Armidale Animal Breeding Summer Course 2023
Venue: University of New England, Armidale, NSW Australia
Course Audience: Postgraduate students and other professionals
Methods and Tool for Genomic Predictions and GWAS in
Breeding Programs
Teachers:
Dr
Daniela Lourenco University
of Georgia, USA
Dr
Mehdi Sargolzaei Select
Sires Inc., USA
Dates:
Monday – Friday 20 -24 February 2023
Course Description:
This course encompasses the
background needed to perform genomic analyses used in Animal Breeding and
Genetics. It involves simulation of genomic data using QMSim
(Sargolzaei and Schenkel, 2009), imputation of missing SNP using FImpute (Sargolzaei et al., 2014), and overall genomic
analyses using BLUPF90 programs (Misztal et al., 2014). A program of the course
is below.
Intended Audience
The intended audience is
advanced graduate students, postdocs, and faculty with an interest in breeding
programs and the use of genomic information in prediction of genetic merit or
risk.
Program 2023 (Feb 20- 24 )
Methods and Tool for Genomic
Predictions and GWAS in Breeding Programs
Day 1: Mehdi
1.
Introduction to Genomic data
a.
History of the use of genomic data
b.
Genomic markers
c.
Statistics of genomic data
d.
Genomic files
e.
Quality control of SNP data
2.
Simulation of genomic data
a.
Simulated vs. real data
b.
QMSim for genomic
data simulation
3.
Introduction to Unix environment and tools
4.
Exercise: Simulate a genomic dataset with QMSim
and use Unix tools for data
manipulation
and statistics
Day 2: Mehdi
1.
Introduction to imputation
a)
Implications of missing genomic data
b)
Methods for imputation to medium and large density
c)
State-of-the-art in imputation
2.
Imputation
a)
Best practices before and after imputation
b)
FImpute for imputation
c)
Accuracy of imputation
3.
Exercise: Impute missing genotypes with and without pedigree
information,
and
compute imputation accuracy
Day 3: Daniela
1.
Introduction of BLUPF90 family of programs for the analyses
of mixed models
including single and multiple traits, maternal effects, and
repeatability models
a)
Renumbering datasets: renumf90
b)
Estimation of breeding values and VCE: blupf90+
c)
Estimation of breeding values and VCE - Bayesian: gibbsf90+
2.
Exercise: use of BLUPF90 programs with real data for single
and multiple trait models
Day 4: Daniela
1.
Introduction to Genomic Selection
2.
Theory of Single-step GBLUP (ssGBLUP)
3.
Creation and handling of genomic relationship matrices with
preGSf90
4.
Quality control for genomic and pedigree relationships
a)
Calling rate
b)
Parental exclusions
c)
Distributions of diagonals and off-diagonals of G
d)
Differences between matched G
and
A22
e)
Eigenvalues/eigenvectors – population stratification
5.
Validation techniques for testing genomic models
6.
Exercises: Application of quality control and use of single-step
with BLUPF90
programs
in simulated data sets
Slides 3 Day 4 Best Practice BLUPF90
Day 5:
1.
Base allele frequencies from Gengler’s
method
2.
Estimating SNP effects from GBLUP-based models
3.
Indirect predictions using SNP effects
4.
Weighted GBLUP and ssGBLUP
5.
Genome-wide association studies (GWAS)
6.
Accounting for unknown relationships in ssGBLUP
(UPG and metafounders)
7.
Exercises: Compute SNP effects from ssGBLUP,
run indirect predictions for
young animals, and do ssGWAS
(variance explained by SNP and p-values) with
BLUPF90 programs
Exercise Day 5 (Indirect SNP effects, GWAS)
Coursephoto
Material of previous years:
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 2003 Materials