Societal Impact Statement Plant breeding for agroecological transition (AET) holds the potential to transform agriculture by fostering crop diversification and empowering farmers through collaborative, inter‐ and transdisciplinary research. By adopting a systemic, co‐learning approach, we can deepen our understanding of the complex interactions between plant diversity, management practices and socio‐ecological contexts. Achieving this transition requires responsible governance to co‐design cropping systems and ensure sustainable, safe and resilient agricultural systems with healthy nutrition. Embracing these integrative practices will not only advance plant breeding science for the transformation of sustainable food systems but also strengthen food security, safety and resilience in the face of pressing environmental and societal challenges. Summary This opinion paper advocates for a transformative approach to plant breeding to support the agroecological transition (AET), essential for addressing global challenges such as biodiversity loss and climate change. It emphasizes the need for inter‐ and transdisciplinary, collaborative and inclusive research to enhance plant and crop diversity while empowering farmers. Key strategies include co‐designing agroecological systems with stakeholders, leveraging crop inter‐ and intraspecies diversity and establishing responsible governance. The participatory approach encourages collaboration between farmers and researchers to co‐develop solutions that enhance crop inter‐ and intra‐species diversity within cropping systems. Through responsible governance, we aim to ensure inclusivity, participation and equitable access to knowledge at individual and institutional levels. In addition, researchers and institutions must collaborate with farmers to co‐design systems that prioritize context‐specific solutions, sustainability and diversity. Enhancing plant diversity for AET requires plant breeding tailored to diverse agroecological contexts and farming needs, supported by collaborative networks, participatory methods and appropriate experimental and modelling tools. We conclude with a call for inter‐ and transdisciplinary training to better prepare future researchers in plant breeding for AET.

In the current polycrisis era, plant science, particularly when applied to agronomy, becomes instrumental: because our main substantial and renewable resource is plant biomass, many future solutions will depend on our ability to grow and transform plant material in a sustainable way. This also questions the way we conduct plant research and thus quantitative plant biology. In response to the increasing polarization between science and society, participatory plant research offers a pertinent framework. Far from moving away from quantitative approaches, participatory plant research builds on complexity associated with biology and situated knowledge. When researchers and citizens work together on societal issues, such friction becomes more fertile, quantitative questions become more complex, societal issues are addressed at their roots and outcomes often exceed that of top-down strategies. This article serves as an introduction to this ongoing bifurcation in plant science, using plant breeding as a key example.

Background and ObjectivesMinor species of wheat, including einkorn (Ei), emmer (Em), and spelt (Sp), are believed to have different gluten compositions compared to common wheat (CW). Given the limited research on these resources, and as a result of a collaboration with a collective of farmers, we aimed to provide insights into their gluten compositions. We focused on varieties readily accessible to farmers and bakers within the region of Lyon, France.FindingsWe compared gluten compositions in 31 wheat varieties, revealing significantly lower glutenin and protein aggregate contents in Ei and Em than in CW. Similar trends, though milder, were observed for Sp. Additionally, we observed intra-species variability, especially for Em, and identified varieties within each species with noteworthy protein profiles.ConclusionsEach species showed characteristic protein contents, yet with intraspecies variability. Utilizing an innovative approach to analyze the full information provided by chromatograms, we successfully identified varieties with unusual characteristics.Significance and NoveltyThe specific protein compositions of Ei and Em, and to a lower extent Sp, may impact their processability and digestibility. Our study also highlights that considering complete chromatographic profiles can reveal differences that remain unnoticed when using traditional analytical approaches.

CropMetaPop is a new simulation tool to model the genetic evolution of crop diversity under on-farm dynamic management. Under this type of conservation and use of varieties, seeds are resown and exchanged between farmers and the set of connected populations is described as a crop metapopulation. CropMetaPop is therefore at the interface of genetic and social processes. We used sensitivity analyses to check the behaviour of the model and to identify which parameters and range of values for them induce the most variability in the outputs. CropMetaPop was found to behave as expected. Depending on the type of locus studied (neutral or selected), the parameters related to drift or selection were those that induced the most variability in the outputs. Colonisation, migration, and network topology parameters were less influential. Looking at the detailed results will help setting the parameters to relevant values in the future utilisation of the model.

