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In this episode with Kai Voss-Fels we dive into the complex world of grapevine breeding. Discover the unique challenges of breeding grafted crops. Enhancing genetic gain becomes multifaceted due to the fact that grapevines consist of two genetically distinct parts, the scion (upper) and rootstock (lower). Our discussion centers on addressing challenges such as water limitation, and drought stress for the lower section, while simultaneously focusing on improving sustainability by introgression of resistances in the uppper part. Moreover, we explore the ACGG (Accelerating Crop Genetic Gain) program, an international research initiative funded by the DFG in Germany, aimed at training PhD students and postdocs to tackle different questions with relevance to speeding up the varietal development process.
Kai Voss-Fels is Professor of Grapevine Breeding at Geisenheim University where he leads a team of researchers, students and technical staff working on genetics, genomics and breeding of grapevine. After completing his PhD in plant breeding and quantitative genetics at Justus Liebig University Giessen in 2016, he was a senior research fellow and group leader at the University of Queensland, Australia from 2017-2021. In 2021, he moved to Geisenheim University to develop a new research program focussed on genomics-assisted rootstock improvement and clonal selection in grapevine.
More:
Department of Plant Breeding, HS Geisenheim ACGG (Accelerating Crop Genetic Gain -
In this episode Jörg Hagmann, Product Manager Pantograph, explores the concept of pangenomes, a collection of individual whole genome sequences. Discover the reasons why pangenomes and their associated research field is experiencing growth and increasing significance. Jörg discusses the vision behind the development of the interactive browser Pantograph and illustrates practical applications in pre-breeding and the identification of gene editing targets. Join us as we delve into the landscape of DNA exploration and the promising future of genomic navigation with Pantograph.
Dr. Jörg Hagmann, Product Manager Pantograph, joined Computomics 8 years ago. He studied Bioinformatics at University of Tübingen and McGill, Montréal, and graduated with researching the evolution of epigenetic marks in plants at the Max Planck Institute for Developmental Biology, Tübingen. Besides his broadexperience in multiple omics data analysis, Jörg is now working on propelling the representation, use, and visualization of pangenomes forward. He develops anovel interactive pangenome browser called Pantograph.
Contact Jörg for more information: [email protected]
Pantograph
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In this episode Helen Brabham, Team Lead at 2Blades, provides a glimpse into the diverse projects of 2Blades. As a nonprofit organization 2Blades is bridging academia and industry, focusing on advancing scientific technologies for disease-resistant crops. Explore how they translate research into practical solutions for smallholder farmers, such as their Africa Soybean Program combating soybean rust. Delve into the NLRseek initiative, aimed at identifying crucial resistance genes to bolster crop resilience against threats like stem rust. Discover their utilization of gene sequences, harnessing machine learning and protein modeling to enhance predictions.
Helen is a Team Leader at 2Blades, a non-profit organisation dedicated to delivering sustainable and environmentally-friendly genetic solutions to protect crops from plant pests and disease. Helen is based with the 2Blades research team embedded at The Sainsbury Laboratory in Norwich, UK and develops a platform for rapidly identifying resistance genes from plants. Helen completed her PhD at The Sainsbury Laboratory part of the University of East Anglia in 2020, and her BSc in Biology from the University of Bristol. Helen’s research focuses on understanding plant-microbe interactions to build disease resistant crops.
Links:
https://2blades.org/
https://computomics.com/news-reader/2blades-computomics.html -
In this episode Addie Thompson, Assistant Professor in the Plant, Soil & Microbial Sciences Department at Michigan State University, discusses her research on disease resistance to tar spot, a fungal pathogen affecting maize. Learn about different modeling prediction techniques and data collection approaches, ranging from manual measurements to high-throughput lidar data obtained via drones. Emphasizing an interdisciplinary approach,Thompson underscores the pivotal role of collaboration in staying at the forefront of research. Additionally, Addie touches on her educational approach in science, teaching her students on how to think about science, how to ask the right questions, and then how to work together in a collaborative group and how to communicate.
