2024 Summer Institute in Plant Breeding

Summer Institute in Plant Breeding (in person)

10 - 14 June 2024

Saint Paul, Minnesota, USA

Offered by the

Plant Breeding Center at the University of Minnesota, also featuring instructors from the University of Wisconsin-Madison

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

• Plant Breeding 101 (James A. Anderson)
• Mixed-Model Analysis in Plant Breeding (Lucia Gutierrez)
• Professional Skills for Scientists (Rex Bernardo)

SET 2

• Polyploid Genomics (Laura M. Shannon)
• Participatory Plant Breeding (Julie Dawson)
• Data Bootcamp for Genomic Prediction in Plant Breeding (Aaron J. Lorenz)

Target Audience

Plant Breeding 101 is intended for those who seek a course in the fundamentals of plant breeding (technicians, data scientists, managers, non-plant breeding graduate students, etc.).

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

Costs

US $490 for graduate students, postdocs, and faculty

US $650 for industry participants

Cost includes lunch and morning and afternoon breaks. Breakfast, dinner, and accommodations are not included. We regret that scholarships or reduced fees are unavailable.

Questions?

Contact Rex Bernardo by email ([email protected])

-------------

Module descriptions

Plant Breeding 101. This course is for those who seek to learn the fundamentals of plant breeding (e.g., technicians, data scientists, managers, non-plant breeding graduate students, etc.). Each session will include lecture/discussion, demonstrations, and problem-solving with sample data.

Session 1: Genetic variation, qualitative and quantitative inheritance, heritability

Session 2: Phenotyping, experimental design, genotype x environment interaction, data analysis and summary

Session 3: Modes of reproduction, types of cultivars, parent selection, breeding methodologies

Session 4: Genetic mapping, breeding using major genes/markers, genomic prediction

Session 5: Polyploidy, breeding for pest resistance, breeding asexually propagated species, intellectual property protection

Mixed-Model Analysis in Plant Breeding. This course provides an introduction to mixed-model analysis will cover the following topics: matrices and matrix manipulations; linear models; mixed effects models and their development; covariance structures; mixed-model equations; shrinkage; properties of estimates and predictions; analysis software; and applications in experimental designs and in plant breeding. The course will involve lectures, problem sets, and hands-on data analysis activities.

Professional Skills for Scientists. This course will cover what a group of former graduate students said is “Stuff I wish I learned in graduate school, but that I instead had to learn the hard way in [company X].” The overall goal of this course is to help prepare graduate students for their future careers. Specific goals are to increase student awareness and improve student skills in leading people, and in managing money, time, operations, and projects.

Session 1: Life cycle of a scientist; industry versus academe versus nonprofit; company structure; budgeting

Session 2: StrengthsFinder; differences in the workplace; building a high-functioning team

Session 3: Managing yourself; preparing for your job interview; hiring, motivating, evaluating, and transitioning employees

Session 4: Managing your bosses; resolving conflict

Session 5: Work-life harmony; messaging; written and oral communication

Polyploid Genomics. Polyploidy (and accompanying rediploidizaion) is a major component of plant evolution. All flowering plants have undergone at least one whole genome duplication event in their history. Furthermore, a wide variety of important crop plants are current polyploids. Despite the ubiquity of polyploidy, polyploid genomes are difficult to analyze. They complicate many of the tools and models most commonly used in genomics and breeding. This course will involve lectures, discussions, problem sets, and hands-on data analysis activities.

Session 1: Polyploid evolution

Sessions 2-3: Challenges presented by genotyping and sequencing polyploids; tools to overcome them; ways of determining ploidy

Sessions 4-5: Population and quantitative genetic theory for autopolyploids; new tools for polyploidy research

Participatory Plant Breeding. This course is for plant breeders who are evaluating the advantages (and disadvantages) of incorporating participatory methods into their breeding program. Each session will include lecture/discussion, demonstrations, and problem-solving with case studies.

Session 1: Overview of participatory plant breeding, including different types of PPB and examples; types of engagement and participation, PPB programs internationally and domestically

Session 2: Determining when participatory methods are advantageous to a breeding program; crops and markets, environments, seed markets, seed regulation and intellectual property

Session 3: Design of participatory breeding programs; types of trial designs, types of varieties released, commercialization methods

Session 4: Experimental design and analysis for different types of participatory programs; applying core concepts, methods for decentralized and unbalanced trials

Session 5: Practical aspects of managing a participatory program; engagement, logistics, troubleshooting, scaling-up, evolution of goals and methods

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. This course will include lectures and hands-on activities. (Prerequisite: basic knowledge of programming in R)

Sessions 1-2: Formatting and quality control of genotype/phenotype data for genomic prediction, model implementation and exploration of various types of models, techniques in cross validation for assessing prediction accuracy

Sessions 3-4: Training population optimization, multi-trait prediction, genomic prediction for genotype x environment interaction, predictions of all possible crosses

Session 5: Other special topics in genomic prediction, tour of available tools for implementing genomic prediction

Host or Publisher Rex Bernardo