2012 Summer Institute in Statistical Genetics, Seattle, Washington/University of Edinburgh: Mixed Models in Quantitative Genetics

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since 29 June 2012

INSTRUCTORS:

· William Muir, Department of Animal Sciences, Purdue University bmuir@purdue.edu

· Bruce Walsh, Department of Ecology & Evolutionary Biology, University of Arizona. jbwalsh@u.arizona.edu

Notes

· Lecture 01: Introduction to matrix algebra and calculus (Walsh)

o pdf of powerpoint

o Background reading: LW, Chapter 8

o Additional reading: LW Appendix 3; <ul

o WL Appendix 4 - matrix geometry

o WL Appendix 5 - matrix derivatives

o Matrix calculations in R

· Lecture 02: The General Linear Model (Walsh)

· pdf of powerpoint

· Background reading: LW Chapter 8

· Additional reading: LW Appendices 3, 4; <ul

· WL Appendix 2 - Intro to Bayesian Stats

· WL Appendix 3 - MCMC

· Lectures 03 to 05 : Overview and Derivation of the mixed model, BLUP breeding values and Genomic selection (Muir)

· pdf of powerpoint

· Additional reading: LW Chapters 26, 27

· Lecture 06: Application: QTL/association mapping (Walsh)

· pdf of powerpoint

· Additional reading: LW Chapters 14, 16

· Lecture 07: Application: BLUP maternal genetic (Walsh)

· pdf of powerpoint

· Lecture 08: Application: Associative effects (Muir)

· pdf of powerpoint

· Additional reading:

o WL Chapter 21

· Lecture 09: Application: G x E (Walsh)

· pdf of powerpoint

· Additional reading:

o WL Chapter 32

o WL Chapter 33

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Code

Bill Muir's SAS code

· BLUP cytoplasmic Genetic -- code

· BLUP Maternal Environmental (2) -- code

· BLUP Maternal Environmental correlated residual-- code

· BLUP Maternal Environmental negative between-- code

· BLUP Maternal Environmental negative correlated residual-- code

· BLUP Maternal Environmental -- code

· BLUP Maternal Genetic and Environmental -- code

· BLUP Maternal Genetic and negative Environmental -- code

· BLUP Maternal Genetic -- code

· BLUP Sex Limited -- code

· IML selection index (2) -- code

· IML selection index -- code

· OLS proc iml -- code

· BLUP by proc iml -- code

· BLUP Competitive effects -- code

· BLUP corr residuls Competitive effects -- code

Bill Muir's Excel code

· Genomic selection using Relationship matrix -- code

· Genomic Selection using Marker effects BLUP-- code

Gras Alexandru's R code

· maternal-full -- code

· maternal-brushed -- code