Computomics Podcast - In Conversation

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

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?

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.

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

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:

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.

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].

Anthony Hall is giving comprehensive insights into the Earlham Institute, the research projects he is working on and why it is important to surf the wave of data. Learn how technology helps in integrating all data – genomic, phenotypic and environmental data - and which role AI plays. Generating data, analyzing it and making it reusable is key to Anthony. Get insights into projects on circadian regulations of the transcriptome in polyploid crops, introgression breeding in wheat and GWAS on heat tolerance in wheat in collaboration with CIMMYT.

Anthony is the head of Plant Genomics at Earlham Institute. He moved from the University of Liverpool where he held the Holbrook Gaskell Chair of Botany at the University of Liverpool. He was research lead for the Institute of Integrative Biology. Was director at the Centre for Genomic Research (CGR) and academic lead of the Liverpool GeneMill (£3.8M investment). He received his PhD from the University of Leicester in 1997 from the Botany Department and has worked as an Arabidopsis molecular geneticist for 18 years, focusing on the field of plant circadian biology.

If you want to learn more about the latest research projects you can reach out to Anthony here.

Links to papers and preprints mentioned in episode:

Circadian regulation of the transcriptome in a complex polyploid crop

Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Am. muticum introgression lines

Exotic alleles contribute to heat tolerance in wheat under field conditions.

In this episode, Alessio D’Antino, the founder of Forward Fooding tells us about the start of the platform – from the very beginning of the idea to how it developed. Why is it important to connect all the players in the food and beverage ecosystem? How can we contribute positively to a system that leverages new technologies and makes it more efficient? What is the methodology behind the FoodTech 500 (FT500) - the fortune 500 of AgriTech?. Why is sustainability such an important criteria for FT500? On top of this, receive insights into the trends and future of AgriTech. Alternative proteins, AI and microbiome are just a few examples. What are future game changers and what are challenges startups are facing?

In this episode, Karsten Borgwardt gives insights into his current research projects. In two examples, Karsten explains how machine learning algorithms are being developed specifically in the medical sector. Learn about the importance of massive amounts of data, and how this data is used to train a machine learning model to predict the probability of a sepsis of individual patients. Understand the various challenges, the importance of big datasets, the importance of validation, and why it’s a huge undertaking to make machine learning in medicine work. Apart from the Sepsis Study hear how Karstens career started in plant genetics and how the field has grown in importance.

In this episode we talk to Tom Koch, research manager at Beck’s Hybrids. Tom talks about the challenges of a mid-size breeding company and gives insights into how technology helps Beck’s stay ahead of competition. Apart from technology, learn what else is important in corn breeding and what role data plays especially for phenotyping.