Population genetics with applications in plant-microbe interactions
Course description
When and how can population genetic tools be applied studies regarding plant-microbe interactions? If you are working within plant pathology, this course will help you understand life cycles and pathogen population structure in an evolutionary context. The course combines theoretical population genetics with hands-on bioinformatic analyses, using real data from pant-pathogen systems.
Ecological and evolutionary processes influence pathogen population dynamics and disease development. Studies on the population genetics of plant pathogens provides important information about processes of disease epidemics such as the generation and spread of virulence factors. In addition, surveys of genetic variation and population structure are valuable to generate hypotheses about evolutionary processes in disease-causing organisms, and can often directly contribute to informed decisions in disease management. The topics of the course are also applicable in other contexts where questions pertaining to population genetics are of interest.
The course will provide students with a theoretical background on population genetics and also give practical experience demonstrating where to apply tools in data analyses during practical exercises.
The course is intended for PhD students within the SLU Graduate School Organism Biology, and is open for all interested SLU PhD students. If space permits, other SLU staff and PhD students from other universities are also welcome to apply.
Course facts
P000185, Population genetics with applications in plant-microbe interactions, 4.0 Hp
Print syllabus
Syllabus
Valid from : Autumn semester 2026 (2026-08-31)
Level
Third cycle
Subject
Biology
Grading Scale
The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.
Course language
English
Entry Requirements
- Experience of statistical analysis in R from introductory course (or equivalent) is required
Objectives
Population genetics is an important tool to understand the life cycles of microorganisms causing diseases in plants and is an important part of plant-microbe interactions. The aim of this course is to equip students with knowledge and tools to carry out a population genetic study in any pathosystem. After this course, the student will be able to:
- Discuss and critically evaluate population genetic theory and how it can be applied when studying disease causing organisms.
- Design sampling strategies to address a given problem and plan an experiment for molecular-based population biological analysis to answer population genetic and evolutionary questions.
- Be able to work in High-Performance-Computing (HPC) environments for population genetic data analysis
- Use a scientific workflow systems for bioinformatic, such as Nextflow, to run basic population genetic pipelines
- Apply and interpret core methods and analytical tools available in population genetics.
- Reflect on assumptions, limitations and ethical aspects when drawing conclusions from population genetic analysis
Content
A theoretical block will introduce and discuss population genetic principles including evolutionary forces acting on pathogen populations and the theoretical background on various analyses. This will be realized using flipped classroom, i.e., the literature and lectures will be available online and discussed during thematic online seminars.
The second part will be more hands-on where the theoretical knowledge will be applied on real data. It will start with a lecture describing state-of-the art molecular tools that can be used in population genetics. The students will then be trained in tools available in population genetics during three practical exercises, each with a specific theme: Read mapping, Using a variant call file (VCF) and Population structure.
The examination task will give students the opportunity to apply their knowledge to a prepared dataset and address a relevant population genetic question relating to plant-microbe interactions. This activity will allow them to demonstrate and reflect on the skills they have acquired during the course.
Examination Formats and Requirements for Passing the Course
The following is required for a pass mark on the course: - Active participation in at least half of the online discussion seminars and practical exercises. - Approved written or oral report of the examination assignment demonstrating achievement of the intended learning outcomes.
Responsible Department/Equivalent
Department of Forest Mycology and Plant Pathology
Supplementary information
Other Information
Self-studies: 50 h
Lectures: 16 h
Discussion seminars: 6 h
Practical exercises: 20 h
Examination: 8 h
The first half of the course will take place on Zoom. A Canvas-page will be organized where course information, literature, lectures, self-assessing quizzes and other resources will be available. The practical exercises will be held at Ultuna during 4-days in early December.
The course program is designed for maximum 15 students per course occasion.