Training for Student

1^ST STUDENT TRAINING WORKSHOP UNDER THE BUILDING CAPACITY IN PLANT BREEDING AND BIOTECHNOLOGY EDUCATION AND RESEARCH THROUGH PARTNERSHIP PROGRAM IN AFRICA, THE MIDDLE EAST, AND EUROPE FOR AGRICULTURAL TRANSFORMATION (BREEDTECH) INITIATIVE

1. INTRODUCTION

The target group addressed by the BREEDTECH Student Training Workshop consisted of undergraduate and graduate students from Kenyan, Ethiopian, and Palestinian higher education institutions. These students were selected based on their academic focus in agricultural sciences, plant breeding, genetics, and biotechnology. A total of 8 students participated in the workshop, representing diverse academic backgrounds, including plant genomics, crop science, and biotechnological applications in agriculture. We had a total of 9 participants from Kenya (Laikipia and Egerton) and Palestine (An-Najah and Al-Quds). Unfortunately, we did not have participants from Ethiopia since the appointed students failed to receive the visa in due course. In order not to lose their opportunity, the team in Pisa agreed to host these students during the Staff Training event planned for September 2025.

2. TRAINING COURSE

This training was structured over a period of five consecutive days, each designed to build progressively from foundational genetic concepts to hands-on laboratory skills and applied analysis. The training combined theoretical lectures, interactive discussions, and practical sessions, with each day focusing on a specific theme. The outcomes reflected participants’ improved understanding of molecular genetics, enhanced technical competencies, and preparedness to apply these techniques in their own research or institutional settings. The following sections provide a day-by-day breakdown of the training activities, key topics covered, and the corresponding outputs and outcomes.

Day 1: Fundamental Principles of Genetics and Molecular Biology

The first day of the training workshop began with an introductory roundtable session designed to set the tone for the days ahead. Participants and trainers introduced themselves, shared their academic or professional backgrounds, and discussed their expectations for the workshop. This session helped establish a sense of community and laid the groundwork for open dialogue and collaborative learning throughout the training.

The morning lecture sessions focused on fundamental principles of genetics, structured into three thematic parts to progressively build participants’ understanding: i) the uniqueness of the genetic approach, ii) the relationship between genotype and phenotype, the molecular role of DNA, and iii) the application of genetic markers and maps. In the afternoon, the focus shifted to practical preparations. A lecture introduced the principles and workflow of DNA extraction and PCR, highlighting key techniques, challenges, and the importance of accuracy. The session also included a comprehensive orientation on laboratory safety, ensuring participants were well-prepared for the hands-on sessions to follow.

Day 2: Practical Sessions on Fundamental Molecular Biology Techniques

On the Second day, students engaged in a comprehensive hands-on laboratory session focused on fundamental molecular biology techniques. The day began with sampling leaf material from bean and maize plants, followed by sample preparation using liquid nitrogen, mortars, and pestles. Students then carried out DNA extraction and quantified the DNA using a Nanodrop spectrophotometer. This was followed by setting up PCR reactions, preparing agarose gels, and performing gel electrophoresis to visualize the amplified DNA. The session concluded with a preliminary discussion of the results. The training approach combined brief theoretical introductions with practical activities. Each method was clearly explained before the hands-on exercises to ensure students understood the objectives and procedures. Participants were divided into small groups, each supported by a facilitator who guided them through the tasks and provided individual support where needed.

Student participation was generally strong, with many showing high levels of interest and enthusiasm. However, it was noted that student engagement levels varied perhaps due to different levels of practical experience. In future, the working groups could be organized according to participants’ varying levels of education and practical experience to better address individual learning needs and optimize engagement. Nonetheless, most students demonstrated a solid grasp of the scientific concepts and confidently applied the techniques introduced as showcased by the successful completion of planned activities for the day. The following day, the results were revisited through an interactive discussion session, which encouraged critical thinking and peer learning. Students not only acquired new technical skills but also explored how these could be applied within their own research or areas of interest.

Day 3: Genomics and Transcriptomics

This session aimed to bridge foundational genetic knowledge with advanced technologies, demonstrating how these approaches can be used to unravel complex trait regulation, improve crop performance, and address challenges in agriculture and biotechnology. The lectures on day three provided a comprehensive overview of genomics, covering the basics of the genome, its physical composition, and structure, including the genomes of cell organelles. It explored genomic features such as coding sequences (genes), repeat regions (including tandem and interspersed repeats, with a focus on transposable elements). The second part introduced transcriptomics, emphasizing the importance of coding and non-coding RNAs in the functioning of living organisms. It discussed how dynamic gene expression regulation impacts cell differentiation and phenotypic plasticity, with examples of non-coding RNAs and their significance. The lecture also reviewed the development of techniques for studying the transcriptome, highlighting dominant modern technologies.

