2003 Nordic postgraduate courses in Animal Breeding: Quantitative Genetics in Animal Breeding

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since 21 June 2002

Class picture

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 on-line 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 right-click 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 right-click 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 Least-squares Regressions
  - Regressions and Correlations
- Maximum Likelihood
  - Large-sample 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
  - Parent-offspring regressions
  - Collateral relationships: ANOVA
- Causes of Phenotypic Covariance Among Relatives
  - Genetic Covariance Between Relatives
  - Offspring and one parent
  - Half-sibs
  - Full-Sibs
  - 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 h² 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: One-way ANOVA and the simple full-sib design
  - Estimating Variances and Variance Components
  - Estimating heritability
  - Worked Example of a Full-sib Design
- Estimation: The Nested Full-sib, Half-sib Analysis
  - Worked Example of a Nested Design
- Estimation: Parent-Offspring 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
  - Mixture Models
- Complex Segregation Analysis
  - Likelihood Functions Assuming a Single Major Gene
  - Common-family Effects
- Genetic Maps and Candidate Genes
  - Map Distances vs. Recombination Frequencies
  - Linkage Disequilibrium Mapping
  - Fine-mapping 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
  - Haseman-Elston 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:
- Lynch and Walsh: Chapter 10
- Walsh and Lynch WL Chapter 12 [ link to pdf file ]
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: Short-term Response Selection (Walsh)

pdf file of lecture (15 pages)
powerpoint file of lecture
Reading:
- Walsh and Lynch : Chapter 4 [ link to pdf file ]
- Walsh and Lynch : Chapter 5 [ link to pdf file ]
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
- Short-term changes in the variance

Day 5 (Friday, 8 August)

Lecture 9: Analysis of short-term selection experiments (Walsh)

pdf file of lecture [ 19 pages ]
Reading:
- Walsh and Lynch : Chapter 6 [ link to pdf file ]
- Walsh and Lynch : Chapter 7 [ link to pdf file ]
Topics:
- Variance in response
- Realized heritabilitites
  - Estimators for Several Generations of Selection
  - Weighted Least-Squares 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
  - Nicholas' Criterion
- Mixed-model 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 Goodness-of-fit and Hypothesis Testing
  - Chi-square and F-distributions
  - Sums of Squares
  - Hypothesis Testing

Day 6 (Monday, 11 August)

Problems for Lectures 11-19 --- 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
- page 25
- page 34
Topics:
- Drift Variances
- Prediction Error Variance

Day 7 (Tuesday, 12 August)

Lecture 13: Maternal Effects I: Non-inherited (Muir)

pdf file of lecture [ 22 pages ]
Reading: Lynch and Walsh, Chapter 6.
SAS code
- page 13
- page 18
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
- page 11
- page 24
Topics:
- Maternal Genetic
- Cytoplasmic
- BLUP Model
- Selection program

Day 8 (Wednesday, 13 August)

Lecture 15: Genotype-Genotype interactions (Muir)

pdf file of lecture [ 81 pages ]
SAS code
- page 64
Topics:
- Competition
- BLUP Model
- Selection Programs

Lecture 16: Genotype-Environment interactions (Muir)

pdf file of lecture [ 34 pages ]
Reading:
- Lynch and Walsh: Chapter 24
- Muir, Nyquist and Xu, TAG 84: 193-200. [ 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 genotype-by-environment 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
- page 31
Topics:
- Relevance
- Estimation
- Interpretation

Day 9 (Thursday, 14 August)

Lecture 17: Multi-trait selection: (Muir)

pdf file of lecture [ 56 pages ]
Reading:
- Walsh short notes of correlated traits and multivariate selection -- pdf file of notes [9 pages]
- Xu and Mui r TAG 83: 451-458. [ pdf file of reprint ]
- Walsh and Lynch : Chapter 23 [ link to pdf file ]
- Walsh and Lynch : Chapter 24 [ link to pdf file ]
SAS code
- page 46
- Index updating code
Topics:
- Genetic covariances
- Indirect Selection
- Index selection
- Economic weights

Lecture 18: Marker Assisted Selection (Muir)

pdf file of lecture [ 58 pages ]
Reading: Deckers and Hospital, 2002. Nature Reviews Genetics 3: 22-32[ pdf file of reprint ]
Topics:
- When
- Where
- How

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 Quantitative-genetic 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: 175--184.. TBP [ pdf file of reprint ]
- Uses of microarray in animal breed -- powerpoint file of talk at 2003 ASAS meeting
Topics:
- Transgenics
- Cloning
- micrroarrays
- Genomics

Useful References

D. Falconer and T. Mackay. 1996. Introduction to Quantitative Genetics, 4th Edition. Longman

The classic introduction to the field

H. N. Turner and S. S. Y Young. 1969. Quantitative Genetics in Sheep Breeding. Cornell University Press.

A great classic which is unfortunately out of print.

G. Simm. 1998. Genetic Improvement of Cattle and Sheep. Farming Press.

A nifty compact introduction

B. Kinghorn, J. van der Werf, and M. Ryan. 2001. Animal Breeding. Use of New Technologies. Twynam Press.

A nice review treatment of recent advances

Wyman Nyquist's Notes on Statistical Genetics . On line at: http://nitro.biosci.arizona.edu/Nyquist/Nyquist.html
J. I. Weller. 2001. Quantitative Trait Loci Analysis in Animals CABI Publishing.
N. D. Cameron. 1997. Selection Indices and the Prediciton of Genetic Merit in Animal Breeding CABI Publishing.
R. A. Mrode. 1996. Linear Models for the Prediction of Animal Breeding Values CABI Publishing.
J. I. Weller. 1994. Economic Aspects of Animal Breeding Chapman and Hall.
D. Sorensen and D. Gianola. 2002. Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics Springer.