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Mass selection is increasingly promoted in viticulture to enhance resilience by restoring intra-varietal diversity, yet its effects on the structure and inheritance of plant-associated microbiomes remain poorly understood. Here, we investigated bacterial and fungal communities associated with old grapevine mother plants and their progeny across four Bordeaux estates practicing mass selection, using a fully in situ experimental design. Root and leaf microbiomes were characterized by metabarcoding and analyzed using multivariate ordination, hierarchical clustering, and assembly-process metrics (βNTI and NST). Microbial community composition and structure were primarily shaped by plant compartment and vineyard origin, whereas generation effects were significant but weak. Microbial resemblance between mother vines and their offspring was limited and highly context-dependent, occurring mainly under comparable environmental conditions. Assembly-process analyses revealed heterogeneous deterministic signals, particularly in root-associated bacterial communities, but did not consistently result in phylogenetic similarity between generations. Although inheritance signals were generally weak, their recurrence across multiple vineyards and contrasted field conditions highlights their ecological relevance. By integrating environmental variability, this in situ approach mitigates the adaptive bias in plant–microbiome interactions and shows that mass selection does not rely on systematic microbial transmission but rather operates within a nuanced framework of environmentally mediated interactions.

The context of global ecological crisis has led to the rediscovery and reuse of landrace crop cultivars. Many recent studies testify the high-quality value of landraces, as well as their agronomic interest in terms of adaptability to pedoclimatic environments. The aim of this study was to highlight the differences between modern varieties and landraces for their mixing and intercropping capabilities. An on-farm experiment, in low input conditions, took place in five different sites in Western France (3 repetitions per site) during three seasons (from seedling 2014 to harvest 2017). Three landraces and three modern varieties were compared in three mixing modalities: monoculture, cultivar mixture and legume intercropping. This on-farm experiment with no chemical input has offered new insights on the differences between modern varieties and landraces: (1) Landraces yielded around 2.8 t ha −1 while modern varieties yielded around 3.0 t ha −1 , a difference that was not significant. (2) Landraces’ yields were more stable over sites. (3) Wheat straw dry matter yields were 1.5 t ha −1 higher for landraces than for the modern ones. (4) The grain nitrogen content for landraces was 13.5% while it is 12.3% for modern varieties. (5) Landraces were healthier than modern varieties; (6) Arbuscular mycorrhiza fungi wheat root colonisation was 5% higher in landraces (35.2%) than modern varieties (29.4%) in these conditions unfavourable to mycorrhiza due to ploughing. (7) Wheat lodging was 38.5% for landraces while it was around 1% for modern varieties. Intercropping wheat with legumes decreased wheat grain yield by around 25%, but increased wheat grain nitrogen content from 12.7 to 13.8%, independently between landraces and modern varieties. This study provides novel evidence of the interests of diversifying crops, either through intra-varietal genetic diversity (the use of landraces) and inter-specific diversity (intercropping of wheat and legumes), for both wheat performance and stability.

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.

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.

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. Root endosphere microbiota composition differed among modern (M) and ancient (A) wheat cultivars considering both bacteria (a) and fungi (b)

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.

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 ploïdy 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 in Brassica is controlled by a single, highly polymorphic locus that extends over several hundred kilobases and includes several expressed genes. Two stigma proteins, the S locus receptor kinase (SRK) and the S locus glycoprotein (SLG), are encoded by genes located at the S locus and are thought to be involved in the recognition of self-pollen by the stigma. We report here that two different SLG genes, SLGA and SLGB, are located at the S locus in the class II, pollen-recessive $S_{15}$ haplotype. Both genes are interrupted by a single intron; however, SLGA encodes both soluble and membrane-anchored forms of SLG, whereas SLGB encodes only soluble SLG proteins. Thus, including SRK, the S locus in the $S_{15}$ haplotype contains at least three members of the S gene family. The protein products of these three genes have been characterized, and each SLG glycoform was assigned to an SLG gene. Evidence is presented that the S2 and S5 haplotypes carry only one or the other of the SLG genes, indicating either that they are redundant or that they are not required for the self-incompatibility response.

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.