Addie Thompson is an Assistant Professor in the Plant, Soil & Microbial Sciences Department at the Michigan State University, and affiliated with the Plant Resilience Institute and NRT-IMPACTS. She earned a BS in Genetics from Iowa State University in 2008 and a PhD in Plant Breeding and Molecular Genetics from the University of Minnesota in 2014. Prof. Thompson’s research focuses on using quantitative genetics, high-throughput phenotyping, and statistical and physical models to predict how varieties will grow in diverse and challenging environments, and to discover genes contributing to these differences.
Link:https://www.thompsonmaizelab.org/
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Our guest in this episode is Randall (Randy) Barker – Co-Founder and CEO at INTENT and Strategic Advisory Board Chairperson at Computomics. He discusses the challenges of adaptinginnovative agriculture products to the diverse practices and environments of different farmers and how technology helps farmers adopt products more effectively. Get insightsinto the global adoption of AgTech, highlighting the varying technological landscapes in different regions. And finally receive tips for startups in the ag tech space. Barker shares his views on the complexities and opportunities in the intersection of agriculture, technology, and innovation.
Randy is the co-founder and CEO of INTENT, an agricultural company focused on the use of technology to accelerate customer adoption of emerging ag products and solutions. Randall has more than 25 years of experience in agribusiness and has worked in over 30 countries, helping launch a number of agtechnologies on a global scale. He holds a bachelor’s degree in Seed Technology from Olds College, a Bachelor of Science in Agriculture and Economics from the University of Lethbridge, and an MBA from the University of Guelph.
Our guest in thisepisode is Randall (Randy) Barker – Co-Founder and CEO at INTENT and Strategic AdvisoryBoard Chairperson at Computomics. Hediscusses the challenges of adaptinginnovative agriculture productsto the diverse practices and environments of different farmers and how technology helps farmersadopt products more effectively. Get insightsinto theglobal adoption of ag tech, highlighting the varying technological landscapesin different regions. And finally receive tips for startups in the ag tech space. Barker shares his views on the complexities and opportunitiesin the intersection of agriculture, technology, and innovation.
Randy is the co-founder and CEO of INTENT, an agricultural companyfocused on the use of technology to accelerate customer adoption of emerging agproducts and solutions. Randall has more than 25 years of experience inagribusiness and has worked in over 30 countries, helping launch a number of agtechnologies on a global scale. He holds a bachelor’s degree in Seed Technologyfrom Olds College, a Bachelor of Science in Agriculture and Economics from theUniversity of Lethbridge, and an MBA from the University of Guelph.
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In this episode, we talk to Jim Schwartz, Director of Research, Agronomy and PFR and Jason Gahimer, PFR Manager, both working for Beck’s Hybrids about the Practical Farm Research (PFR) program. Learn what the PFR program is, why it is important, and how farmers can get involved. Dive into the origins of the Practical Farm Research (PFR) program, tracing its roots back to 1964 when Sonny Beck started this unbiased research program to help farmers succeed by providing them with reliable information on agronomic practices, equipment, and other inputs.
Jason Gahimer, PFR Manager at Beck’s Hybrids grew up on a small family farm in Milroy, IN. He attended Ball State University and graduated with a degree in Computer Technology. Jason has been with Beck‘s for over 12 years and served in many different roles within the Practical Farm Research department.
Jim Schwartz, Director of Research, Agronomy, and PFR at Beck’s grew up in Southern Indiana and went to Purdue University. His career in the seed business for 38 years has included a 17 year stent with Monsanto. Jim‘s last role there was as the U.S. agronomy lead for the regional brands. He was also a partner and co-owner in a seed company called Icorn that he eventually sold to Monsanto. Jim has been at Beck's for 6 1/2 years.Links:
https://www.beckshybrids.com/research/practical-farm-research -
Today’s guest is Kalliopi Rantsiou, professor at the University of Turin. Kelly is sharing insights into the SAFFI - Safe Food for Infants – project. This European funded project evaluates how pathogenic microorganisms may contaminate food for infants, and how we can understand ways of controlling these microorganisms. Learn what role next-generation sequencing technologies play in understanding the microbiota. In a second project, Kelly delves into fermented olives trying to understand what the influence of the microbiota during primary production is and how inoculating a microbial community can foster certain health promoting characteristics.
