2023 Summer Institute in Plant Breeding

Summer Institute in Plant Breeding (in person)

3 - 7 July 2023

Ghent, Belgium

Offered by the

Plant Breeding Center at the University of Minnesota

VIB | International Plant Biotechnology Outreach at the Ghent University

Modules

Participants can register for one module in Set 1 (Monday to Wednesday noon) and one module in Set 2 (Wednesday afternoon to Friday afternoon):

SET 1

• Genomewide Markers in Plant Breeding (Dr. Rex Bernardo)
• CRISPRing in Plants (Dr. Thomas Jacobs)
• Machine Learning Applied to Plant Science (Dr. Tolutola Oyetunde)

SET 2

• Genetic Analysis in Understudied Plants (Dr. Laura Shannon)
• The Many Dimensions of Plant Phenotyping (Dr. Hilde Nelissen)
• Data Bootcamp for Genomic Prediction in Plant Breeding (Dr. Aaron Lorenz)

Target Audience

The other modules are intended for M.Sc. and Ph.D. students, postdocs, researchers, and industry scientists

Costs

US $475 (~€450 as of December 2022) for graduate students, postdocs, academic researchers, and faculty

US $625 (~€595 as of December 2022) for industry participants

Cost include lunch and morning and afternoon breaks. Breakfast, dinner, and accommodations are not included.

Disclaimers

A module might not be held if a minimum class size is not met. In this situation, participants can choose a different module or be refunded the full cost of the cancelled module.

The organizers are not responsible for losses due to unforeseen circumstances (e.g., a resurgence of COVID-19), and travel insurance is strongly recommended.

Questions?

Contact Dr. Rex Bernardo by email (bernardo@umn.edu)

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Module descriptions

Genomewide Markers in Plant Breeding. Principles, concepts, and practices regarding the use of molecular markers to improve quantitative traits in plants. The course will include both theory and hands-on computer sessions in an active-learning format.

CRISPRing in Plants. The objective of this course is to provide students with the fundamental theory and experience to perform genome editing (CRISPR) experiments in their own projects. Using a combination of lecture and hands-on computer work, students will learn the fundamentals of performing a CRISPR experiment; the variety of techniques and editing outcomes, best practices and quality control steps throughout the whole pipeline, and how to analyze genotyping results.

Machine Learning Applied to Plant Science. This short course provides an introduction to core concepts in machine learning and data science. It will separate hype from fact, demystify machine learning, and critically examine prospects and limitations of data science as applied to plant science. Lectures, demonstrations, and hands-on exercises are designed to encourage the participants to think of ways of applying machine learning to solve practical problems in their current and future research.

Genetic Analysis in Understudied Plants. Genetic analysis is an incredibly powerful tool in crop breeding and research, allowing us to predict breeding values, simplify selection processes, identify causative loci and pathways for traits of interest, and describe and assess diversity. However, many important plants lack prerequisites, like reference genomes or genetic maps, for commonly used analyses. New technologies have made it relatively cheap and easy to generate genetic data on these organisms, but effectively analyzing this data is more complicated. We'll use case studies from my research and yours to talk about some of the challenges of working on non-model systems. This course will be heavily discussion based with lectures, problem sets, and hands on data analysis activities.

The Many Dimensions of Plant Phenotyping. Plant phenotyping is a very broad field. Everyone involved in plant breeding or plant research will at one point, knowingly or unknowingly, deal with plant phenotyping. Plant phenotyping occurs at many scales, from the field down to the cell, at different temporal resolutions, from one-off measurements to time-series of constant measurements, at varying levels of details. Continuous advancements in technology keep extending the borders of what is possible, allowing us to take measurements in ever-higher detail or at an ever-higher throughput. In this course you will get an overview of plant phenotyping at the different scales, followed by a deep-dive at each level, to show you what is possible.

Data Bootcamp for Genomic Prediction in Plant Breeding. This course will cover common data structures, analysis techniques, and tools used for genomic selection in plant breeding. The sessions will include lectures and hands-on activities.