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Understanding microbial dispersal is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about their vectors of migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal along the sourdoughs bread-making chain using a participatory research approach. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analysed the potential of wheat grains and flour to serve as an inoculum for sourdough microbial communities using 16S rDNA and ITS1 metabarcoding. First, in an experiment involving farmers, a miller and bakers, we followed the microbiota from grains to newly initiated and propagated sourdoughs. Second, we compared the microbiota of 46 sourdough samples collected everywhere in France, and of the flour used for their back-slopping. The core microbiota detected on the seeds, in the flour and in the sourdough was composed mainly of microbes known to be associated with plants and not living in sourdoughs. No sourdough yeast species were detected on grains and flours. Sourdough lactic acid bacteria were rarely found in flour. When they were, they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. However, the low sequencing depth for bacteria in flour did not allow us to draw definitive conclusion. Thus, our results showed that sourdough yeasts did not come from flour, and suggest that neither do sourdough LAB.

Modern plant breeding and agrosystems artificialization could have altered plants’ ability to filter and recruit beneficial microorganisms in its microbiota. Thus, compared to modern cultivars, we hypothesized that root‐endosphere microbiota in modern wheat cultivars are less resistant to colonization by fungi and bacteria and thus more susceptible to also recruit more pathogens. We used an in‐field experimental design including six wheat varieties (three ancient vs. three modern) grown in monoculture and in mixture (three replicates each). Endospheric microbiota of wheat roots were analyzed on four individuals sampled randomly in each plot. Composition‐based clustering of sequences was then characterized from amplicon mass‐sequencing. We show that the bacterial and fungal microbiota composition in wheat roots differed between ancient and modern wheat cultivar categories. However, the responses observed varied with the group considered. Modern cultivars harbored higher richness of bacterial and fungal pathogens than ancient cultivars. Both cultivar types displayed specific indicator species. A synergistic effect was identified in mixtures of modern cultivars with a higher root endospheric mycobiota richness than expected from a null model. The present study shows the effect of plant breeding on the microbiota associated plant roots. The results call for making a diagnosis of the cultivar's endospheric‐microbiota composition. These new results also suggest the importance of a holobiont‐vision while considering plant selection in crops and call for better integration of symbiosis in the development of next‐generation agricultural practices.

International audience; Microorganisms associated with plants are determinant for their fitness, but also in the case of vine grapes, for the quality and quantity of the wine. Plant microbiota is, however highly variable in space despite deterministic recruitment from the soil reservoir. Therefore, understanding the drivers that shape this microbiota is a key issue. Most studies that have analysed microorganisms associated with vines have been conducted at large scales (e.g., over 100 km) and have analysed the bulk soil and the rhizosphere. In this study, we focused on the root-microbiota endosphere, the most intimate fraction of microorganisms associated with plants. We sampled vine roots in 37 fields distributed throughout a vineyard to investigate drivers shaping the grapevine microbiota at the alpha-(i.e., within-field) and gamma-(i.e., between-field) diversity scales. We demonstrated that vine endospheric microbiota differed according to both the edaphic and plant-specific parameters including cultivar type and age. This work supports the idea of an existing microbial terroir occurring within a domain and offers a new perspective for winemakers to include the microbial terroir in their management practices.

Presentation of Carrot and Buckwheat tasting

Cauliflower and Cabbage participatory breeding in Brittany

EnglishBy exploring the case of an association of artisanal seed producers, Les Croqueurs de Carottes, this paper sheds light on how these stakeholders interconnect management of crop biodiversity and governance of plant health. Faced with European phytosanitary regulations that prohibit the sale of bean seeds carrying “quarantine pests”, these artisanal seed producers defend their practices, which consist of “living with” diseases by regarding them as an integral part of the production process. Through their efforts to gain recognition for their methods and acceptance of plant diseases, they are not only promoting their management practices, but are also building and asserting their professional identity. francaisEn se saisissant du cas d'une association d'artisans semenciers, les Croqueurs de carottes, cet article a pour objectif d’eclairer l'articulation entre gestion de la biodiversite cultivee et gouvernance de la sante des plantes par ces acteurs. Face a un reglement phytosanitaire europeen interdisant la commercialisation de semences de haricot porteuses d’un « organisme de quarantaine », les artisans semenciers defendent leurs pratiques qui consistent a « vivre avec » les maladies en les considerant comme partie integrante de leur systeme de production. Par leurs efforts pour faire reconnaitre leurs modes d’attachement aux maladies des plantes, ils ne font pas seulement valoir leurs pratiques de gestion, mais construisent et defendent aussi leur identite professionnelle.