AbstractEstablishing linkage among data of diverse domains (e.g. biological, environmental, socio-economical, and geographical) is critical to address complex multidimensional issues such as food security or sustainable agriculture. The complexity of this challenge increases with the level of heterogeneity of the data but also with the social context of production of datasets, a dimension usually less considered. Building on the experience of a transdisciplinary project on the diversity of crop diversity management systems in West Africa (CoEx), this chapter reflects on the importance to better account for agency for more meaningful, responsible and efficient plant data linkage. The chapter addresses sequentially the cognitive and political challenges related to data work and the way they could be addressed simultaneously within the same social unit. To do this, we rely on the concept of community of practice (CoP) which gained enormous popularity in relation to data and knowledge management. More than simply a social mechanism for community knowledge management, we show in this contribution that CoP needs to be approached as a social experiment and a terrain of collective situated learning in order to address each challenge and their linkages with respect to data work.

This paper rethinks the governance of genebanks in a social and political context that has significantly evolved since their establishment. The theoretical basis for the paper is the commons conceptual framework in relation to both seed and plant genetic resources. This framework is applied to question the current policy ecosystem of genetic research and breeding and explore different collective governance models. The concept of crop diversity management system (CDMS) commons is proposed as the new foundation for a more holistic and inclusive framework for crop diversity management, that covers a broad range of concerns and requires different actors. The paper presents a multi-stakeholder process established within the context of the two recent projects CoEx and Dynaversity, imagining possible collective arrangements to overcome existing deadlocks, foster collective learning, and design collaborative relationships among genebanks, researchers, and farmers’ civil society organizations involved in crop diversity management.

Stochastic simulation programs are useful to study the evolution of crop populations in changing environments. These programs require to take into account some specific features characterizing farmers’ practices such as seed circulation or seed mixing. However such human-mediated evolutionary processes are different from the classical colonization or migration models used in most existing stochastic simulation programs for quantitative population genetics. To fill this gap, CropMetaPop is an individual based forward-time simulation program for quantitative population genetics developed to represent a diversity of socially established rules underlying seed circulation between farmers. For instance, one farmer can give seeds to neighbours according to his stock and receive from them according to his needs. Crop-Metapop also takes into account other important evolutionary forces encountered in crop diversity management systems, such as different population sizes and selection modalities for different populations. CropMetaPop makes it possible to study the impacts of different crop biodiversity management strategies. For this purpose, it simulates the genetic evolution over time of several crop populations submitted to genetic drift and selection and linked by explicitly modeled seed circulation and mixtures.

MotivationIn 2005, researchers from the French National Research Institute for Agriculture, Food and Environment (Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, INRAE) started a collaboration with the French farmers' seed network Réseau Semences Paysannes (RSP) on bread wheat participatory breeding (PPB). The aims were: (1) to study on-farm management of crop diversity, (2) to develop population-varieties adapted to organic and low-inputs agriculture, (3) to co-develop tools and methods adapted to on-farm experiments. In this project, researchers and farmers' organizations needed to map the history and life cycle of the population-varieties using network formalism to represent relationships between seed lots. All this information had to be centralized and stored in a database.ResultsWe describe here SHiNeMaS (Seeds History and Network Management System) a web tool database. SHiNeMaS aims to provide useful interfaces to track seed lot history and related data (phenotyping, environment, cultural practices). Although SHiNeMaS has been developed in the context of a bread wheat participatory breeding program, the database has been designed to manage any kind and even multiple cultivated plant species. SHiNeMaS is available under Affero GPL licence and uses free technologies such as the Python language, Django framework or PostgreSQL database management system (DBMS). ConclusionWe developed SHiNeMaS, a web tool database, dedicated to the management of the history of seed lots and related data like phenotyping, environmental information and cultural practices. SHiNeMaS has been used in production in our laboratory for 5 years and farmers' organizations facilitators manage their own information in the system.