The session culminated with PhD students from ISP sharing their current research projects, academic backgrounds, and personal journeys in research. They provided valuable insights into how they selected their research focus, particularly highlighting the use of genomics and related technologies in advancing their studies. Their presentations illustrated practical applications of genomics in addressing real-world scientific questions and showcased strategies for pursuing research goals, inspiring participants through authentic examples of academic and professional growth.

The session used a mix of lectures, videos, presentations, student questions, and open discussions between presenters and students. About half of the students participated actively, with many questions, especially on transposable elements and the case studies presented by PhD students. They asked insightful questions, showing interest and understanding of the lecture content. However, the animated videos on sequencing techniques were less successful, with some students expressing difficulty in following them. It was suggested that explaining via whiteboard could allow for better interaction.

Day 4: Hands-On Genome-Wide Association Analysis using TASSEL Software

The fourth day of the training was dedicated to building a comprehensive understanding of trait and genotype association analysis. The session began with an in-depth overview of the theoretical foundations and biological relevance of identifying genetic markers linked to phenotypic traits. This background was followed by clear and intuitive explanations of key methodologies, particularly Genome-Wide Association Studies (GWAS) and Quantitative Trait Loci (QTL) mapping. These concepts laid the foundation for a practical, hands-on segment using the TASSEL software platform. The training walked participants through a full association mapping workflow. This included the installation of the TASSEL software, quality control checks for genotype data, and relatedness analyses using kinship matrices, principal component analysis (PCA), and multidimensional scaling (MDS). The session culminated in performing GWAS using TASSEL.

The training employed a blended teaching approach. Theoretical sessions were delivered through visually rich tutorials that used diagrams and graphics to explain complex concepts. These were complemented by live, step-by-step demonstrations that helped participants gain confidence in using the software.

Participant engagement was high throughout the session. Enthusiastic involvement was particularly evident during the installation and GWAS exercises, with trainees frequently seeking clarification and guidance. Master’s and PhD students found the content especially relevant and accessible, as demonstrated by their active participation during the question-and-answer sessions. Many were able to connect the material directly to their own research projects, showing a strong intent to apply what they had learned.

Undergraduate participants, however, appeared to find some of the advanced content more challenging, which was reflected in their more reserved participation. The varied academic backgrounds of the trainees resulted in different learning speeds and levels of comprehension. Trainers had to make an extra effort to ensure that all participants, regardless of prior knowledge, could keep up with the exercises and achieve the core learning objectives.

By the end of the day, most participants had acquired a solid foundational understanding of genotype-trait association analysis and felt confident in navigating the TASSEL interface to carry out basic GWAS analyses. The session not only improved technical skills but also sparked interest in applying these methods to ongoing and future research projects.

Day 5: Advanced genetic tools for plant breeding

The final day of the training focused on advanced genetic tools for plant breeding, specifically Genome-Wide Association Studies (GWAS), genomic prediction, and genome editing. Building on day 4, the session aimed to deepen understanding of how these genomic techniques can improve crop traits and productivity, particularly for smallholder farmers in developing economies. The day included a blend of lectures, discussions, and real-world case studies to connect theory with practical applications. This approach allowed participants to engage with both the scientific principles and the practical use of these technologies in breeding programs. Active participant engagement fostered a collaborative learning environment, enhancing the relevance of the content.

Key outcomes included discussions on improving genomic prediction accuracy through advanced statistical models and integrating participatory variety selection data. Participants also explored CRISPR-Cas systems for genome editing, learning about its mechanisms, applications, and ethical considerations. Case studies demonstrated the successful use of these technologies to improve crop resilience and productivity.

In conclusion, day five equipped participants with both theoretical insights and practical tools to apply modern genomic techniques in plant breeding, emphasizing their role in enhancing global food security while remaining accessible for smallholder farmers.

3. CONCLUSION

This BREEDTECH training workshop received overwhelmingly positive feedback. Participants rated both the content and delivery highly, especially appreciating the practical, relevant, and expertly led sessions. The students expressed strong interest in long-term engagement and collaboration. As an output, SSSA presented students with attestations recognizing their participation. Additionally, all training materials used during the workshop were provided to the students to support their ongoing learning.

First Student Training Course: Advanced Applications of Genetics and Genomic Tools In Crop Improvement: Scuola Superiore Sant’Anna Pisa, Italy, 5th to 9th May 2025:

Training Course Programme

Fig. 1: A photo of workshop participants alongside some of the trainers who facilitated the session on Day 1, marking the beginning of a productive and engaging workshop.

Fig. 2: Students participating in a hands-on molecular biology training session. During this practical, they extracted DNA, performed PCR amplification, and conducted gel electrophoresis to visualize the amplified DNA. The session provided foundational skills in molecular lab techniques and reinforced theoretical knowledge with real-world application.