Managing complexity within agro ecological systems requires new research organization, such as action or participatory researches. The integration of empirical knowledge remains a challenge for such approaches and should ease the understanding of complex issues and the formulation of new hypothesis. The case study of the quality management of hand-made breads in the farmer-baker sector offers relevant conditions for methodological studies, since empirical knowledge has developed through individual experiments. In this paper, empirical knowledge was gathered from 11 grain farmers (farmer-bakers) via semi-structured interviews aiming at identifying breeding strategies linked to end-use quality. In parallel, morphological and sensory characterization of some farmers' wheat was then used to validate the patterns identified in the interviews. The interviews identified three breeding strategies related to end-use quality: the genetic diversity to stabilize performance, the typicality strategy to differentiate bread and the genetic adaptation by growing landraces. To help breeding, quality markers as dark kernel color or awns presence should be relevant. Those phenotypes show specific aromas, such as the roasted flavor, during sensory property evaluations. Our approach connected objective data with qualitative data from interviews related to practices and cultural values. This last point is of importance as non-measurable variables such as human values should impact significantly farmers' strategies. These results will help to better connect both forms of knowledge required for participatory approaches by integrating empirical and scientific knowledge so as to implement experiments and to analyze complex issues.

Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces.

International audience; Organic and low-input food systems are emerging worldwide in answer to the sustainability crisis of the conventional agri-food sector. Alternative systems are based on local, decentralized approaches to production and processing, regarding quality and health, and short supply-chains for products with strong local identities. Diversity is deeply embedded in these food systems, from the agrobiodiversity grown in farmers' fields, which improves resilience and adaptation, to diverse approaches, contexts and actors in food manufacturing and marketing. Diversity thus becomes a cross-sectoral issue which acknowledges consumers' demand for healthy products. In the framework of the European project CERERE, CEreal REnaissance in Rural Europe: embedding diversity in organic and low-input food systems, the paper aims at reviewing recent research on alternative and sustainable food systems by adopting an innovative and participatory multi-actor approach; this has involved ten practitioners and twenty-two researchers from across Europe and a variety of technical backgrounds in the paper and analysis stages. The participatory approach is the main innovation and distinctive feature of this literature review. Partners selected indeed what they perceived as most relevant in order to facilitate a transition towards more sustainable and diversity based cereal systems and food chains. This includes issues related to alternative food networks, formal and informal institutional settings, grass root initiatives, consumer involvement and, finally, knowledge exchange and sustainability. The review provides an overview of recent research that is relevant to CERERE partners as well as to anyone interested in alternative and sustainable food systems. The main objective of this paper was indeed to present a narrative of studies, which can form the foundation for future applied research to promote alternative methods of cereal production in Europe.

The “transfer of technology”, typical of a top-down linear process of innovation cannot be used in the new contexts of sustainability, characterised by uncertainty and complexity. There is a need to redefine categories and concepts around which innovation and agricultural policies are built, as those currently in use provide only a partial representation of reality. Innovation paradigms underpinning technological development and public policies design will have a direct impact on decisions regarding which agricultural models will ultimately be supported. Looking at local learning capacity and systems of relations can help to understand the potential to develop innovation within a specific context. This work contributes to the definition of new actors who are developing innovation for sustainability in rural areas. The study focuses on the knowledge systems of farmers who are applying alternative breeding strategies: it uses a network approach to explore the knowledge system in which individual farmers are embedded in order to understand their specific relational features. Three main conclusions emerge from the study: for enhancing the agro-ecological innovation paradigm there is a need to define the ‘innovation broker’, to revise the evaluation system of public research and to integrate innovation and agricultural policies.

OPVs (open pollinated varieties) of cross pollinated crops are genetically heterogeneous and therefore likely to evolve over generations, under natural and human selection, which gives them a strong potential for organic and low input farming. OPVs of maize were cultivated and selected by different farmers in France and Italy for 2 generations. The third year, they were phenotypically evaluated for evolution, adaptation and level of diversity (estimated with Nei index) across evolution in a combined on farm and on station experimentation. The results showed that the varieties evolved and even adapted over 2 generations only (especially on maturity traits) but conserved their identity (no evolution of ear morphological traits). They all conserved their diversity, which demonstrated the pertinence of farmers’ selection (it is not a bottleneck). These results suggested that the genetically heterogeneous nature of OPVs is an asset for farmers because they can adapt these varieties to specific local conditions and production objectives. Therefore, farmer OPVs should receive more support through social and regulatory recognition, as well as further interest from research.

Recognizing both the stakes of traditional European common bean diversity and the role farmers' and gardeners' networks play in maintaining this diversity, the present study examines the role that local adaptation plays for the management of common bean diversity in situ. To the purpose, four historical bean varieties and one modern control were multiplied on two organic farms for three growing seasons. The fifteen resulting populations, the initial ones and two populations of each variety obtained after the three years of multiplication, were then grown in a common garden. Twenty-two Simple Sequence Repeat (SSR) markers and 13 phenotypic traits were assessed. In total, 68.2% of tested markers were polymorphic and a total of 66 different alleles were identified. F-ST analysis showed that the genetic composition of two varieties multiplied in different environments changed. At the phenotypic level, differences were observed in flowering date and leaf length. Results indicate that three years of multiplication suffice for local adaptation to occur. The spatial dynamics of genetic and phenotypic bean diversity imply that the maintenance of diversity should be considered at the scale of the network, rather than individual farms and gardens. The microevolution of bean populations within networks of gardens and farms emerges as a research perspective.