As the effects of climate change begin to be felt on yield stability, it is becoming essential to promote the use of genetic diversity in farmers’ fields. The presence of genetic variability in variety could fulfil this purpose. Indeed, the level of intra-varietal genetic diversity influences the spatio-temporal stability of yields and the disease susceptibility of crop species. Breeding history of varieties and their management practices are two factors that should influence intra-varietal genetic diversity. This paper describes the genetic diversity of eight wheat samples covering a gradient from modern single varieties to on-farm mixtures of landraces. This gradient discriminates between landrace, historical and modern varieties, considering the breeding history of varieties, between single-varieties and mixtures of varieties, and between ex situ and in situ de facto strategy in terms of management practices. Genetic diversity of these samples was analyzed with the help of 41 single nucleotide polymorphism markers located in neutral regions, through computing genetic indices at three different levels: Allelic, haplotypic and genetic group level. Population structure and kinship were depicted using discriminant analysis and kinship network analysis. Results revealed an increase in the complexity of the genetic structure as we move on the gradient of variety types (from modern single variety to in situ on-farm mixtures of landraces). For the landraces, the highest levels of genetic diversity have been observed for a landrace (Solina d’Abruzzo) continuously grown on-farm in the region of Abruzzo, in Italy, for many decades. This landrace showed an excess of haplotypic diversity compared to landraces or the historical variety that were stored in genebanks (ex situ conservation). Genetic analyses of the mixtures revealed that, despite a very high selfing rate in wheat, growing in evolutionary mixtures promotes recombination between different genetic components of the mixture, a second way to increase the level of haplotype diversity. When management practices such as growing in mixture and on-farm management are combined, they substantially increase the different levels of genetic diversity of the populations (allelic, haplotypic, genetic group diversity), and consequently promote their adaptability. Our results confirm the need to develop and manage evolving diversified large populations on-farm. These results invite crop diversity managers such as genebank curators, community seed bank managers and farmers’ organizations to adapt their management strategies to the type of variety they wish to manage, because we have shown that their choices have a strong influence on the genetic composition of the crop populations.

Agroecology calls for a global approach, integrating scientific, practical, and advocacy dimensions, to redesign agricultural systems based on ecological and socio-cultural processes and emphasizing biodiversity. This review is grounded on the results of DIVERSIFOOD, a European H2020 multi-actor research project, and explores the concept of cultivated diversity using various dimensions relevant to foster sustainable organic food systems and agro-ecological transition. From the evaluation of underutilized genetic resources and forgotten crops, DIVERSIFOOD has proposed plant breeding strategies, on-farm experimentation, and statistical tools to create new populations, landraces, and organic cultivars with intra-varietal diversity. The added value of Community Seed Banks and forms of collective seed management in Europe have been described in terms of goals and activities, and their value for improving seed regulations, treaties, and genetic resources management is discussed. In the context of the current agro-food system characterized by standardization, DIVERSIFOOD raised awareness of qualities of ‘biodiverse food systems’ in which all actors have a role to play. It highlighted the critical capacity to preserve a diversity of cultural values embodied in ‘biodiverse products’, thereby involving consumers in collective strategies for reviving diversity, and empowering all actors of organic food systems to really and efficiently implement research within their farms and networks.

