Training materials on organic plant breeding

Deliverable 1.1 Funded by the European Union (grant no. 101059872), the Swiss State Secretariat for Education, Research and Innovation (Contract no. 22.0412) and UK Research and Innovation (UKRI). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or REA, nor SERI or UKRI. Training materials on organic plant breeding Authors: Adrian Rodriguez-Burruezo (UPV), Riccardo Bocci, (RSR), Véronique Chable (INRAe), Yannick De Oliveira (INRAe), Isabelle Goldringer (INRAe), Francesca Gori (RSR), Kostas Koutis (Aegilops), Mariano Iossa (FiBL Europe), Mariateresa Lazzaro (FiBL-CH), Gabriele Maneo (EC-LLD), Vladimir Meglic (KIS), Pedro Mendes Moreira (IPC), Stephanie Mothes (ITAB), Neus Ortega-Albero (UPV), Barbara Pipan (KIS), Michael Schneider (FiBL-CH), Eva M. Solbes-Garcia (UPV) Deliverable Number D1.1 Work Package WP1 Deliverable type DEC Dissemination level Public Deliverable Lead partner UPV Due date 31 May 2025 Submission date 2 June 2025 Version V4 Reviewers Mariateresa Lazzaro (FiBL CH), Vladimir Meglic (KIS), Mariano Iossa (FiBL Europe) Contact Adrian Rodriguez Burruezo, [email protected] D1.1, Training in Organic Breeding 1 History of changes Version Date Author Comments V1 May 15th, 2025 Adrian RodriguezBurruezo First draft V2 May 19th, 2025 Mariateresa Lazzaro and Vladimir Meglic Contributions to the first draft V3 May 23rd, 2025 Adrian RodriguezBurruezo Integration of the contribution of authors V4 May 30th 2025 Mariano Iossa Final revision and quality check D1.1, Training in Organic Breeding 2 LiveSeeding - Organic seed and plant breeding to accelerate sustainable and diverse food systems in Europe is a 4-year Innovation Action funded by the European Union, the Swiss State Secretariat for Education, Research and Innovation (SERI) and UK Research and Innovation (UKRI). The project started in October 2022 and brings together 37 organisations operating in 16 European countries. LiveSeeding provides science-based evidence and best practice solutions to help achieve 100 % organic seed. LiveSeeding contributes to the transition towards environmentally-friendly, climateneutral, healthy and fair food systems through a PUSH-PULL-ENABLE strategy to enhance the availability and adequacy of organic seeds of cultivars appropriate to organic farming (PUSH), increase and stabilise the market demand for organic seeds of cultivars appropriate to organic farming (PULL), foster an enabling policy and regulatory environment where both demand and supply can harmoniously and productively negotiate without irrelevant constraints due to legal restrictions and/or regulatory fragmentation (ENABLE). LiveSeeding addresses the topics in a holistic multi-actor, multi-stakeholder, participatory approach involving stakeholders along the value chain in 17 local Living Labs (LLs) and 3 established networks of organic breeders (ECO-PB), seed savers (ECLLD) and Milan Urban Food Policy Pact (MUFPP). 15 European countries cover the different pedoclimatic zones and socio-economic contexts, including countries with a low level of development in organic seed and breeding in East and South Europe. D1.1, Training in Organic Breeding 2 Table of Contents SUMMARY .............................................................................................................. 4 1. JUSTIFICATION AND MAIN OBJECTIVES ........................................................ 5 2. DESCRIPTION OF THE TRAINING MODULES ................................................... 6 2.1 MODULE 1 - PLANT GENETIC RESOURCES (PGRS): COLLECTION, CONSERVATION AND EXCHANGE TO SUPPORT THE INCREASE OF AGROBIODIVERSITY IN FARMING SYSTEMS ................. 7 2.1.1 Unit 1 - Public/Institutional seedbanks: PGRs collection, conservation and exchange ........................................................................................................................ 8 2.1.2 Unit 2 - Pre-breeding: from genetic resources characterisation to their use in breeding programmes ............................................................................................ 8 2.1.3 Unit 3 - Community seed banks: collection, dynamic management and exchange ................................................................................................................................ 8 2.2 MODULE 2 - PHENOMICS: APPROACHES AND TOOLS FOR GENETIC RESOURCES AND BREEDING MATERIAL CHARACTERIZATION ..................................................................................... 