Site web Techniques de l'ingénieur - Ressources documentaires - Innovation - Éco-conception et innovation responsable; National audience; Organic farming is growing apace, but little research is specifically dedicated to it in France. The organic approach unites a range of different concepts in an agricultural context dominated by conventional farming and a policy of "agro-ecological transition". Cultivated biodiversity has shrunk by intensification of agriculture for a century, yet is key to the performance of organic systems founded on respect for, and optimization of, natural processes. To overcome the lack of well-adapted, diverse varieties, a collaboration with organic farmers was initiated. This paper describes the experience of these professional ”Engineers of Life", and how their activities have evolved, with a look at local food systems and their stakeholders through a transdisciplinary, multi-actor approach.; L'agriculture biologique connaît un fort développement mais peu de recherches lui sont dédiées en France. La notion d'agriculture biologique regroupe des conceptions très diverses dans un contexte d'agriculture conventionnelle dominante et d'une politique de « transition agroécologique ». La biodiversité cultivée, réduite par l'intensification de l'agriculture, est la clé de la performance des agrosystèmes « bio » basés sur le respect et la maximisation des processus vitaux. Pour pallier le manque de variétés adaptées et diversifiées, une collaboration avec les paysans « bio » a été initiée. Cet article présente les expériences et les évolutions du métier d'«ingénieur du vivant » élargi aux systèmes alimentaires locaux et leurs acteurs, avec une approche transdisciplinaire et multi-acteurs.

In this study, we used LCA to test the influence of practicing low-input farming, on-farm processing and direct distribution on the environmental impact of bread consumption. Primary data were collected from four commercially active producers (two in France, one in Italy and one in Portugal) who cultivate cereals under low levels of inputs, process grains on farm and distribute their products directly to end consumers. Environmental impacts of products were compared to equivalents from supermarkets, characterised by higher rates of applied inputs at the agricultural stage, industrial processing and centralised distribution. The scope of LCA was from cradle to the consumer. The study revealed a high variability of results between individual cases. At the agricultural stage, products from a low-input cropping system integrated with livestock production in France and from a small-scale labour intensive production in Portugal showed similar or better performance on most impact categories to those from high-input agriculture, while horse farming in France and a stockless cultivation of ancient wheat cultivars in Italy revealed mostly higher environmental burdens. Decentralised processing and distribution in France had similar or slightly higher impacts to conventional supply chains, while Italian and Portuguese cases revealed clearly higher environmental burdens for most impact categories. Results demonstrate that while there might be a positive relationship between the scale and eco-efficiency of processing and distribution, the level of agricultural inputs, yields and transport distances cannot be used as proxies of environmental performance. Products of low-input systems can have much higher, similar or lower impacts to their high-input counterparts due to the influence of site conditions and the management. More research assessing the effectiveness of context-specific management systems is needed as oppose to the generic comparisons between labelling schemes (i.e. organic and conventional farming). (C) 2014 Elsevier Ltd. All rights reserved.

Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces.

The lack of seeds and varieties suited to organic agriculture has been a problem for a long time. Conventional breeding strategies do not fit the needs of organic agriculture, which requires specific adaptation to the environment. Moreover, several current breeding methods do not respect the principles of organic agriculture. To overcome these limitations, organic farmers and their organisations initiated participatory plant breeding (PPB) programmes, together with researchers.

All organic agricultural systems suffer from a lack of plant cultivars adapted to organic production. Within the framework of the European project SOLIBAM (Strategies for Organic and Low Input Breeding and Management) a study was undertaken to determine which cultivars farmers grow, why they grow them, and the expectations in plant breeding of organic stakeholders. A comprehensive range of investigations carried out between 2010 and 2012 provided information on the state of organic seed in France. Results fit with the hypothesis that the market is a significant factor influencing the choice of seeds and cultivars (local cultivars, landraces, modern cultivars). Expectations and practices of producers selling on a local market (i.e., direct sale) differ radically from those of producers selling to long food supply chains. This study shows that the availability and use of organic seeds have significantly improved over the last three years. A vast majority of organic producers willingly use organic seeds, with, on average, 45-70% (cereals) and 75%-100% (vegetables) of organic seeds being planted on farms. However, the total number of derogations remains quite high: there is still space for improvement in organic seed use and supply in France. Several limiting factors and levers were identified during the study, as well as farmers' expectations for the future on horticultural crops. The case study on tomatoes states the differences between producers selling on a local market and those of producers selling in long food supply chains regarding their practices (open field vs greenhouses) and the kind of cultivar they use or wish to have.