Kalliopi Rantsiou graduated from the University of Athens in Greece in 1997 with a degree in Biology and continued her education at the University of Davis, USA obtaining a PhD in Food Science in 2002. She then returned to Greece and from 2003 to 2005 was scientific advisor regarding microbial hazards for the Hellenic Food Safety Authority. In 2006 she moved to Italy and initiated her researcher career first at the University of Udine and then at the University of Turin. In 2008 she became researcher/lecturer, in 2016 Associate Professor and in 2022 Professor in Food Microbiology at the same University. Her main research interest is microbial ecology of foods with particular emphasis on combining culture dependent and culture independent approaches to describe the microbiota and its function in foods.
Links:
Safe Food for Infants (SAFFI)
DOMINO project on fermented food
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In this episode, we continue our conversation about barley with Matthias Nachtmann, Sustainability Business Development Lead at BASF. Matthias gives us insights into the "Better Barley" project, which has the goal to reduce greenhouse gas emissions in barley cultivation while supporting farmers to meet the high protein standards for malting barley.
Learn how companies can work with farmers to overcome the challenges of balancing sustainability and productivity. By developing new barley varieties that are both high-yielding and sustainable, the project is helping to ensure that the food industry can continue to produce food in a way that is both environmentally friendly and profitable.
Matthias explains their 3-step approach to the project:
What do you want? How will the first hectare look like? How is the scale-up plan?Better Barley Project:
https://www.agricentre.basf.co.uk/en/Crop-Solutions/Better-Barley/
Podcast with Brent Atthill: Diving into the world of barley
https://podcasters.spotify.com/pod/show/computomics/episodes/Diving-into-the-world-of-barley-e26qe6o
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In this episode Brent Atthill, managing director of RMI Analytics GmbH delves into the fascinating world of barley. Explore the entire supply chain, uncovering the challenges and emerging trends within the industry. Brent provides valuable insights into why having the best quality barley is crucial for the malting process in the brewing industry and gain a better understanding of the role of technology and data in this sector. With his dedication to fostering exchange and sharing best practices, Brent takes the lead in engaging with all stakeholders in the barley network, ensuring a collaborative and thriving industry.
Brent Atthil is an accomplished global professional with over 25 years experience in the grain, malting, and brewing industries, with a proven track record in strategic procurement, team leadership, and business integration. In his current position as principal owner, board member, and managing director for RMI Analytics GmbH, he focuses on driving RMI’s content delivery through their Journal publication, webinars, and global Insights Tours. He is a leader in the development of extensive supply chain strategies designed to deliver continuous, real business value through optimization and a constant challenge to the status quo. Brent is absolutely passionate about agriculture and sustainability!
https://www.rmi-analytics.com/
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In this episode Cyrill Stachniss, professor at the University of Bonn and spokesperson of the DFG Cluster of Excellence “PhenoRob - Robotics and Phenotyping for Sustainable Crop Production” sheds light on the purpose and focus of PhenoRob. Gain insights into the importance of optimizing field management with digital technologies like robotics or machine learning. How can we analyze every plant at high speed to provide management and automatic target actions for every plant. Are there different complexity levels in analyzing and taking actions? What methods, applications and technologies are used to analyze the data? What's the technological outlook for the next 5-10 years?