8 2.2.1 Unit 1 - Main descriptors used worldwide in characterizing plant genetic resources ................................................................................................................................ 9 2.2.2 Unit 2 - Intro to SHiNeMaS : a web tool dedicated to Seed Lots History, Phenotyping & Cultural Practices .................................................................................. 10 2.2.3 Unit 3 - Guidelines and examples of good practices in data management 10 2.2.4 Unit 4 - Methods for phenotyping & selection of agronomic traits of interest in organic farming .............................................................................................. 10 2.3 MODULE 3 - BREEDING METHODS FUNDAMENTALS ...................................................... 10 2.3.1 Unit 1 – Generation of new diversity ............................................................ 11 2.3.2 Unit 2 - Common methods and strategies in organic breeding ............. 12 2.3.3 Unit 3 - Calculation and evaluation of key breeding parameters .......... 12 2.3.4 Unit 4 - Fundamentals in participatory plant breeding ............................ 12 2.4 MODULE 4 - DEVELOPMENT AND APPLICATION OF MOLECULAR METHODS IN ORGANIC BREEDING .................................................................................................................................... 12 2.4.1 Unit 1 – Genome Wide Association (GWA) and its potential for understanding the genetic basis of complex traits .................................................... 13 2.4.2 Unit 2 - Genomic Selection and its potential in organic breeding ........ 14 2.4.3 Unit 3 - Application of molecular marker-based selection in practical breeding 14 2.4.4 Unit 4 - Overview on experimental populations (e.g. NILs, RILs, introgression families, MAGIC) and their role in molecular breeding approaches 14 D1.1, Training in Organic Breeding 3 2.5 MODULE 5 - ORGANIC HETEROGENEOUS MATERIAL (OHM) DESIGN AND DEVELOPMENT 14 2.5.1 Unit 1 – Composite Cross Populations: setting-up & selection .............. 15 2.5.2 Unit 2 - Dynamic mixtures: setting-up & selection ................................... 16 2.5.3 Unit 3 - Fundamentals of populations genetics applied to OHM development and use ........................................................................................................ 16 2.5.4 Unit 4 - Using genomics to track the evolution of heterogeneous organic materials ............................................................................................................................... 16 3. MATERIALS ................................................................................................... 17 4. ATTENDEES NUMBER AND PROFILES ........................................................... 18 D1.1, Training in Organic Breeding 4 Summary Current agricultural production systems face great challenges. Climate change and its far-reaching impacts—such as erratic rainfall patterns and rising global temperatures – combined with unsustainable farming practice - based on intensive monocrop, highinput agriculture, that disrupts soil health, accellerates erosion of agrobiodiversitycompromise the future of our food security and sovereignty in Europe. Organic agriculture, when combined with the deliberate enhancement of cultivated biodiversity, offers a powerful means of mitigating and even reversing these threats. This approach contributes to the development of globally sustainable food systems that are less polluting and more genetically diverse, and therefore inherently more resilient and adaptable in confronting these complex challenges. A key pillar in achieving this transformation lies in the improvement of seeds and crop varieties through targeted plant breeding. Seeds are fundamental to agricultural production, and their enhancement—especially under organic conditions—provides vast potential for fostering sustainability. Organic plant breeding, which includes the recovery and improvement of traditional landraces as well as the creation of new genetic variations, is essential for cultivating robust and diverse plant populations suited to organic systems. The LiveSeeding project, aims to enhance the availability and adequacy of organic seeds of cultivars appropriate to organic farming. Training in organic seed and plant breeding key concepts, terms, strategies and tools available represents a key approach to change farming practices. Deliverable 1.1 