Section 1: General Topics Related to Organic Plant Breeding. Chapter 8; The developments of plant breeding and the emergence of seed laws in Europe and in USA Variety registration: origin, history and procedures (DUS and VCU) Seed quality control and certification: Rules for truth-in-labelling in USA; Operation of seed quality control and certification Special needs for Organic Agriculture: VCU testing in organic context; DUS testing in organic context; Organic seed market and the current rules; Evolution of seed standards in Europe. A recent development in Europe: conservation varieties: EU-rules on ‘Conservation Varieties’; Quality control, production and marketing Intellectual Property Rights and plant breeding: historical origin, Breeder’s Rights from Europe to the USA, Plant breeders rights and organic agriculture Discussion : EU and US comparison; Organic farming, seed policy and agricultural biodiversity

Because of the lack of varieties for organic agriculture, associations of organic farmers in several European countries have begun cultivating landraces and historic varieties, effectively practicing in situ conservation of agricultural biodiversity. To promote agrobiodiversity conservation, a special list for ‘‘conservation varieties’’ was implemented in 2008 by the EU because for any exchange and marketing of seeds in the EU, a variety must be registered in an official catalog. Our study aimed at improving knowledge on the phenotypic diversity and evolution of such varieties when cultivated on organic farms in Europe, in order to better define their specific characteristics and the implications for the registration process. We assessed multi-trait phenotypic evolution in eight European landraces and historic varieties of bread wheat and in two pureline variety checks, each grown by eight organic farmers over 2 years and then evaluated in a common garde experiment at an organic research farm. Measurements on each farmer’s version of each variety included several standard evaluation criteria for assessing distinctness, uniformity and stability for variety registration. Significant phenotypic differentiation was found among farmers’ versions of each variety. Some varieties showed considerable variation among versions while others showed fewer phenotypic changes, even in comparison to the two checks. Although farmers’ variety would not satisfy uniformity or stability criteria as defined in the catalog evaluation requirements, each variety remained distinct when assessed using multivariate analysis. The amount of differentiation may be related to the initial genetic diversity within landraces and historic varieties.

The importance of genetic diversity in cultivated varieties for organic and low-input agriculture has attracted increasing attention in recent years, with a need to identify relevant sources of diversity and strategies for incorporating diversity in plant breeding for organic systems. However, the regulatory system in many countries, particularly in the European Union, restricts the varieties available to farmers to those registered in an official catalogue, and most countries require varieties to go through official tests under conventional management, which has resulted in a lack of suitable varieties available to organic farmers. This study characterized a sample of wheat (Triticum aestivum L.) landraces, historic varieties and varietal mixtures currently of interest to organic farmers in a diverse range of organic conditions on farms in Italy, France and the Netherlands. These varieties were assessed for individual plant and spike characteristics and compared to modern registered wheat varieties grown under the same on-farm conditions. Significant differences in mean values were found among varieties for many plant and spike traits, as well as significant variety-by-environment interactions. There were often similar levels of intra-varietal variability between farmer and modern varieties, indicating that the strong selection for genetic homogeneity to meet regulatory criteria has little impact on the phenotypic variability of certain traits when assessed on-farm. Several farmer varieties had high values of traits related to productivity outside their region of origin, which underlines the need for experimentation with diverse types of varieties in order to find and develop appropriate varieties for organic systems.

Organic and low-input agriculture needs flexible varieties that can buffer environmental stress and adapt to the needs of farmers. We implemented an experiment to investigate the evolutionary capacities of a sample of spinach ( Spinacia oleracea L.) population varieties for a number of phenotypic traits. Three farmers cultivated, selected and multiplied one or several populations over two years on their farms. The third year, the versions of the varieties cultivated and selected by the different farmers were compared to the original seed lots they had been given. After two cycles of cultivation and on-farm mass selection, all the observed varieties showed significant phenotypic changes (differences between the original version and the version cultivated by farmers) for morphological and phenological traits. When the divergence among versions within varieties was studied, the results show that the varieties conserved their identity, except for one variety, which evolved in such a way that it may now be considered two different varieties. The heterogeneity of the population varieties was assessed in comparison with a commercial F1 hybrid used as control, and we found no specific differences in phenotypic diversity between the hybrid and population varieties. The phenotypic changes shown by the population varieties in response to on-farm cultivation and selection could be useful for the development of specific adaptation. These results call into question the current European seed legislation and the requirements of phenotypic stability for conservation varieties.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; Aberrant phenotypes of cauliflower were detected throughout the cultivation period and in any variety type. The rate of these phenotypes in the field has recently increased. We reported previously on the first part of our results which showed that (1) the rate of aberrant plants varied with genotype and cultivation area, (2) the aberrant phenotypes can evolve or reverse to normality during the plant cycle and (3) the capacity to express a variant phenotype can be transmitted to the progeny. An epigenetic hypothesis has been proposed to explain the determinism of the phenomenon. Further investigation on the "aberrant" character focussed on the flow cytometric estimation of ploidy levels and on the parallel observation of meiosis. Only a fraction of aberrant plants did show aneuploidy and various plo < dy levels were found for the same phenotype. Indeed, aneuploidy could not be related to the aberrant phenotype although it could probably be a consequence of the aberration phenomenon. HPLC analysis of global DNA methylation rates showed that DNA hypermethylation occurred in plants which exhibited an evolution of their phenotype during vegetative cycle. The epigenetic origin of aberrant phenotypes in cauliflower is discussed with reference to epigenetic diseases described in human beings.