In 2007, Rete Semi Rurali (RSR), the Italian farmers' seed network, facilitated the emergence of a broad movement of seeds re-appropriation and on-farm diversity management by farmers by creating a bread wheat Community Seed System (RSR-CSS). RSR-CSS is now facing changes in farmers' seed demand in the context of the current seed regulation for heterogenous material in Europe (2014/150 & 2018/848 EU). One major issue for the RSR-CSS is to organize seed circulation among farmers in order to foster local adaptation of wheat populations, while maintaining a sufficient level of genetic diversity over generations. To address this issue, we started an iterative participatory simulation-based approach with RSR-CSS, consisting in: i) the description of the CSS' functioning; ii) the co-construction of scenarios; iii) the scenario simulation using a population genetics model of crop metapopulations and the output analyses. Discussions and meetings with RSR farmers and facilitators, helped to describe the CSS' functioning and to co-design scenarios. These included different characteristics of the seed circulation network based on longitudinal data and three ways of representing the local selective pressures due to the pedo-climatic conditions and farming practices: 1) a single environment; 2) an environmental gradient; and, 3) two contrasting environments. The functioning of the model and the results were shown and discussed with RSR-CSS actors, allowing us to iteratively co-construct: a) more accurate scenarios to represent the current functioning of the CSS; and, b) new scenarios to explore alternative management practices and organisation modes. We found that the way environmental selective pressures were represented in relation to the seed circulation network strongly affected genetic diversity and genetic differentiation, whilst the gradient scenario maintains more genetic diversity over generations. These results will feed into the RSR-CSS discussion on the best practices for seed distribution/ciruclation among an increasing number of farmers.

Sustainable agriculture in a context of global change should be based on diversified agro-ecosystems with the possibility for actors of community seed systems to exchange seeds. Although several studies have shown that seed flows among actors strongly impact the evolution of crop genetic diversity, there is a lack of knowledge on how seed circulation, farmers' practices and local selective pressures interact together to shape diversity pattern over time. Simulation-based approaches offer an attractive alternative to experimental studies, surveys, and analytical approaches. In the framework of the EU project DIVERSIFOOD, we developped a model called CropMetaPop that simulates the evolution of multilocus and multiallelic genomes. It allows to represent the evolution of different annual crop species by their mating system, along with the management practices of the populations by changing population sizes and selection pressures. It is particularly intented to represent the seed circulation using different network topologies. In order to better understand the functioning of the model, we performed a sensitivity analysis, which allowed us to determine the parameters that have the largest impact on the outputs of the model. We designed three different scenarios to test the behaviour of the model focusing: (i) on the impact of genetic drift, selection and mutation of isolated populations, (ii) on previous scenario plus colonisation and extinction, and (iii) on first scenario with migration. This allowed us to test the impact of 11 related parameters of these scenarios on several demographic and genetic output variables (e.g. survival rate, Nei's genetic diversity, genetic differentiation among sub-populations...). This allowed us to check that the outputs fit the theoretical expectations and to identify the parameters and their interactions that are the most influencial in the different responses. CropMetaPop can now be used as a support for companion modeling of genetic diversity management in community seed systems.

Chapter 4 Network Analysis: Linking Social and Ecological Dynamics Vanesse Labeyrie, Vanesse LabeyrieSearch for more papers by this authorSophie Caillon, Sophie CaillonSearch for more papers by this authorMatthieu Salpeteur, Matthieu SalpeteurSearch for more papers by this authorMathieu Thomas, Mathieu ThomasSearch for more papers by this author Vanesse Labeyrie, Vanesse LabeyrieSearch for more papers by this authorSophie Caillon, Sophie CaillonSearch for more papers by this authorMatthieu Salpeteur, Matthieu SalpeteurSearch for more papers by this authorMathieu Thomas, Mathieu ThomasSearch for more papers by this author Book Editor(s):Roger Waldeck, Roger WaldeckSearch for more papers by this author First published: 09 December 2019 https://doi.org/10.1002/9781119681519.ch4Citations: 2 AboutPDFPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShareShare a linkShare onFacebookTwitterLinked InRedditWechat Summary This chapter introduces the basic principles of network analysis and provides an overview of the main types of questions that can be answered in the field of ecological and social systems studies. Social interactions between actors affect ecosystem dynamics via their role in the circulation of biological resources and of the knowledge associated with their management. The application of network analysis methods to the study of these two main types of mechanisms is illustrated by three case studies whose results have been published and analyzed in the articles by Thomas and Caillon, Labeyrie et al., and Salpeteur et al. These examples highlight the need to associate network analysis with qualitative approaches, which are essential to understand the social rules and norms regulating interactions between individuals, and are also necessary to understand how these interactions fit into the general system of interactions in the studied social systems. Citing Literature Methods and Interdisciplinarity, Volume 1 RelatedInformation

