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


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