Self-incompatibility (SI) is thought to have played a key role in the evolution of species as it promotes their outcrossing through the recognition and rejection of self-pollen grains. In most species, SI is under the control of a complex, multiallelic S-locus. The recognition system is associated with quantitative variations of the strength of the SI reaction; the origin of these variations is still not elucidated. To define the genetic regulations involved, we studied the variability of the SI response in homozygous S 15 S 15 plants in cauliflower. These plants were obtained from a self-progeny of a self-compatible (SC) plant heterozygous for S 15 , which was generated after five selfing generations from one strongly self-incompatible initial plant. We found a continuous phenotypic variation for SI response in the offspring plants homozygous for the S 15 haplotype, from the strict SI reaction to self-compatibility, with a great proportion of the plants being partially self-compatible (PSC). Decrease in SI levels was also observed during the life of the flower. The number of pollen tubes passing through the stigma barrier was higher when counted 3 or 5 days after pollination than one day after pollination. Analysis of the expression of the two key genes regulating self-pollen recognition in cauliflower, the S-locus receptor kinase (SRK) and S-locus cysteine-rich (SCR/SP11) genes, revealed that self-compatibility or PSC was associated with decreased SRK or SCR/SP11 expression. Our work shows the particularly high level of phenotypic plasticity of the SI response associated with certain S-haplotypes in cauliflower.

The myth of technological progress in agriculture and then modern plant breeding have resulted in a separation of farming from breeding activities. Seed laws have also contributed to this outcome (e.g. by imposing strict rules for the entry of varieties in the official catalogue). Nowadays, some pioneers, among them farmers rejecting industrialized agriculture and more often practising organic agriculture, are proposing a different option. In Europe, since the beginning of this century, they have been organizing themselves in networks: the Réseau Semences Paysannes in France, the Red de Semillas in Spain and the Rete Semi Rurali in Italy. Their members are farmers, consumers and scientists working together in order to reconsider the scientific, technical and legal aspects of seed production. These new varieties are designated ‘peasant varieties’, a concept that encompasses two main aspects: the seed, the reproductive part of the plant linked to its terroir, and the variety, shaped by history and coevolved with farmers. Scientists working with these networks are developing participatory plant breeding projects, which aim to broaden agrobiodiversity by creating so called new peasant varieties. The basis of these projects comes from old local varieties and landraces conserved in seed banks. In Europe, the legal framework has evolved since the establishment of ‘conservation varieties’ by directive 98/95. The European research project Farm Seed Opportunities is under way to support new seed policies, in the light also of the different national contexts. The debate in Europe now offers a range of seed systems models. It is time to enlarge this debate to southern countries through the sharing of knowledge between farmers of the North and the South, aiming at conserving agrobiodiversity and promoting rural innovation.

Plant breeding for organic agriculture (OA) was stimulated when it came under the European Organic Agriculture Regulation (2092/91) in 2004. In Brittany, the need for specific varieties for organic farming arose early for the Brassica species because of the unsuitability of most of the modern varieties to the principles of OA. Moreover, the private sector of plant breeding finds it economically difficult to satisfy the demands of OA. The aim of the present study is to provide varieties and seed for organic farmers for two vegetable Brassica crops, and to show how genetic resources can contribute to this purpose in the framework of a Participatory Plant Breeding (PPB) programme. The emergence of PPB in Brittany is the result of several concomitant and favourable circumstances: the will of the professionals (represented by IBB, Inter Bio Bretagne), their organization (an experimental station, the PAIS, Plateforme Agrobiologique d’IBB à Suscinio), the research initiative in INRA and the availability of genetic resources. From genetic resource observations, our experience showed several breeding situations: reviving a traditional activity (Roscoff cauliflower and local cabbages), extending tradition (autumn cauliflower), diversifying production by new introductions (coloured cauliflowers), and creating new forms of population varieties (broccoli and coloured cauliflowers). Farmers have taken charge of population breeding by mass selection and the PAIS, with INRA scientific support, has taken up innovative selection and the improvement of varieties completing the farmers’ initiatives. The PAIS remained the central point for information and for providing the seed for trials. Seed production will be managed in a collective way. Until now, the exchange of seed remained an experimental dimension of PPB. French seed legislation represents a limitation on the development of seed exchange by PPB.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; For more than a decade, the number of "aberrant plants" showing various developmental abnormalities in cultivated cauliflowers has dramatically increased, thus hampering the registration of new varieties in some cases. The aberrant phenotype occurred during the cultivation period and in any variety type (pure line or F1 hybrid). The number of aberrant plants increased considerably from 1994 onwards. The rate of aberrant plants observed among F1 hybrids in the field was found to vary according to genotype and cultivation area. Besides morphological changes, aberrant phenotypes showed various patterns of evolution, i.e. stable, evolving toward another phenotype or reversing toward normality. Vegetative and seed progenies were obtained in order to investigate the genetic control of these phenotypic variations. Given that the aberrant phenotypes can evolve towards either normality or another abnormality during the life cycle of the plant and that the aberration capacity and/or the "acquired morphological disorder" can be transmitted to the progeny, an epigenetic hypothesis has been proposed for the determinism of this phenomenon.

