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
Content:
Day 1 The
building blocks: single trait selection
Introduction
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
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
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. 2:105–39
Exercises, spreadsheets and
software used in the course
SelAction software (Wageningen University) can be
downloaded from
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
BLUP_EBV.XLS PseudoBlup JD
Multrunc.xls Trucation
Selection JD
GENETIC_GAIN.XLS JD
Bulmer.xls Simple
Illustration Bulmer Effect JvdW
MTINDEX.XLS JvdW
MTINDEX_DESGAINS.XLS JvdW
MTINDEXELLIPSE.XLS JvdW
Day2 2-trait example.d1s Input 2 traits SelAction
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
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
Inquiries
Julius van der Werf
Animal Genetics, UNE
phone: 02 6773 2092
fax 02 6773 3922
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
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IBD
inference in genome association studies: Elizabeth Thompson
Armidale Animal Breeding Summer Course 2010 Materials
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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
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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
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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 2003 Materials