2003 Nordic postgraduate courses in Animal Breeding: Quantitative Genetics in Animal Breeding
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 since 21 June 2002

Names, addresses and emails of 2003 students (
word.doc file)
Tons of excellent
class photos from
Veijo Vilva
A list of useful references appears at the bottom of this page.
Main Nordic 2003 website
Course Schedule, Readings and Lecture Notes
Walsh and Lynch refers to online draft chapters from our (yet to be finished) volume, Evolution and Selection on Quantitative Traits. Chapters can be viewed at
http://nitro.biosci.arizona.edu/zbook/volume_2/vol2.html
Problems downloading pdf/powerpoint files?
On Internet Explorer in some windows environments, the pages show up as blank. They are really there. Either try reloading or
rightclick on the link and select "Save Target" . The powerpoint files (.ppt) were generated on a Mac and hence some of the fonts might not transfer over to PCs. I also use EXTENSIVE animation, and again I make no claim this transfers over to a windows environment. Again, in some environments, clicking on the files opens them as an encoded text file.. Once again, try to rightclick trick.
FTP site
All of this material is also on our ftp site,
ftp://Nordic2003:Nordic2003@eeb19.biosci.arizona.edu
There are five folders: pdf of lecture notes, powerpoint files,
reprints/reading materials (References), Datasets (SAS code is here),
amd mastersd, which has all of the files on the CD that will be handed out in class.
For those this wish to use a strict ftp server, the site is
eeb19.biosci.arizona.edu, user = Nordic2003, password=Nordic2003
Day 1: (Monday, 4 August )
Lecture 1: Basic statistical machinery (Walsh)
 pdf file of lecture notes (10 pages)
 powerpoint file of lecture
 Reading: Lynch and Walsh: Chapters 2, 3, A4
 Topics:
 Probabilities, Distributions, and Expectations
 Discrete and Continuous Random Variables
 Joint and Conditional Probabilities
 Bayes' Theorem
 Expectations of Random Variables
 The Normal Distribution
 Covariances
 Useful Properties of Variances and Covariances
 Regressions
 Properties of Leastsquares Regressions
 Regressions and Correlations
 Maximum Likelihood
 Largesample Properties of MLEs
 Likelihood ratio tests
 Bayesian Statistics
Lecture 2: Basic Population and Quantitative Genetics (Walsh)
 pdf file of lecture notes (7 pages)
 powerpoint file of lecture
 Reading: Lynch and Walsh: Chapters 5, 6
 Topics:
 Allele and Genotype Frequencies
 Gamete Frequencies, Linkage, and Linkage Disequilibrium
 Contribution of a Locus to the Phenotypic Value of a Trait
 Example: the Booroola (B) gene
 Fisher's Decomposition of the Genotypic Value
 Average Effects and Breeding Values
 Genetic Variances
 Epistasis
Day 2: (Tuesday, 5 August)
Lecture 3: Resemblances Between Relatives (Walsh)

