V. Chable

Terroir is a key driver of seed-associated microbial assemblages

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.

Organic varieties for cauliflowers and cabbages in Brittany: from genetic resources to participatory plant breeding

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.

Diversity of different farmer and modern wheat varieties cultivated in contrasting organic farming conditions in Western Europe and implications for European seed and variety legislation

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.

Seeds for Organic Agriculture: Development of Participatory Plant Breeding and Farmers’ Networks in France

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.

Short-Term Local Adaptation of Historical Common Bean (Phaseolus vulgaris L.) Varieties and Implications for In Situ Management of Bean Diversity

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. FST 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.

“Aberrant” plants in cauliflower: 1. Phenotype and heredity

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.

“Aberrant” plants in cauliflower: 2. Aneuploidy and global DNA methylation

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.