2^nd STUDENT TRAINING WORKSHOP UNDER THE BUILDING CAPACITY IN PLANT BREEDING AND BIOTECHNOLOGY EDUCATION AND RESEARCH THROUGH PARTNERSHIP PROGRAM IN AFRICA, THE MIDDLE EAST, AND EUROPE FOR AGRICULTURAL TRANSFORMATION (BREEDTECH) INITIATIVE

Second Student Training Course: Classical and Modern Approaches in Crop Breeding 22-26 September 2025, IFVCNS, Novi Sad, Serbia:

1. Introduction

In IFVCNS, participants took part in theoretical, field and laboratory sessions on classical breeding, tissue culture, molecular breeding, high-throughput phenotyping, seed production and data analysis. The training also offered students opportunity to learn more on commercial breeding, practical application of -omics tools in crop improvement, as well as get first-hand experience and information form the IFVCNS staff involved both in development and commercial application of new tools and technologies in breeding. In addition to the technical sessions, the workshop provided opportunities for networking, and discussions on actual problems and challenges in crop improvement and agriculture in Mid-East and Africa, and possibilities of the application and transfer of the knowledge gained during the training in the student’s respective countries.
The trainees consisted of 5 master and PhD students from Kenyan (2 participants), Ethiopian (2 participants), and Palestinian (1 participant) higher education institutions with backgrounds in plant breeding, plant production and crop protection.

2. Course Structure

This training was done during five consecutive days, designed to provide student theoretical basis in crop improvement methods, tools and data analysis and then enable students to gain practical skills and hands-on training in the lab and in the field. The training combined theoretical lectures, interactive discussions, as well as practical sessions, with each day focusing on specific themes.

Day 1: Fundamental molecular biology techniques

First day was a hands-on laboratory session focused on fundamental molecular biology techniques. The day began with sampling leaf material from wheat plants, followed by sample preparation using mortars and pestles. Student then carried out DNA extraction and quantified the DNA using a Nanodrop spectrophotometer. This was followed by preparing agarose gel, and performing gel electrophoresis to visualize the extracted DNA. Each step was explained in detail as to ensure that student understood the objectives and procedures.

Day 2: Classical breeding

Tuesday began with tour-de-table and participants and trainers introduced themselves, shared their academic or professional backgrounds, and discussed their expectations for the workshop. The lectures on the second day were devoted to classical breeding and were structured into four thematic parts: i) use of genetic resources in breeding, ii) inbred line breeding, iii) hybrid breeding and iv) breeding for resistance. Those sessions enabled students to learn about principle of plant breeding, different tools and approaches used, and were supported by practical examples and solutions that could be applied in their respective countries.

Day 3: Modern applied tools in plant breeding

Lectures on the Wednesday aimed to build up on what was learned on the second day and demonstrate to students modern tools that are applied in breeding as to accelerate it and make it more efficient. The lectures comprised: i) tissue culture, ii) molecular breeding and iii) HTPP in lab and in the field. The lectures were interactive with demonstrations of the actual experiments and work in the lab and field, along with some mobile phone applications that could be used for plant phenotyping. Students also took part in quiz where they were asked questions related to the lectures.

Day 4: Seed Production

Thursday, the fourth day of the training, was dedicated to seed production as the final stage in breeding process, along with the different aspects of the data analysis. From practical examples students learned on important factors for successful seed production and the rules and regulations that need to be respected. They were shown how Excel could be used for complex data analysis, as well as basic principles of integrated analysis of different data. The lectures were interactive with lecturers using examples from their own work, as to make the lectures more understandable to the students.

Day 5: Visit to germplasm collection and breeding nurseries

In the morning session of the Friday students visited germplasm collection and breeding nurseries of different field crops. There they were introduced to the basic principles of the field work and learned particularities of the both non-commercial and commercial breeding of different crops. They were also able to see in the practice the application of the methods they were introduced to on the second day of the training. During this session students were also shown speed breeding facility, along with the demonstration of the use of drones for HTPP in the field. In the afternoon, the students prepared in vitro grown plants for phenotyping and scanned prepared samples using WinRHIZO. They also learned how to analyse and interpret obtained data. They were also shown the basic of root phenotyping and steps and requirements to successfully prepare rhizotrons for imaging and data analysis. This session, along with the morning session related to speed breeding and use of drones for HTTP enabled students to see in practice the application of the modern breeding tools they were introduced to in the third day of the training. scanning a hands-on training on plat emasculation, which is one of the crucial steps in breeding process.

3. Conclusion

The evaluation feedback showed high satisfaction with the competence of trainers and their ability to transfer knowledge, course content, structure of the course, and the quality of the practical sessions. These results underscored the strong demand for continued capacity-building workshops and ongoing engagement to further support research development.
In the open-ended responses, Participants appreciated the structure and organization of training course. They also appreciated the high level of trainers’ qualification and experience. Trainees suggested for future training courses, more practical sessions especially for data analysis.