Dans les annees 2000, des agriculteurs desireux de cultiver des bles correspondant a leurs besoins et soucieux d’affirmer leur autonomie vis-a-vis de l’industrie semenciere, ont entrepris de relancer la selection paysanne a la ferme. Des collaborations ont ete tissees avec des geneticiens de l’Inra, et se sont progressivement developpees dans le cadre de projets finances. Or les financements de recherche impliquent une formalisation des partenariats, des engagements en termes de resultats academiques et une augmentation significative de la taille des projets. Dans ce nouveau contexte, comment preserver les valeurs d’emancipation paysanne et de justice cognitive sur lesquelles la collaboration paysans-chercheurs s’est originellement construite ? Cet article aborde la facon dont ce defi se pose concretement aux acteurs de ces projets, et les precautions qu’ils mettent en oeuvre pour y faire face.

Dans les années 2000, des agriculteurs désireux de cultiver des blés correspondant à leurs besoins et soucieux d’affirmer leur autonomie vis-à-vis de l’industrie semencière, ont entrepris de relancer la sélection paysanne à la ferme. Des collaborations ont été tissées avec des généticiens de l’Inra, et se sont progressivement développées dans le cadre de projets financés. Or les financements de recherche impliquent une formalisation des partenariats, des engagements en termes de résultats académiques et une augmentation significative de la taille des projets. Dans ce nouveau contexte, comment préserver les valeurs d’émancipation paysanne et de justice cognitive sur lesquelles la collaboration paysans-chercheurs s’est originellement construite ? Cet article aborde la façon dont ce défi se pose concrètement aux acteurs de ces projets, et les précautions qu’ils mettent en œuvre pour y faire face.

Recent studies investigating the relationship between crop genetic diversity and human cultural diversity patterns showed that seed exchanges are embedded in farmers' social organization. However, our understanding of the social processes involved remains limited. We investigated how farmers' membership in three major social groups interacts in shaping sorghum seed exchange networks in a cultural contact zone on Mount Kenya. Farmers are members of residence groups at the local scale and of dialect groups clustered within larger ethnolinguistic units at a wider scale. The Chuka and Tharaka, who are allied in the same ethnolinguistic unit, coexist with the Mbeere dialect group in the study area. We assessed farmers' homophily, propensity to exchange seeds with members of the same group, using exponential random graph models. We showed that homophily is significant within both residence and ethnolinguistic groups. At these two levels, homophily is driven by the kinship system, particularly by the combination of patrilocal residence and ethnolinguistic endogamy, because most seeds are exchanged among relatives. Indeed, residential homophily in seed exchanges results from local interactions between women and their in-law family, whereas at a higher level, ethnolinguistic homophily is driven by marriage endogamy. Seed exchanges and marriage ties are interrelated, and both are limited between the Mbeere and the other groups, although frequent between the Chuka and Tharaka. The impact of these social homophily processes on crop diversity is discussed.