The holobiont concept considers the functional unit composed of plants and these microorganisms. It promotes a holistic approach to crop management and, more generally, to the vision of macroorganisms. However, this concept is subject to debate due to the lack of experimental evidence of its existence. Moreover, a better understanding of the mechanisms governing the assembly of microbial communities associated with plants remains one of the major challenges of microbial ecology and agriculture. The overall objective of this thesis was to test the validity of the concept of holobiont, to study the factors that impact the assembly of root-endosphere microbial communities and to analyze the intra- and inter-annual dynamics of the grapevine microbiota. Thanks to an experiment set up in association with a vine nursery (grafting and chimeric plants), we demonstrated the existence of an active and determined recruitment of microorganisms by the plant, under the dominant effect of the rootstock, which allowed us to increase the experimental evidence for the existence of the holobiont concept. In a second part, thanks to a large sampling design set up in a single vineyard, we investigated the dynamics of grapevine microbiota assembly. We highlighted the fundamental role of environmental factors, age and grape variety (cultivar) in the assembly of the root-endosphere microbiota of grapevine on a small geographical scale and evidence of clear intra- annual temporal patterns in the structuring of these communities. This thesis provides a body of new knowledge in the field of microbial ecology, supports the existence of the microbial terroir and underlines the importance of taking this microbial terroir into account in the context of sustainable vineyard management., Le concept d’holobionte considère l’unité fonctionnelle composée des plantes et de ces microorganismes. Il promeut une approche holistique à la gestion des cultures et, plus généralement, à la vision du vivant. Cependant, ce concept est sujet à débat en raison du manque de preuves expérimentales de son existence. De plus, la compréhension fine des mécanismes régissant l’assemblage des microorganismes associés aux plantes reste un des enjeux majeurs de l’écologie microbienne et de l’agriculture. Le but de cette thèse était de tester la validité du concept d’holobionte, d’étudier les facteurs qui impactent l’assemblage des communautés microbiennes de l’endosphère racinaire et d’analyser la dynamique intra- et inter-annuelle du microbiote de la vigne. Grâce à une expérimentation mise en place en association avec une pépinière viticole (greffage et plantes chimériques), nous avons pu démontrer l’existence d’un recrutement actif et déterminé de microorganismes par la plante, sous l’effet dominant du porte-greffe, ce qui nous a permis d’augmenter les preuves expérimentales à l’existence du concept d’holobionte. Dans le cadre d’une seconde partie, nous nous sommes intéressés aux dynamiques d’assemblages du microbiote de la vigne, grâce à un vaste plan d’échantillonnage mis en place au sein d’un domaine viticole. Nous avons mis en avant le rôle fondamental des facteurs environnementaux, de l’âge et du cépage dans l’assemblage du microbiote endosphérique racinaire de la vigne à petite échelle géographique et l'existence de patrons temporels intra-annuels marqués dans la structuration de ces communautés. Ces travaux fournissent un ensemble de connaissances nouvelles dans le domaine de l’écologie microbienne, soutiennent l’existence d’un terroir microbiologique et soulignent l’importance de la prise en compte de ce terroir microbien dans le cadre d’une gestion durable de la vigne.

Within the framework of the European project LIVESEED, this study aims at establishing the influence of the type of pruning applied to trees in an agroforestry system and of the grown variety of tomato on the composition of the tomato root microbiome, as well as the effect of the microbiome's structuration on the physical-biochemical quality of tomatoes. The results show an effect of pruning intensity on the biochemical profile of tomatoes, which have higher amounts of sugars, vitamin C and phenolic compounds in the non agroforestry control environment, and higher concentrations of acids under tree shade. The two tomato varieties tested (Rose de Berne and Coeur de Boeuf) have different biochemical profiles, resulting from farmer selection. The fungal communities are little influenced by the tomato variety but reveal different assemblages depending on the intensity of tree pruning, both at the community and phyla levels (Ascomycetes, Basidiomycetes and Glomeromycetes). These differentiations are explained from an ecological point of view in order to lead to a better understanding of plant-microorganism interactions in agroforestry systems. The correlations between the physico-biochemical quality of the fruits and the structuration of the mycobiome show an impact of the diversity of Ascomycetes and the specific richness of Glomeromycetes on the biochemical profile of tomatoes. The results are discussed under the holobionte hypothesis and its influence on plant breeding, in connection with on-farm selection.; Dans le cadre du projet européen LIVESEED, cette étude a pour objectif d'établir l'influence du type de taille appliquée aux arbres dans un système agroforestier et de la variété de tomate cultivée sur la composition du microbiome racinaire de la tomate, ainsi que l'effet de la structuration du microbiome sur la qualité physico-biochimique des tomates. Les résultats montrent un effet de la taille des arbres sur le profil biochimique des tomates, qui possèdent des quantités plus importantes de sucres, vitamine C et composés phénoliques dans le milieu témoin non agroforestier, et des concentrations plus importantes en acides sous l'ombrage des arbres. Les deux variétés de tomates testées (Rose de Berne et Coeur de Boeuf) présentent des profils biochimiques différents, résultant d'une sélection paysanne. Les communautés fongiques sont peu influencées par la variété de tomate mais révèlent des assemblages différents selon l'intensité de coupe des arbres, aussi bien à l'échelle des communautés que des phyla (Ascomycètes, Basidiomycètes et Gloméromycètes). Ces différenciations sont expliquées d'un point de vue écologique afin d'amener à une meilleure compréhension des interactions plante/micro-organismes dans les systèmes agroforestiers. Les corrélations entre la qualité physico-biochimique des fruits et la structuration du mycobiote montrent une incidence de la diversité des Ascomycètes et de la richesse spécifique des Gloméromycètes sur le profil biochimique des tomates. Les résultats sont discutés sous l'hypothèse holobionte et son influence sur l'amélioration des plantes, en lien avec la sélection paysanne.