is an exhaustive compilation of training materials in organic breeding. Training materials are divided into five thematic modules, structured in 34 units each, covering from the basic aspects of organic breeding to the most sophisticated available tools, all respectful of the principles of organic production. Each training module has a training outline that clearly identifies the scope of the training, the learning objectives and target audience, the learning modalities, methodology and materials, as well as the learning assessment method. The training outline has been developed as a common approach for all training materials and training-related deliverables in the project. The supporting materials include i) PowerPoint presentations prepared by the lecturers; ii) the recordings of the sessions; iii) other support learning materials such as videos, exercises, case studies etc. & iv) the training outline for each Module. D1.1, Training in Organic Breeding 5 1. Justification and main objectives Current agricultural production systems face great challenges. Climate change and its pedoclimatic consequences (e.g. drought, scarcity and worse quality of water for irrigation, erratic rains, increase in temperatures), the negative impacts of intensive monoculture production systems, the genetic erosion of cultivated biodiversity exacerbated in recent decades, pollution and alteration of soil balances, among other aspects, seriously compromise the sovereignty and food security of the future. In this context, organic production, together with the promotion of greater cultivated biodiversity, can contribute to significantly mitigate these risks and even reverse them, contributing positively towards more sustainable productive systems, less demanding on inputs and less polluting, more genetically diverse and consequently more adaptable, resilient and dynamic. Seeds are the foundation of life and the cornerstone of food production. To advance organic farming, we must take a synergistic approach based on two key pillars for enhancing agrobiodiversity: - by preserving, improving, and valuing genetic resources; - by genetic improvement of plant populations and development of new cultivars within organic production systems—a process known as organic breeding. Whenever possible, it is essential to encourage the active and informed participation of all stakeholders in the value chain—farmers, breeders, technicians, retailers, consumers, end users, and public authorities. Their collective knowledge can support effective decision-making in organic breeding through participatory plant breeding, while also helping to build or strengthen the socioeconomic networks that support sustainable agriculture. The aim of Task 1.4 of LiveSeeding project is to contribute to training in the main concepts, terms, strategies and tools available in organic breeding, with a considerable amount of training materials aimed at a wide range of actors. These materials have initially been generated as online courses, taught in five sessions between the months of January and March 2025, and include i) the PowerPoint presentations prepared by the lecturers (covering concepts, practical examples, demonstrations, tutorials, additional materials suggested to work on in the sessions themselves, questionnaires and homework), ii) the recordings of these sessions; iii) other support learning materials & iv) the training outline for each Module that can be used by trainers that want to deliver lectures based on LiveSeeding materials. Our training materials are divided into five thematic modules, one for each session. Each module consists of three or four units that cover all aspects, from the basics of organic breeding to the most sophisticated available tools, while respecting the principles of organic production and organic breeding (i.e. target molecular breeding D1.1, Training in Organic Breeding 6 tools for diagnostics use only, not to substitute the direct selection in the target environment). These materials offer a comprehensive perspective on organic breeding knowledge, concepts, strategies, tools and opportunities, adapted to a diverse group of target trainees, from organic farmers to PhD students of different levels (high school, undergraduates and/or MSc students) and scientists, seed producers, , organic breeders, and any others involved in the value chain of organic systems with interest in some (or all) the main issues in organic breeding. Some units are suitable for most of the mentioned trainee profiles (particularly those in Modules 1 and 2), while other materials are aimed at more technical and advanced audience (from Module 3 onward), such as MSc and PhD students, breeders or scientists. More details on the specific units and training objectives are provided in the next section. 