pdf file of lecture notes (14 pages)
 powerpoint file of lecture
 Reading: Lynch and Walsh: Chapter 7
 Topics:
 Phenotypic Resemblance Between Relatives
 Parentoffspring regressions
 Collateral relationships: ANOVA
 Causes of Phenotypic Covariance Among Relatives
 Genetic Covariance Between Relatives
 Offspring and one parent
 Halfsibs
 FullSibs
 General degree of relationship
 Environmental Causes of Relationship Between Relatives
Lecture 4: Basic Designs for Estimation of Genetic Parameters (Walsh)
 pdf file of lecture notes (10 pages)
 powerpoint file of lecture
 Reading: Lynch and Walsh: Chapters 17, 18
 Topics:
 Heritability
 Why h^{2} instead of h?
 Heritabilities are Functions of a Population
 Increasing the Heritability
 Heritability and the Prediction of Breeding Values
 Heritability Values and Population Divergence
 Estimation: Oneway ANOVA and the simple fullsib design
 Estimating Variances and Variance Components
 Estimating heritability
 Worked Example of a Fullsib Design
 Estimation: The Nested Fullsib, Halfsib Analysis
 Worked Example of a Nested Design
 Estimation: ParentOffspring Regressions
Day 3: (Wednesday, 6 August)
Lecture 5: Major Genes, Polygenes, and QTLs
(Walsh)
 pdf file of lecture
(16 pages)
 powerpoint file of lecture
 Reading: Lynch and Walsh: Chapters 13
 Topics:
 Major and Minor Genes
 Major Genes and Isoalleles
 Polygenic Mutation and the Mutational Variance
 Simple Tests for Detecting Major Genes
 Complex Segregation Analysis
 Likelihood Functions Assuming a Single Major Gene
 Commonfamily Effects
 Genetic Maps and Candidate Genes
 Map Distances vs. Recombination Frequencies
 Linkage Disequilibrium Mapping
 Finemapping Major Genes Using LD
 The Transmission/Disequilibrium Test
 Example: Mapping Type 1 Diabetes
Lecture 6: QTL Mapping
(Walsh)
 pdf file of lecture
(16 pages)
 powerpoint file of lecture
 Reading: Lynch and Walsh: Chapters 15, 16
 Topics:
 Mapping Using inbred line crosses
 Experimental designs
 Conditional Probabilities of QTL Genotypes
 Example:
Conditional Probabilities for an F2
 Expected Marker Means
 Linear Models for QTL Detection
 Maximum Likelihood Methods for QTL Mapping and Detection
 Likelihood Maps
 Precision of ML Estimates of QTL Position
 Interval Mapping with Marker Cofactors
 Power and Repeatability: The Beavis Effect
 Mapping in Outbred Populations
 QTL Mapping Using Sib Families
 General Pedigree Methods
 HasemanElston regression
 Affected sib pair methods
Day 4 (Thursday, 7 August)
Lecture 7: Inbreeding and Heterosis (Walsh)
 pdf file of lecture notes (11 pages)
 powerpoint file of lecture
 Reading:
 Topics:
 Changes in the Mean and Variance Under Inbreeding
 Inbreeding
 Inbreeding Depression in Fitness Traits
 Computing the Inbreeding Depression Coefficient, B
 Why do traits associated with fitness show inbreeding depression?
 Minimizing the Rate of Inbreeding
 Change of Variance With Inbreeding
 Changes in the Mean Under Crossbreeding
 Heterosis: Change in the Mean Under Crossbreeding
 Heterosis in F2
 Crossbreeding in Animals: General Concepts
 Synthetics and Rotational Crossbreeding
 Estimating the Amount of Heterosis in Maternal Effects
Lecture 8: Shortterm Response Selection (Walsh)
 pdf file of lecture (15 pages)
 powerpoint file of lecture
 Reading:
 Topics:
 Short Terms changes in the mean: the breeder's equation
 The Selection Differential S and Response R
 The Selection intensity i
 Truncation Selection
 Selection Intensities and Differentials Under Truncation Selection
 Correcting the Selection Intensity for Finite Samples
 Selection on Threshold Traits
 Permanent Versus Transient Response
 Response with Epistasis
 Maternal Effects: Response Under Falconer's Model
 Gene Frequency Changes Under Selection
 Shortterm changes in the variance
Day 5 (Friday, 8 August)
Lecture 9: Analysis of shortterm selection experiments (Walsh)
 pdf file of lecture
[ 19 pages ]
 Reading:
 Topics:
 Variance in response
 Realized heritabilitites
 Estimators for Several Generations of Selection
 Weighted LeastSquares Estimates of Realized Heritability
 Standard Errors for Realized Heritability Estimates
 Experimental Evaluation of the Breeders' Equation
 Asymmetric Selection Response
 Control Populations and Experimental Designs
 Basic Theory of Control Populations
 Divergent Selection Designs
 Variance in Response
 Control Populations and Variance in Response
 Optimal Experimental Design
 Mixedmodel Estimation
 The Relationship Matrix Accounts for Drift and Disequilibrium
 Model Validation
Lecture 10: Linear Algebra and Linear Models (Walsh)
 pdf file of lecture (23 pages)
 powerpoint file of lecture
 Reading: Lynch and Walsh: Chapter 8, Appendix A3
 Topics:
 Elementary Matrix Algebra
 Basic Notation
 Partitioned Matrices
 Addition And Subtraction
 Multiplication
 Dimensional Properties and Matrix Multiplication
 Transposition
 Inverses and Solutions to Systems of Equations
 Expectations Of Random Vectors And Matrices
 Covariance Matrices Of Transformed Vectors
 The Multivariate Normal Distribution
 Properties of the MVN
 Example: The Regression of Offspring Value on Parental Value
 Example: Regression of Offspring Breeding Value on Parental Breeding Values
 Overview Of Linear Models
 Examples of GLMs
 Ordinary Least Squares
 Example: Partial Regression
 Polynomial Regressions and Interaction Effects
 Fixed vs. Random Effect
 Example: Fixed vs. Random Effects in the Sire Model
 Generalized Least Squares
 Example: Weighted Least Squares
 Model Goodnessoffit and Hypothesis Testing
 Chisquare and Fdistributions
 Sums of Squares
 Hypothesis Testing
Day 6 (Monday, 11 August)
Problems for Lectures 1119  pdf file.
Lecture 11: BLUP Estimation I (Muir)
 pdf file of lecture
[ 33 pages ]
 Reading: Lynch and Walsh: Chapter 8
 Data set (saved as text file with comma separated variables)
 SAS code
 Topics:
 Breeding Values
 Genetic and Environment Trends
Lecture 12: BLUP Estimation II (Muir)
 pdf file of lecture
[ 38 pages ]
 Reading: Lynch and Walsh: Chapter 26
 Sample Pedigree Data set
 Link to Windows program amatnew.exe.. This is a windows executable file that computes inbreeding coefficient and the relationship matrix for any pedigree given in ped.dat
 SAS code
 Topics:
 Drift Variances
 Prediction Error Variance
Day 7 (Tuesday, 12 August)
Lecture 13: Maternal Effects I: Noninherited (Muir)
 pdf file of lecture
[ 22 pages ]
 Reading: Lynch and Walsh, Chapter 6.
 SAS code
 Topics:
 Permanent Environmental effects
 BLUP Model
 Selection Program: Optimal Between vs within Family Selection
Lecture 14: Maternal Effects II: Inherited (Muir)
 pdf file of lecture
[ 28 pages ]
 Reading: Lynch and Walsh: Chapter 23
 SAS code
 Topics:
 Maternal Genetic
 Cytoplasmic
 BLUP Model
 Selection program
Day 8 (Wednesday, 13 August)
Lecture 15: GenotypeGenotype interactions (Muir)
Lecture 16: GenotypeEnvironment interactions (Muir)
 pdf file of lecture
[ 34 pages ]
 Reading:
 Lynch and Walsh: Chapter 24