Genetic and species-level diversity maximization is a cru cial stake of the agro-ecological transition. Alternative Agri-Food Systems flourish to acheive this goal. The RCM project is an action-based and multi-actor research project aiming at enhancing minor cereals production via farmers seeds networks. This study uses the innovation theoretical framework to describe the trajectories of theses cereals, as well as on-going initiatives to restore them in the agricultural landscape of North Western France. We find that the industrialization process as well as the creation of a formal seed system amplified the marginalization of minor cereals. Yet they were already looked down uppon due to the social status of those who were eating them. However, the quality and proximity turn happening in consuming trends offers opportunity for their rehabilitation. We observed four types of transitions. 1. Traditional actors of the regime use standard strategies of investment and marketing. 2. Producers regroup at the regional and participate in the construction of shared governance schemes. 3. Margin actors circumvent the traditional circuit and create a territorial network. 4 The local farmers seeds network is a driving force of this network and it questions the relevance of seed marchandization, as well as a top-down model of knowledge production. To foster this innovation we advise for the maximization of network members participation, the local anchoring in territorial structures and alliances with other regional networks such as organic grain producers.; La maximisation de la diversité inter et intra spécifique en agriculture est un levier central de la transition agro-écologique. Pour y parvenir, des systèmes agri-alimentaires alternatifs se structurent. RCM est un projet multi-acteurs visant le développement des céréales « mineures », via les semences paysannes. A l’aide de la sociologie de l’innovation, ce travail décrit la trajectoire de ces céréales, ainsi que les initiatives dont elles font l’objet dans le quart Nord-Ouest de la France. Nous trouvons que l’industrialisation de la production alimentaire et la mise en place du système semencier formel ont amplifié un phénomène de marginalisation « sociale » de ces céréales. La transition vers une économie de la qualité et de la proximité ouvre toutefois une fenêtre pour leur retour. Sur le territoire d’étude, nous avons identifié quatre types de transitions. 1. Les acteurs traditionnels du régime utilisent stratégies standard d’investissements et de marketing 2. Des agriculteurs se regroupent à l’échelle régionale et participent à la construction d’une gouvernance participative 3. Des acteurs contournent le système dominant par la création d’un réseau territorial 4. Le réseau local des semences paysannes est un élément moteur de cette reconfiguration. En outre, il constitue une remise en cause de la marchandisation de la semence et du modèle centralisé de la production de savoirs. Pour consolider la démarche, ce travail propose la maximisation de la participation des membres, la décentralisation via des partenariats locaux et l’association avec d’autres réseaux régionaux.

All over the globe, networks of seed growers are cultivating crop diversity in fields and gardens. Their contribution to the maintenance of this diversity has been studied, but research has widely left aside their management of plant health. The governance of bean health practiced by an association of artisanal seed companies, Croqueurs de Carottes, is approached as a case study in the objective of specifying how management of crop diversity and governance of plant health are articulated. Their concern for the governance of bean health is elucidated from an agroecological perspective, taking an interdisciplinary and transformative approach. Actor-network theory constitutes the backbone of the thesis, situated between agronomy and sociology and drawing upon a threefold research device: on-farm experiments, semi-directive interviews and participant observation.The Croqueurs' approach to bean health is described as in situ approach, in which plant populations are considered healthy if they are able to live with potential plant pathogens and adapt to their growing environments. Relying on ecological interactions, competences of plant health management are distributed throughout the production system. Both for plant health and crop diversity management, a seed lot is determined by a complex system of interactions. A clear boundary distinguishing plant populations from their growing environment cannot be drawn. This implies (i) that plant health must be judged upon in situ in the plants' growing environment and (ii) that the governance of plant health must be considered at the, De multiples réseaux d'agriculteurs et de jardiniers maintiennent la biodiversité cultivée dans le monde. Leurs pratiques de gestion de la santé des plantes demeurent peu étudiées. La thèse a pour objectif de caractériser l'articulation entre gestion de la biodiversité cultivée et gouvernance de la santé des plantes, se saisissant du cas d'une association d'artisans semenciers, les Croqueurs de Carottes. Elle développe une approche interdisciplinaire et transformatrice pour décrire et comprendre la gouvernance de la santé du haricot par ces acteurs, dans une perspective agroécologique. La théorie de l'acteur-réseau est mobilisée pour situer l'analyse à l’intersection entre approches agronomique et sociologique, reposant sur les données produites par un triple dispositif : expérimentations à la ferme, entretiens semi-directifs et observation participante.Nous qualifions d’in situ l'approche de la santé des plantes des Croqueurs dont l’objectif est de vivre avec les agents pathogènes potentiels. Fondées sur des interactions écologiques entre plantes et terroir, les compétences contribuant à la gestion de la santé des plantes sont distribuées à travers le système de production. Que ce soit en termes de santé ou de biodiversité, un lot de semence est l'expression d'un jeu complexe d'interactions. Il est alors difficile de délimiter des populations de plantes de leur terroir de manière précise. Par conséquent, (i) la santé des plantes ne peut être jugée qu'in situ, dans l'environnement dans lequel elles évoluent et (ii) la gouvernance de la santé des plantes doit être prise e