2. Description of the training modules The training courses were organized into five thematic modules. Each training module is divided into three or four units. The units were implemented as online webinars and included a presentation, as well as dynamic interactions with trainees, in the form of quizzes, general discussions, and tutor-led work and hands-on exercises during sessions and/or homework assignments. These modules and corresponding links in Organic Eprint and ECO PB are: Module 1: Plant Genetic Resources (PGRs): collection, conservation and exchange to support the increase of agrobiodiversity in farming systems (3 units). Organic Eprint link: https://orgprints.org/id/eprint/54728/ ECO PB: https://www.eco-pb.org/trainings.html Module 2: Phenomics: approaches and tools for genetic resources and breeding material characterization (4 units). Organic Eprint link: https://orgprints.org/id/eprint/54984/ ECO PB: https://www.eco-pb.org/trainings.html Module 3: Breeding methods fundamentals (4 units) Organic Eprint link: https://orgprints.org/id/eprint/54985/ ECO PB: https://www.eco-pb.org/trainings.html Module 4: Development and application of molecular methods in organic breeding (4 units) ECO PB: https://www.eco-pb.org/trainings.html Organic Eprint link: https://orgprints.org/id/eprint/55664/ Module 5: Organic heterogeneous material (OHM) design and development (4 units). Organic Eprint link: https://orgprints.org/id/eprint/55665/ ECO PB: https://www.eco-pb.org/trainings.html D1.1, Training in Organic Breeding 7 All training modules have a common training outline that clearly identifies the scope of the training, the learning objectives and target audience, the learning modalities, methodology and materials, as well as the learning assessment method. The training outline and the modular approach have been developed as a common approach for all training materials and training-related deliverables in the project (each work package as a training task) in order to create better learning paths that can support knowledge transfer and can also ensure easy replicability of trainings. The modular approach also allows to create new trainings in the future that make use of individual modules or units from various work packages in order to create new trainings targeted to specific groups and learning needs. The framing of common training outline and the learning methodology has been curated by Stephanie Mothes (ITAB, FR) with the support of Mariano Iossa (FiBL Europe) and Francesca Gori (RSR) within the work of the Training Task Force (T7.2) 2.1 Module 1 - Plant Genetic Resources (PGRs): collection, conservation and exchange to support the increase of agrobiodiversity in farming systems Topics: Plant genetic resources (PGRs) are essential for breeding. The agrobiodiversity encompassed in modern varieties, landraces and ecotypes as well as wild relatives must be preserved i) to mitigate genetic erosion and, therefore, ii) to ensure that these resources are available to face future challenges (e.g. climate change, new pathogens, new preferences) and iii) contribute to a diverse and resilient agrifood sector. Seedbanks as ex situ conservation structures, community seedbanks (CSBs), breeding and pre-breeding collections, are among the most usual ex situ conservation methods. Community seed banks and farmers´ collections are examples of in situ conservation. Target groups: In this module, the targeted actors learn about methodologies and strategies related to the conservation, use and exchange of genetics resources. This module is open to (although not limited to) farmers (and more specifically to the ones committed with agroecology, preservation of landraces and involved in selection and plant breeding) and students (from the high school level to MSc level, especially students in plant breeding, plant production or agronomy). Learning objectives: At the end of the training, the trainee received input and contacts to support: - Management of own genetic resources; D1.1, Training in Organic Breeding 14 2.4.2 Unit 2 - Genomic Selection and its potential in organic breeding Lecturer(s): Dr. Michael Schneider (FiBL) LIVESEEDING partner(s): FiBL Topics: The basis of genomic selection and its applications in organic breeding. The course will explain the simplest aspects of genome selection procedures and provide practical examples, online tutorials, and presentations. There will also be practical exercises with trainees. Unit duration: 1:30 h 2.4.3 Unit 3 - Application of molecular marker-based selection in practical breeding Lecturer(s): Dr. Barbara Pipan (KIS) and Dr. Mariateresa Lazzaro (FiBL) LIVESEEDING partner(s): KIS and FiBL Topics: how molecular-based selection can be applied and be useful in organic breeding, practical examples from projects managed by KIS and FiBL (lupins, common bean). Unit duration: 1:30 h 2.4.4 Unit 4 - Overview on experimental populations (e.g. NILs, RILs, introgression families, MAGIC) and their role in molecular breeding approaches Lecturer(s): MSc Neus Ortega-Albero (UPV) and Dr. Vladimir Meglic (KIS) LIVESEEDING partner(s): UPV and KIS Topics: review of the most common experimental populations used in plant breeding and genetics (NILs, RILs, MPPs, MAGIC), several practical examples for Solanaceae crops (tomato, eggplants, peppers) from UPV activities, and wheat from KIS activities (Ecobreed project), cucumber, introgression/genome transfer of Solanum lycopersicoides into S. lycopersicon , QTL mapping based on these populations, etc. Unit duration: 1:30 h 2.5 Module 5 - Organic heterogeneous material (OHM) design and D1.1, Training in Organic Breeding 15 development Topics: Organic Heterogeneous Material is a cultivar type that contributes to a more diverse, dynamically adaptable and resilient farming system. These populations, while showing uniformity for many morphological traits (e.g. fruit size and appearance, plant development), also preserve a heterogeneous genetic background for other traits which could be useful for adaptation to a wide range of pedoclimatic conditions. Thus, they are of particular interest in the context of organic farming and low input farming, as well as to face the climate change. This module includes examples of OHMs already obtained, procedures to start the initial populations (composite cross populations or dynamic mixtures), breeding strategies and tools for genomic tracking of their evolution, as well as fundamentals on population genetics to understand their evolution. The present module is aimed at training on the fundamentals of all these concepts. Target groups: In this module, the targeted trainees will learn about the main issues related to Organic Heterogeneous Materials (OHMs) concepts, fundamentals and development. From basic knowledge and population genetics dynamics to their development and tracking. This module is mainly aimed at organic breeders, researchers and students (at least University undergraduates on Agronomy, Biology, Biotechnology, MSc or even PhD students in plant breeding and biotechnology). Learning objectives: At the end of the training, the trainee: - knows the main methods to develop OHMs; - understands how they evolve during their selection and development; - has an overview of the main applications and opportunities of OHMs in organic farming. Number of units: 4 2.5.1 Unit 1 – Composite Cross Populations: setting-up & selection Lecturer(s): Prof. Adrian Rodríguez-Burruezo (UPV) and Dr. Isabelle Goldringer (INRAe) LIVESEEDING partner(s): UPV and INRAe Topics: what is a CCP, uses in genetics and organic breeding, contribution for a more diverse and resilient farming system, creation of CCPs, development towards OHMs, examples in vegetables and crop species, tutorized work based on research papers. Unit duration: 2:00 h D1.1, Training in Organic Breeding 16 2.5.2 Unit 2 - Dynamic mixtures: setting-up & selection Lecturer(s): Prof. Pedro Mendes Moreira (IPC) LIVESEEDING partner(s): IPC Topics: explain mixtures in the context of breeding, uses in genetics and organic breeding, contribution for a more diverse and resilient farming system, creation of mixtures and further dynamic development, examples in vegetables and crop species. Unit duration: 1:30 h 2.5.3 Unit 3 - Fundamentals of populations genetics applied to OHM development and use Lecturer(s): Prof. Adrian Rodríguez-Burruezo (UPV) and Dr. Isabelle Goldringer (INRAe) LIVESEEDING partner(s): UPV and INRAe Topics: basis to understand population genetics, gene and genotype frequencies estimation, micro-evolutionary forces, practical example with online available simulator (PopGen). Unit duration: 1:30 h 2.5.4 Unit 4 - Using genomics to track the evolution of heterogeneous organic materials Lecturer(s): Dr. Michael Schneider (FiBL) LIVESEEDING partner(s): FiBL Topics: in connection with unit 3, in-depth review on genomic tracking of OHMs evolution, main parameters, practical examples from FiBL projects, etc. Unit duration: 1:30 h D1.1, Training in Organic Breeding 17 3. Materials The available materials for each Module include: - The Training Outline summarizing concepts and learning objectives for each training module; - The corresponding presentations for each unit; - The additional materials suggested in the presentations intended to widen the learning process( i) papers, ii) online available tutorials, iii) links to online available software and simulators, iv) links to projects, etc.); - The live recordings of the courses, with the lecturers explaining in a dynamic way the different units, answering questions, solving the quizzes in common discussion, proposing activities and homework. Table 1. List of training materials available in Organic EPrints repository. Links to Organic EPrints Module 1 https://orgprints.org/id/eprint/54728/ Module 2 https://orgprints.org/id/eprint/54984/ Module 3 https://orgprints.org/id/eprint/54985/ Module 4 https://orgprints.org/id/eprint/55664/ Module 5 https://orgprints.org/id/eprint/55665/ D1.1, Training in Organic Breeding 18 4. Attendees number and profiles A considerable number of people attended the webinars of the different modules , reflecting a wide geographic distribution and diverse profiles. Overall, around 140 unique individuals from 28 different countries attended at least one of the five modules offered (Table 2). Table 2. Representation of participants by country Country Number of attendees Spain 14 France 13 Greece 12 Italy 12 Portugal 9 Germany 8 Poland 7 Hungary 7 Lithuania 6 Switzerland 6 Other1 48 As expected, some modules and units were open to more diverse profiles, like Modules 1 and 2, which were more basic and easily understandable for farmers, seed savers, breeders, students, and even MSc and PhD students. As a consequence, the number of people attending was much higher for those Modules (Table 3). Specifically, Module 1 engaged predominantly students (30%), breeders (28%), and researchers (24%). Module 2 attracted up to 70 participants, mostly researchers and students (Figure 1 and 2). 1 Other countries include: Belgium, Ireland, United Kingdom, Netherlands, Norway, Serbia, Bosnia & Herzegovina, Latvia, Burkina Faso, Croatia, Tunisia, Nigeria, Nepal, Cabo Verde, Czech Republic, Slovenia, Austria. D1.1, Training in Organic Breeding 19 In contrast, Modules 3, 4 and 5 presented content that was more technical and closer to the frontiers of knowledge and, therefore, appealing to more specialized profiles (academics, MSc and PhD students, breeders and molecular breeders). Module 4, for example, engaged predominantly researchers and breeders. Similarly, Module 5 maintained the same profile of attendees (Figures 3 and 4). It is noticeable that a significant number of participants selected the “Other” category when indicating their actor profile. Entries grouped under “Other” included terms such as “seed activist,” “landscape/seed manager,” “NGO leader,” “field agent,” etc. This trend was particularly pronounced in Modules 2 and 3, where the share of “Other” 27% 26% 30% 17% Distribution of participants by actor groups - Module 1 Breeder Researcher Student Other Figure 1 Distribution of participants by actor groups - Module 1 21% 27% 23% 29% Distribution of participants by actor groups - Module 2 Breeder Researcher Student Other Figure 2 Distribution of participants by actor groups - Module 2 24% 46% 15% 15% Distribution of participants by actor groups - Module 4 Breeder Researcher Student Other 20% 57% 14% 9% Distribution of participants by actor groups - Module 5 Breeder Researcher Student Other Figure 4 Distribution of participants by actor groups - Module 4 Figure 3 Distribution of participants by actor groups - Module 5 D1.1, Training in Organic Breeding 20 profiles came close to 30%, reflecting both the diversity of the audience and the limitations of the registration form. Table 3. Number of attendees on the webinars for each Module and Unit. Date Unit 1 Unit 2 Unit 3 Unit 4 Module 1 Jan 27th 105 102 96 --- Module 2 Feb 3rd 70 70 65 60 Module 3 Feb 13th 60 55 58 55 Module 4 March 4th 59 57 46 36 Module 5 March 7th 44 38 35 35