Muir, Nyquist and Xu, TAG 84: 193200. [ pdf file of reprint ]

Emebiri and Moody, 2001. Quantitative characterisation of malting barleys for consistency in grain protein concentration. In
Proceedings of the 10th Australian Agronomy Conference, Hobart.
[ html file of reprint ]

Matassa, 2001. Statistical methods for partitioning genotypebyenvironment interactions: an empirical evaluation of Muir's method using a GenStat program. from Australasian Biometrics and New Zealand Statistical
Association Joint Conference 2001
[ html file of reprint ]
 SAS code
 Topics:
 Relevance
 Estimation
 Interpretation
Day 9 (Thursday, 14 August)
Lecture 17: Multitrait selection: (Muir)
 pdf file of lecture
[ 56 pages ]
 Reading:
 SAS code
 Topics:
 Genetic covariances
 Indirect Selection
 Index selection
 Economic weights
Lecture 18: Marker Assisted Selection (Muir)
Day 10 (Friday, 15 August)
Lecture 19: Long Term Selection (Muir)
 pdf file of lecture
[ 66 pages ]
 Reading:
 Robertson, 1960. A theory of limits in Artifical Selection.
[ link to pdf file ]
 Meuwissen and Sonesson, 1998. Maximizing the response of selection
with a predefined rate of inbreeding
[ link to pdf file ]

Walsh and Lynch : Chapter 16
[ link to pdf file ]

Walsh and Lynch : Chapter 17
[ link to pdf file ]

Walsh : Population and Quantitativegenetic models of selection limits (ms for Plant Breeding Reviews )
[ link to pdf file ]
 Topics:
 Selection limits
 Avoidance of inbreeding
Lecture 20: The Future (Walsh/Muir)
 Optional Reading:
 Walsh , 2001 Quantitative Genetics in the Age of Genomics, Theoretical Population Biology 59: 175184.. TBP [ pdf file of reprint ]
 Uses of microarray in animal breed  powerpoint file of talk at 2003 ASAS meeting
 Topics:
 Transgenics
 Cloning
 micrroarrays
 Genomics