Cyrill Stachniss is a full professor at the University of Bonn and heads the Photogrammetry and Robotics Lab. He is additionally a Visiting Professor in Engineering at the University of Oxford and is with the Lamarr Institute for Machine Learning and Artificial Intelligence. Cyrill is a spokesperson of the DFG Cluster of Excellence “PhenoRob - Robotics and Phenotyping for Sustainable Crop Production” at the University of Bonn. Before his appointment in Bonn, he was with the University of Freiburg and the Swiss Federal Institute of Technology, ETH Zurich. The research activities of the Photogrammetry and Robotics Lab focus on probabilistic techniques for mobile robotics, perception, and navigation. This involves developing and applying state estimation, machine learning, and AI algorithms for robots and sensor data interpretation. The team has made several contributions to SLAM, localization, place recognition, semantic scene interpretation, autonomous exploration, and navigation. The main application areas of the lab are autonomous service robots, agricultural robotics, and self-driving cars.
Besides his university involvement, he co-founded three startups: Escarda Technologies, DeepUp, and PhenoInspect.https://www.phenorob.de/
https://www.youtube.com/c/CyrillStachniss?
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In this episode Markus Stetter, group leader at the Institute for Plant Sciences at the University of Cologne and member of CEPLAS (Cluster of Excellence on Plant Science) takes us into the exciting history of Amaranth. Markus combines molecular and computational biology approaches to study the domestication of wild plants. Learn how wild plants became crops and how these crops spread around the globe. Furthermore get insights into CEPLAS, its research mission, focus area and education program.
Since 2019, Markus Stetter is a group leader at the Institute for Plant Sciences and member of CEPLAS (Cluster of Excellence on Plant Science). His group is interested in the domestication and evolution of crop plants. To study how wild plants became crops and how the crops spread around the globe the group combines molecular and computational biology approaches. Within BIPON Markus is interested in the conservation and utilisation of genetic diversity from wild plants and novel crops. Markus did his postdoctoral research in the Department of Plant Sciences at the University of California Davis, USA. Before that he was PhD student at the University of Hohenheim, Stuttgart.
https://cropevolution.org/index.html
https://www.ceplas.eu/en/home/
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In this episode Diego Risso, Executive Director of URUPOV (Uruguayan Plant Breeders Association) and Secretary General of the SAA (Seed Association of the Americas), gives insights into the activities of both organizations. What are the major assets, what are the goals and challenges? Diego talks about the UPOV91 framework, intellectual property rights, plant breeders rights and much more. Which role does technology play for the seed industry? Which technology will be relevant in 2023 for agriculture and the seed industry and has the most impact? Get a recap of the SAA Congress 2022, a short outlook to the congress in 2024 and the importance of gene editing in South America.
Diego Risso got his degree in Agronomy in 1997 and in 2001 completed a postgraduate degree in Marketing and in 2013 a postgraduate in seed technology.He has been the Executive Director of URUPOV (Uruguayan Plant Breeders Association) since 2002 and is responsible for developing royalties’ collection systems and enforcing plant breeder’s rights in Uruguay. In 2005 he took the position of Executive Director of the National Seed Institute (INASE-Uruguay) and returned to URUPOV in 2006. Diego is also the Secretary General of the Seed Association of the Americas (SAA) which headquarters are in Montevideo, Uruguay. He is responsible of assisting the 4 working groups in SAA (Biotech, Phytosanitary, Seed treatment, IP). Diego organizes congresses and workshops where seed industry and governments representatives gather to address common agenda items to agree on a joint work plan.
https://www.urupov.org.uy/
https://www.saaseed.org/
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Hannah Senior is CEO of PBS International, President of NAPB (National Association of Plant Breeders) and a podcast creator. In this episode you will get a glimpse into Hannah’s broad experience. Learn about the process of developing new solutions within PBS International for plant breeding.
On top of that, Hannah shares her story on how she became the first president of the NAPB from outside North America. During her period as president of the NAPB Hannah is focusing on 3 themes: Putting more structure into the organization, fostering exchange with other international plant breeding organizations and communication and advocacy.
