Statistical methods in animal breeding

With a focus on Genomic Selection and Genome-Wide Association Studies

This is a short informal course organized by the NADAS network. If you wish to participate, send an email to lars.ronnegard@slu.se by the 17th of November.

During the course, the students will gain basic knowledge of methods in genomic selections and genome-wide association studies. They will be introduced to R packages for genomic selection and GWAS. They will perform hands-on computer exercises using a subset of these R packages. Several papers on Genomic Selection and GWAS will be discussed. There will be a couple of presentations on advanced topics and in the final home assignment the students will participate in an open genomic-prediction tournament.

Schedule and content

20th of November 2025, online

Introduction to Genomic Selection & GWAS (30 minutes)

• Which research questions do Genomic Selection and GWAS try to answer?
• What are SNP-genotypes and how can they be coded for statistical analysis?
• Introduction to GWAS: a way to find loci with significant effects on a phenotype by fitting a linear regression at each loci.
• Introduction to Genomic Selection: a way to predict phenotypes by modelling all the effects of SNPs along the genome simultaneously.
• A brief overview of useful software for Genomic Selection and GWAS.

Students present their PhD project, and methods on Genomic Selection or GWAS they would like to learn more about (15 minutes each).

Lars presents methods he has developed over the years (30 minutes).

• GWAS analysis when individuals have repeated phenotypic observations implemented in the R package RepeatABEL.
• vGWAS and vQTL methods: finding loci affecting the dispersion of a phenotype.
• Ranking individuals based on their genetic merit for phenotypic dispersion.

We have a discussion on which methods to focus on next time (45 minutes).

4th of December 2025, online

The students are introduced to the method(s) we have decided to focus on. The course leader will guide the participants to understand the methods using examples in R and by discussing papers on the topic.

Ismo Strandén, Research Professor at LUKE, will give an overview of methods in genomic selection he has developed over the years.

We will also try to invite other experts within the field give a short talk depending on the method(s) we decide to focus on.

16-17th of February 2026: lunch-to-lunch in-person meeting in Uppsala

Computer exercises using R on the chosen method(s) to focus on.

By the end of the course the students will be introduced to a prediction competition using genotype and phenotype data. This will be the home assignment for the course.