Based on the hypothesis of “diversity”, SOLIBAM has designed and tested innovative strategies to develop specific and novel breeding approaches integrated with management practices to improve the performance, quality, sustainability and stability of crops adapted to organic and low-input systems. The SOLIBAM project has been carried out by 23 partners, representing 12 countries in Europe and Africa, within the context of a lack of adapted varieties specifically for organic and low input agriculture. A fundamental characteristic of these farming approaches is a wide range of variability within the farming system, combined with a wide range of environmental variation. Having a choice of adapted plants and practices is the only means to build a sustainable farmingsystem which is characterized by a complexity of interactions. As a basis the team - representing several kinds of actors, researchers, seed companies, farmer’s organisations and also involving end-users and consumers - therefore developed tools and methodologies to better understand and manage complexity. From more than 50 field experiments and case studies in 4 countries and 8 major crop models (durum and soft wheat, barley, maize, faba beans, bean, tomato and broccoli), combined with several competencies including genetics, plant breeding, agronomy, ecology, food science, statistics, sociology and economics, SOLIBAM has established 10 major concepts for cultivating diversity (resilience, robustness, functional biodiversity, yield stability, adaptability, intercropping, sustainability, evolutionary processes, organoleptic quality, participatory research), building strongtransdisciplinarity in a dynamic process of knowledge integration. Within SOLIBAM, plant diversity was observed, analysed, developed and enhanced by the creation of new populations and varieties exploited for novel crop management practices. Genetic structure, observed by relevant markers, of the different types of varieties and populations studied strongly reflected the selection / conservation history of the populations showing, in many cases, significant and rapid differentiation due to cultivation in contrasting agro-climatic conditions and to farmers’ breeding practices or breeding. In addition to activities devoted to field and crop studies, the overallfarm system has been assessed at three system levels: the cropping system, the farm and the chain from breeder to farmer (plant breeding and legal aspects) and to consumer (the food supply system). There was a specific focus on resource use efficiency, environmental impacts and socio-economic assessments in case studies from the UK, France, Italy and Portugal. Part of SOLIBAMs research was participatory in nature, based on the experience and skills of a number of partners to improve knowledge sharing and to involve several kinds of actor and their activities. In a number of cases, the transdisciplinarity within SOLIBAM has allowed links to bemade between scientific knowledge and practitioner ‘know-how’ in complementary ways. SOLIBAM has developed various agro-ecological innovations which are at the core of its strategies: - new approaches to plant breeding and development which simultaneously consider diversity and quality, performance and stability, co-breeding for intercropping, or crop-pollinator interactions; - new food products with improved quality properties;- new tools for participatory plant breeding and management (PPBM) in which farmers, researchers and other stakeholders together designed new breeding methods for decentralized programmes, tools for resource and trial management, and for the statistical analysis of results, along with integrating methodologies to better select for flavoursome products; - social innovation and collective action for decentralised and participatory research; - new modelling tools to better understand and assess resilience, viability and sustainability of farms. In conclusion, SOLIBAM identified three key words - Diversity, Participatory Innovation and Locality/Terroir - that should be at the cornerstone of future agricultural propositions for policy makers so as to adapt the seed system, knowledge system and food system to accommodate diverse cultivated crops.

Les semences sont à la base de la production agricole et c’est en quoi elles revêtent une importance essentielle. Les diverses réglementations qui régissent ce secteur sont assez strictes et autorisent le commerce de certains types de semences et en interdit d’autres. En France, le système est centralisé autour de l’inscription des variétés respectant des critères stricts dans un Catalogue officiel et obligatoire, en préalable à la vente. De nombreuses variétés ne respectant pas ces catégories sont rejetées et ne peuvent être cultivées, contribuant à l’érosion de la diversité des espèces. Dans ce cadre-là, quelle place cela laisse-t-il pour les alternatives qui se développement et qui prônent le droit de cultiver d’autres variétés? Quel est le projet de modèle agricole qui est porté par ces mouvements ?, Seeds are at the beginning of agricultural production, that is why they have a particular importance. Regulation about this sector is really strict and authorize some seeds to be sell on the market, and exclude the others. In France, the system is centralized around the official and mandatory register, which establishes the obligation to register the seed to get the authorization to sell them. Several varieties which don’t respect registration criterions are not allowed on the market and disappear. That lead to the biodiversity erosion. In this context, what place can have the alternatives which are developping currently, and whose goal is to claim the right to grow all the seeds ? What is the agricultural project which is lead by these movements ?