Last but not least get to know what made her become a podcast creator and host of the Plant Breeding Stories podcast.Hannah Senior grew up in a farming community but followed a career into corporate life working with multinational companies, including 5 years with Tesco. She completed an MBA at Stanford University before returning to the UK and agriculture when she acquired PBS International, a company which makes specialist pollination control products for plant breeders and seed producers around the globe.
Hannah’s business career brought her into plant breeding but her contribution to this discipline goes further than PBS International. She has championed communication about plant breeding and highlighting the diversity of perspectives through activities like the podcast series she created called Plant Breeding Stories, and as President of the National Association of Plant Breeders (NAPB).
Hannah’s interest in plant breeding sits alongside her interest in AgriTech entrepreneurship more generally.[nbsp] She holds Board and advisory positions with several AgriTech companies including Crop Health and Protection, the UK’s government-backed Agritech centre for Crops.PBS International: https://www.pbsinternational.com/
NAPB: https://www.plantbreeding.org/
Podcast - Plant Breeding Stories: https://www.pbsinternational.com/podcast/
Book recommendation: Braiding Sweetgrass from Robin Wall Kimmerer
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In this episode Stefan Schmitz, Executive Director of the Crop Trust, gives comprehensive insights on the background, history and purpose of the Crop Trust. Learn how conserving seeds works and how it is ensured that the seeds are safe and secure. What is the difference between seed banks in general and the Svalbard Global Seed Vault? Why is the Global Seed Vault located in Svalbard and what is so extraordinary about it?
Stefan Schmitz joined the Crop Trust as Executive Director in January 2020. He previously worked as Deputy Director-General and Commissioner for the “One World – No Hunger” Initiative at the German Federal Ministry for Economic Cooperation and Development (BMZ). He also chaired the Steering Committee of the Global Agriculture and Food Security Program (GAFSP). For more than 10 years, Stefan was leading the food security, agriculture and rural development work at BMZ. From 2007 until 2009 he worked as senior advisor to the Secretariat of the Organization for Economic Cooperation and Development (OECD) in Paris. Before joining the BMZ in 2001, Stefan held various posts in the German federal administration in the fields of geographical information systems, regional planning and international cooperation on urban issues. He received scholarships of the McCloy Fellowship of the American Council on Germany and of the German Academic Exchange Service. After studying in Bonn and St. Andrews, he graduated from Bonn University in geography and mathematics and received a doctorate in geosciences from the Free University of Berlin in 2000.
More information about the Crop Trust: https://www.croptrust.org/
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In this episode, Patrizia Ricca from Computomics gives us comprehensive insights into xSeedScore – a breeders’ tool to develop new crop varieties adjusted to future climates. Learn about how to work with xSeedScore, about the benefits of using machine learning, and how it differs from conventional methods. What data is needed to apply xSeedScore? What role does the interaction between genetics and temperature play for future varieties?
Patrizia Ricca joined Computomics 4 years ago as Bioinformatics Analyst. She studied Plant Molecular Biology and Bioinformatics at the University of Tübingen, graduating at the Center for Plant Molecular Biology and the Max Planck Institute for Developmental Biology, Tübingen. Patrizia has worked in industry and academia in multiple fields. She has comprehensive and unique knowledge in plant biology, genomics, metagenomics, transcriptomics and machine learning. Since beginning of the year 2022, Patrizia is the Scientific Product Manager for xSeedScore – Computomics’ predictive plant breeding technology.
Details xSeedScore: https://computomics.com/services/innovative-plant-breeding.html
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In this episode Thomas Lübberstedt a professor of agronomy from Iowa State University shares his research goals focusing on doubled haploid technology in maize breeding. What are the challenges, what did they achieve already and what are the further research plans? How can doubled haploid speed up the process of getting homozygous lines?
