Statistical Analysis of Genetic and Phenotypic Data for Breeders: - - PowerPoint PPT Presentation

Statistical Analysis of Genetic and Phenotypic Data for Breeders: Hands on Practical Sessions

Paulino Pérez 1 José Crossa 1

1ColPos-México 2CIMMyT-México

June, 2015.

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 1/11

Contents

1

General comments

2

Software

3

Data and models

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 2/11

General comments

General comments

In this section we briefly review some of the statistical models commonly used in Genomic Selection. As you already know, there are a lot of models that have been developed to that end. Two papers from last years, contains an excellent review of the models and practical applications in GS, both in plants and animals.

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 3/11

General comments

Continue...

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 4/11

Software

Software

The software to be used in the practical sessions is R, you can get it freely from http://www.r-project.org

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 5/11

Software

Continue...

We will concentrate on a few pieces of software (some of them created by us) that were developed to deal with the models that we will cover, BGLR: Bayesian Generalized Linear Regression package, r-forge.r-project.org/R/?group_id=1525 BLR: Bayesian Linear Regression package, cran.r-project.org/web/packages/BLR/index.html brnn: Bayesian Regularized Neural Networks, cran.r-project.org/web/packages/brnn/index.html rrBLUP: Ridge regression and other kernels for genomic selection cran.r-project.org/web/packages/rrBLUP/index.html

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 6/11

Software

Continue...

BLR and rrBLUP are explained in these documents,

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 7/11

Software

Continue...

For BGLR you can read the article that describes the package, The document is also available at http://www.genetics.org/content/198/2/483.full

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 8/11

Data and models

Data and models

We will assume that we have a set of Markers (Genotypic information) and a set of phenotypes and we are interested in predicting the phenotypes given those markers. We first show how to deal with Markers in the R environment and then we show how to fit several models. We will review the following models: Ridge Regression-BLUP Bayesian LASSO BayesA BayesB RKHS and GBLUP Modelling multi-environment data

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 9/11

Data and models

Continue...

If the time permits, we will review also Bayesian Regularized Neural networks, G3/Genetics,

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 10/11

Data and models

Continue...

CIMMYT, México-SAGPDB Statistical Analysis of Genetic and Phenotypic Data for Breeders:Hands on Practical 11/11