactions, mathematical modeling, post-genomic data) and will benefit from the strong complementarity between partners.

Climate changes are rapidly modifying the biotic and abiotic environment of cultivated crops. Fast adaptation of crops is therefore necessary to sustain human demand particularly in developing countries. Cereal crops are the major source of food calories worldwide. While maize is the first cereal crop in terms of production, pearl millet produced in the driest environment on earth is a staple crop in Africa and India. Both crops, like most cereals, have undergone genetic bottlenecks as a consequence of domestication and subsequent improvement. Hence, part of the adaptive cryptic variability in their wild progenitors, Zea mays ssp. parviglumis and P. glaucum spp. monodii respectively, has been lost. AdaptInWild proposes to explore the wild reservoir of both crops and evaluate its potential as a contributor to future breeding efforts. The proposed project thus aims at gaining a better understanding of the genetic and epigenetic bases of plant adaptation. We have collected original material along two altitudinal and two humidity gradients in wild maize and pearl millet, respectively. Those gradients mimic slight and continuous climate variation. We will use wild populations sampled along those gradients to undertake an integrative approach revealing the various facets of plant adaptation: natural selection of nucleotide and structural variants, transcriptomic variations (both coding and non-coding), and epigenetic responses to environmental changes. The proposed project is articulated around 4 interconnected main scientific tasks, that will collectively provide an holistic view of adaptive forces. The first task will combine Next Generation Sequencing (NGS) of pooled individuals sampled in two most ‘extreme’ populations of each environmental gradient (2 gradients per species) and Illumina VeraCode genotyping of intermediate populations, i.e. populations located in between the two most ‘extremes’. It will identify candidate adaptive sequence polymorphism (SNPs), and candidate adaptive insertion of Transposable Elements (TE indels). The second task will assess transcriptome and non-coding small RNA variation in each species between 4 parents sampled in the most ‘extreme’ populations and their F1 hybrid progenies. It will address the question of cis versus trans regulation of gene expression, i.e. percentage of cis-regulated genes among selected genes versus genome-wide expectation, as well as paternal and maternal effects. The third task will investigate the immediate epigenetic response of adapted genotypes to environmental changes, and the relationship between the genomic and epigenomic levels in short-term adaptation. For this, we will apply an environmental swap between individuals sampled in the most ‘extreme’ populations and follow their response in term of genome-wide epigenetic remodelling of histones and DNA methylation. The fourth task will establish, using an association mapping framework, a link between sequence variation (SNPs and TE indels) and phenotypic variation at multiple agronomic or adaptive traits measured in the field. AdaptInWild is an innovative project that will make use of the most recent NGS technologies, develop some new experimental and statistical tools to investigate the adaptive variation of the wild gene pools of two cereal crops. By exploring diverse sources of genomic variation, from mutations to epimutations, and linking genotype to phenotype, it will contribute to greatly enhance our knowledge of plant adaptation to environmental changes and also bring more applied insights on the use and conservation of wild genetic resources. In addition, the project will create a long-lasting collaboration opportunity between two partners, the UMR GV at Gif-sur-Yvette (P1) and the UMR DIADE at the Institut de la Recherche pour le Développement in Montpellier (P2) and sustain the training of several students.