A second focus area is on the organic farming industry. Within 2 organic projects, Thomas is working with a sweet corn breeder and a popcorn breeder on different research goals ranging from the use of natural traits instead of GMO to inbred performance under weedy conditions.Thomas Lübberstedt is Professor and K.J. Frey Chair at the Department of Agronomy, Iowa State University (ISU). Thomas serves as Director of the R.F. Baker Center for Plant Breeding, and the Distance M.S. in Plant Breeding program. He is founder of the Doubled Haploid (DH) Facility, and Faculty Scholar of Plant Sciences Institute at ISU. Thomas served as chair of the Plant Breeding Coordinating Committee (PBCC) in 2016/17. He continued to contribute to the PBCC education objective and was co-host of the 2022 NAPB meeting at ISU.
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In this episode Prof. Dr. Dominik Grimm from TUM Campus Straubing and Weihenstephan-Triesdorf University of Applied Sciences gives us insights into CropML, a BMBF funded project. The project evaluates new machine learning techniques for more accurate plant breeding by integrating heterogeneous external factors. Different phenotype prediction models, including basic genomic selection methods to more advanced deep learning-based techniques have been compared. Learn why advanced models are the future and where the challenges are.
Dominik is heading the Bioinformatics department at TUM Campus Straubing. He received his PhD from Max-Planck-Institute for Intelligent Systems & Max-Planck-Institute for Developmental Biology Tübingen in 2015. Dominik did his PostDoc at ETH Zürich. From there he moved on to TUM where is now Head of Bioinformatics. He receved a prize for Excellence in Teaching two years in a row.
Publication: https://www.frontiersin.org/articles/10.3389/fpls.2022.932512/full
git: https://github.com/grimmlab/easyPheno
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The October episode is a special one as we are celebrating 10 years of Computomics! We give a retrospect of Computomics through plants. Get to know 10 different plants Computomics has worked on. The plants range from rather well known ones like rice, soy, corn and banana up to rather unusual ones like the mamala tree which is native to various tropical islands. You will hear some fun facts about the plants before receiving some insights on the challenges and questions Computomics addressed. In the last 10 years Computomics performed genome assemblies, genome annotations, methylation patterns, predictive plant breeding and much more.
Dr. Sebastian J. Schultheiss, Managing Director of Computomics, founded Computomics together with a very experienced board of scientific advisors from ETH Zurich, Max Planck Institute for Developmental Biology and the University of Tübingen. Sebastian studied Bioinformatics at University of Michigan and Tübingen. He worked on Machine Learning research and its application to biological data for his PhD degree at the Max Planck Institute for Developental Biology and FML. He brings startup experience, boinformatics skills and machine learning expertise to Computomics, which brings superior prediction accuracy and unprecedented integration of phenotyping, genotyping, management and environmental data to agriculture, enabling its clients to produce stable, value-added crops.
Links to MethylScore:
- MethylScore
- MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data -
In this episode, listen to Anne Buchwalder, an experienced plant breeder for different crops ranging from pea, cantaloupe, sweet and hot pepper to cocoa. Anne shares her view on sustainable agricultural production, what it implies for the consumer but also the impact on the producing country. Learn about the value chain from farmer to customer. The second part of this episode covers the role technology plays for plant breeding and how it can help plant breeders breed forward. Technology has improved over the last 25 years and plant breeders have much more tools in their [nbsp]toolbox available today.
After her graduation in agronomy, Anne started her career as commercial plant breeder. During 13 years she had been in charge of several vegetable breeding programs for different seed companies: processing pea, cantaloup sweet and hot pepper, in Europe and Middle East. In 2010 Anne joined Nestlé group to support the Global sustainable sourcing of cocoa beans -Nestlé Cocoa Plan. In 2018 she took the head of a research institute center specialized in perfume and medicinal plants. Since the pandemic Anne started a freelance consultancy activity. Today she is helping companies in the horticultural sector to structure their R[&]D teams and to broaden their expertise to achieve their goals to support more sustainable practices and resilient cropping systems.
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To shorten the summer break we take a quick look back what we covered in the last season and give a preview of what to expect in season 4. We already have a great line-up for the next season, stay tuned and don't miss any episode! If there is anyone out there you would like to listen to with interesting stories in agriculture and technology, let us know. Just send us a short message to [email protected].
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