In agro-systems, genetic diversity especially within-population diversity provides a buffering effect against the year-to-year variation of climatic or biotic pressures as well as a resource for the population to respond to selective pressures due to specific local conditions, thus allowing for local adaptation, particularly when a population is introduced into a new location. Wheat was chosen as a model crop in this study due to its high adaptive potential. Flowering time was evaluated as it is a major adaptive trait that has been involved in wheat adaptation. The objective of this study was to gain insights on the influence of within-population diversity onto the short-term response of populations to contrasting agro-climatic conditions, by studying the genetic and phenotypic variation. Wheat populations (seven farmers’ and one modern varieties), that have been grown on seven farms (distributed across Europe) for three years, were studied for their short term response to the contrasting agro-climatic conditions. Genetic diversity at neutral and candidate genes markers, as well as earliness and plant height (two major adaptive traits) were investigated in 54 samples corresponding to the initial and 3rd year populations of these eight varieties. Results revealed that conservation history of these farmer varieties strongly influenced their genetic diversity and fine genetic structure. Ex situ conserved landraces and the modern variety showed low genetic diversity and simpler structure whereas in situ conserved farmers’ varieties and mixtures revealed higher level of genetic diversity and complex genetic structure. Genetic and phenotypic spatio-temporal differentiation depending upon the level of diversity and structural complexity of the farmer variety was observed. The traditional varieties tend to become more differentiated than the modern variety arguing in favour of the use of diverse traditional (farmers’) varieties in organic and low input agriculture systems. This study at large provides useful knowledge on the understanding of farmers’ varieties evolutionary response to be used in the development of different breeding and conservation approaches, taking into consideration the importance of within-population diversity, to satisfactorily address the problems of sustainable agriculture. ∗Speaker †Corresponding author: arehman@ciit.net.pk sciencesconf.org:biodiv2014:46962

We present a detailed ethnographic case study of sorghum seed acquisitions in a smallholder farming society in northern Cameroon. The effects of variability in household demographics and socioeconomic status on observed patterns of seed provisioning are explored alongside other variables such as age and gender. Our data set comprised 223 seed acquisition events. Independence tests (Pearson's chi-square and Fisher's exact tests) were carried out to test for significant dependencies between individual- or household-level characteristics and properties of seed acquisition events (categories of seed source, social relationship of exchange, and type of landrace). Results indicate that wealth is a structuring factor of the local seed circulation network in as much as it is highly correlated with household composition and size. Members from wealthy households benefit from a more diverse set of seed sources. Their greater number of coresidents and the importance of intrahousehold dynamics of seed transactions also play a role in making wealthy farmers more seed secure than others. The methodological implications of our findings indicate that when documenting seed exchange networks, the collection of data through a single informant or the undertaking of social network analyses at the household level may induce important biases.

Analysis of seed exchange networks at a single point in time may reify sporadic relations into apparently fixed and longlasting ones. In northern Cameroon, where environment is not only strongly seasonal but also shows unpredictable interannual variation, farmers' social networks are flexible from year to year. When adjusting their strategies, Tupuri farmers do not systematically solicit the same partners to acquire the desired propagules. Seed acquisitions documented during a single cropping season may thus not accurately reflect the underlying larger social network that can be mobilized at the local level. To test this hypothesis, we documented, at the outset of two cropping seasons (2010 and 2011), the relationships through which seeds were acquired by the members of 16 households in a Tupuri community. In 2011, farmers faced sudden failure of the rains and had to solicit distant relatives, highlighting their ability to quickly trigger specific social relations to acquire necessary seeding material. Observing the same set of individuals during two successive years and the seed sources they solicited in each year enabled us to discriminate repeated relations from sporadic ones. Although farmers did not acquire seeds from the same individuals from one year to the next, they relied on quite similar relational categories of people. However, the worse weather conditions during the second year led to (1) a shift from red sorghum seeds to pearl millet seeds, (2) a geographical extension of the network, and (3) an increased participation of women in seed acquisitions. In critical situations, women mobilized their own kin almost exclusively. We suggest that studying the seed acquisition network over a single year provides a misrepresentation of the underlying social network. Depending on the difficulties farmers face, they may occasionally call on relationships that transcend the local relationships used each year.