Armidale Genetics Summer Course 2024

Venue: University of New England, Armidale, NSW Australia

Course Audience: Postgraduate students and other professionals




Theory and Tools for Designing Breeding Programs

of Animals and Plants



Gregor Gorjanc                   Professor & Royal Society Industry Fellow,

University of Edinburgh / The Roslin Institute

Daniel Tolhurst                   Edinburgh Innovations Fellow, Highlander Lab

                                                The Roslin Institute

Chris Gaynor                       Rice/OSR Quantitative Geneticist at Bayer, O'Fallon, Missouri, United States

Jon Bancic                            Research Fellow at the Highlander Lab/ The Roslin Institute




Dates:     Monday 5 February – Friday 9 February 2024

Course Description:  

This course will focus on theory and practical tools to assist the design and evaluation of breeding programs for genetic improvement. While the course will focus on the fundamental theories and tools, applications will be shown both for animal and plant breeding programs. A program of the course is below

Intended Audience

The intended audience is postgraduate students, postdocs, and faculty with an interest in breeding programs and the use of phenotypic, pedigree, and genomic information in the prediction and utilization of genotypes with high genetic merit.


Program Feb 5 - 9 - 2024


Theory and Tools for Designing Breeding Programs

of Animals and Plants


Day 1 Stochastic simulation of breeding programmes


Slides for Day 1:

Introduction to the Course

Introduction to Simulations

DNA and phenotype Lottery

Response to Selection

Breeding Program Practices


Links to practical material (zip files)


Practical DNA

Practical Selection

Practical Breeding Program


Day 2 Quantitative genetics


Slides for Day 2:


            Additive effects

            Dominance effects

            Epistasis effects




Links to practical material (zip files)



Demos Source code


Day 3 Estimation of genetic parameters using linear mixed models


Slides for Day 3

·         Introduction to genetic evaluation

·         Pedigree-based models

·         Genome-based models


Links to practical material (zip file)


Practicals Day 3  (simulated genome data not included)


Day 4 Spatial variation & Genotype-by-Environment interactions


Slides for Day 4



                        Design of plant breeding field trials

                        Spatial variation in linear mixed models

                        Multi-environment trials

                        A framework for simulating GxE


Links to practical material (zip file)




Further reading material on the topic

Simulate GxE

Simulate Spatial effects


Day 5 Ancestral recombination graphs (ARG)


Slides for Day 5


·         Spatial Smallholders and APY

·         Ancestral Recombination Graphs

·         Linear Models for Trees


Practical for Day 5


·         Practicals Day5





Course photo 2024 summer course


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Julius van der Werf with Gregor Gorjanc, Daniel Tolhurst, Chris Gaynor, Jon Bancic and Hassan Aliloo from UNE



Material of previous years:


Armidale Genetics Summer Course 2023    Materials

·         Methods and Tool for Genomic Predictions and GWAS in Breeding Programs Daniela Lourenco and Mehdi Sargolzaei         


-           COVID break -

Armidale Genetics Summer Course 2020    Materials

·         The Search for Selection: Bruce Walsh and Michael Morrissey


Armidale Genetics Summer Course 2019    Materials

·         Introduction to Graphical Models with Applications to Quantitative Genetics and Genomics: Guilherme Rosa and Francisco Peñagaricano


Armidale Genetics Summer Course 2018    Materials

·         Mathematical modeling of infection dynamics in genetically diverse livestock populations: Andrea Doeschl-Wilson and Osvaldo Anacleto          


Armidale Genetics Summer Course 2017    Materials

·         Genotype by environment interaction in breeding programs: Piter Bijma and Han Mulder           


Armidale Genetics Summer Course 2016    Materials


Investigating the Genetic Architecture of Complex Traits  & Prediction of Phenotype

from Genome-wide SNPs - Doug Speed and David Balding


Armidale Animal Breeding Summer Course 2015   Materials

                    Primer to genomic analysis using R:    Cedric Gondro

                    From Sequence Data to Genomic Prediction:   Ben Hayes and Hans Daetwyler


Armidale Animal Breeding Summer Course 2014    Materials

Breeding Program Design with Genomic Selection: Jack Dekkers, Julius van der Werf


Armidale Animal Breeding Summer Course 2012    Materials

Statistical Methods for Genome-Enabled Selection: Daniel Gianola, Gustavo de los Campos 


Armidale Animal Breeding Summer Course 2011    Materials

·         Statistical methods and design in plant breeding and genomics: Ian Mackay

·        IBD inference in genome association studies: Elizabeth Thompson


Armidale Animal Breeding Summer Course 2010    Materials

·         Application of evolutionary algorithms to solve complex problems in quantitative genetics

and bioinformatics:   Brian Kinghorn, Cedric Gondro

·         Bayesian methods in genome association studies:  Dorian Garrick,  Rohan Fernando


Armidale Animal Breeding Summer Course 2009    Materials

·        Quantitative Genetic Theory and Analysis- Selection Theory:    Bruce Walsh

·         Quantitative Genetic Models for social interaction and inherited variability: Piter Bijma


Armidale Animal Breeding Summer Course 2008      Materials 

·         Genomic Selection:       Ben Hayes


Armidale Animal Breeding Summer Course 2007      Materials

·         Generalized Linear Mixed Models:        Steve Kachman


Armidale Animal Breeding Summer Course 2006    Materials

·         Gene Expression:          Toni Reverter

·         Breeding Program Design:         Graser, James, Van der Werf

Armidale Animal Breeding Summer Course 2005    Materials
·         Breeding Objectives: Gibson, Van der Werf, Kinghorn
·         Scientific Writing:          David Lindsay
·         ASReml:           Arthur Gilmour
Armidale Animal Breeding Summer Course 2004    Materials
·         Bayesian for Beginners               Kerrie Mengersen
·         Bayesian Models for QTL analysis        Michel Perez-Enciso
·         Bioinformatics   John McEwan

Armidale Animal Breeding Summer Course 2003    Materials

·         Scientific Writing:  David Lindsay
·         Linear Models for animal breeding:   Julius van der Werf, Mike Goddard
·         QTL mapping for practitioners, from linkage to gene: Ben Hayes, Julius van der Werf
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