P000145, Genome-wide predictions in plant breeding: genotype-phenotype associations and genomic selection, 3.0 Hp
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Syllabus

Finalized by: Research school Organism Biology, Mattias Thelander chair, 2025-06-23
Valid from : Second half-year 2025 (2025-07-01)

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

Objectives

After completing the course, the students will be able to:

• Use the acquired theoretical background to design genome-wide predictions in breeding.
• Understand the theory and best practices to run genome-wide association studies.
• Design genomic selection analyses adapted to the species of interest.

Content

This course has been designed for PhD students registered in the Organismal Biology Research School, in collaboration with the SLU breeding network. Experts in plant breeding at our university collaborate to answer: (1) how to associate phenotypes and genotypes and (2) how to accelerate marker-assisted selection in the era of high throughput genome sequencing. Along this course, students will be able to review basic principles of association mapping, study in detail the bioinformatic methods today available, and do extensive hands-on work on pre-designed examples.

Aims of the course:

• The course provides the theoretical and statistical framework to apply in GWAS and Genomic Selection.
• Students will analyse pre-designed datasets, testing different methods and ultimately will design in-silico experiments to apply in their own PhD projects.

Pedagogical form

Dual: on campus and on line.

Lectures: basic concepts of mapping populations, phenotyping, sequencing strategies, statistical models, etc.

Journal club – discussion of papers, from classic to frontier science reports.

Genomics laboratories: students will be challenged with pre-designed data sets and protocols, manageable in personal laptops with free software and libraries.

Time table

Week 1: Theoretical background in breeding

*Breeding strategies *

Breeding for resistance and quality

Breeding and biodiversity

**Week 2: Theory and in silico laboratories. **

• GWAS

Population genetics and quality control of genotype data

Experimental design, models and co-variates

Advanced genome-wide association studies

• Genomic selection

Best Linear Unbiased Predictor

Factors affecting Genomic Selection

Cross-Validations

Examination Formats and Requirements for Passing the Course

Pass/Fail. Students must attend at least 80% of the theoretical/practical sessions planned during week 2 of the course. A final evaluation will consist of an oral presentation of the results of the genomics laboratories. The course coordinator and selected instructors will assess the quality and content of the presentations.

Responsible Department/Equivalent

Department of Plant Biology

Supplementary information