Armidale Animal Breeding Summer Course 2014


Teachers:        Professor Jack Dekkers, Iowa State University, USA

Professor Julius van der Werf, University of New England, Australia     


Breeding Program Design with Genomic Selection


Dates:                          Monday 3 February (9am) - Friday 7 February 2014 (4pm)

Venue:                        University of New England, Armidale, NSW Australia

Course Audience:      Postgraduate students and other professionals


·         Content


·         Spreadsheets  & Software used in the course


·         Materials  previous Armidale summer courses





Day 1   The building blocks: single trait selection  


Building Blocks  JD

EBV accuracy  JD

Selection Theory: Change of mean  JD

Selection Theory: Change of Variance  JD


Day 2    Multiple Trait Selection      

Multiple Trait Selection: Prediction of response          

Factors affecting multi trait response                             

Robust response curves, desired gains, risk  


Slides Multi Trait Selection JvdW


Day 3   Design of breeding programs          

Design of animal breeding programs – overview.  JD

Inbreeding JD

Optimizing Design of BP  JvdW         

Multi Stage Selection JD


Day 4   Using Genomic Information           

Accuracy of GBV, Accuracy of GEBV JD                           

Genomic selection on inbreeding    SC

Genomic selection in crossbreeding programs JD        


Day 5   Breeding program designs to exploit GS    

Cost Benefit of Breeding Programs JvdW

Design of reference populations JD

Imputation strategies JD    

Design of reference populations JvdW

Market Share JD  

Scenarios and cases, across species

   Dairy  JD

   Beef US  AvE

   Beef Aus RB

   Pig&Poultry JD

   Sheep  AS


Review Article:

Alison L. Van Eenennaam, Kent A. Weigel, Amy E. Young, Matthew A. Cleveland, and Jack C.M. Dekkers.

Applied Animal Genomics: Results from the Field Annu. Rev. Anim. Biosci. 2014. 2:10539



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Exercises, spreadsheets and software used in the course


SelAction software (Wageningen University) can be downloaded from


Exercises Day1

Genotypic_values_modelsv10.xls Two locus Model JD

STEBVaccurcay.XLS  Single trait Selection Index/with MBV, GEBV/PseudoBLUP EBV JvdW

SELINT.XLS  Selection Intensity JvdW


Multrunc.xls  Trucation Selection JD

Bulmer.xls  Simple Illustration Bulmer Effect JvdW


Exercises Day2




Day2 2-trait example.d1s  Input 2 traits SelAction


Exercises Day3

xGxAX.xls  Optimal Contributions JvdW

TRUNCSEL.XLS Truncation Selection Opt Age Classes JvdW

GeneFlow.xls  JvdW

Day3Inbreeding prediction.d1s                 Input Inbreeding example SelAction

Day3 Two Stage Selection example.d2s                Input 2 stage SelAction



Exercises Day4

GS accuracy.xls   Predicting GS accuracy from Goddard etc formulas JD

STEBVaccurcay.xls  Single trait Selection Indexwith MBV, GEBV JvdW

xGxGx Optimal Contributions with Genomics SC

GS_Index_parameters.xls           multi trait MBV input for SelAction

Day4 Single trait GS.d1s            Example input ST genomic selection  SelAction

Day4 Multi trait GS.d1s             Example input ST genomic selection  SelAction





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Inquiries                      Julius van der Werf 

                                    Animal Genetics, UNE

                                    phone: 02 6773 2092

                                    fax       02 6773 3922

                                    jvanderw  (at) 

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Material of previous years:


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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