David CROS

Teaching (program, download)




Practical – requirements: computer, no prior knowledge of R

50+ slides powerpoint & files:     [download (ver. feb 2018)]

o   What is R?

o   Installing R and RStudio

o   The RStudio environment

o   The R language and commands: elementary operations, objects, functions, graphs, etc

o   Packages

o Make an ANOVA, multivariate plots and various basic exercices




This is not an exhaustive course about plant breeding, but a focus on a common method (reciprocal recurrent selection) and on the state-of-the-art method of marker assisted selection for quantitative traits (genomic selection), with a preliminary presentation of the basics necessary to understand them.

lecture and practical work – requirements (for the practical work): computer, R software, knowledge of R download files here (ver. feb 2018)

o   PART 1 – Basic concepts of genomics (chromosomes, genes, markers), quantitative genetics and breeding (mass selection, RRS, experimental designs)

o   PART 2 – Resemblance between relatives 

o   PART 3 – Linear mixed model,  heritability,  selection accuracy, genetic gain

o   PART 4 – Genomic selection



R FOR GENOMIC STUDIES (starting from a VCF file)

practical – requirements: computer, R software, knowledge of R, knowledge from lecture “Breeding for quantitative traits”

50+ slides powerpoint:             [download]

1.    The Variant Call Format

2.    Using R for genomic studies (with 20K SNP maize data as an example):

·         Importing & exploring a VCF file

·         Missing SNP data

·         Physical map

·         Linkage disequilibrium

·         Population structure

·         Genomic relationships

·         Genomic predictions: GBLUP, Bayesian Ridge Regression, Bayesian LASSO & RKHS




Requirement: knowledge from lecture “Breeding for quantitative traits”

130+ slides powerpoint             [download, (ver. apr 2017)]

1. Introduction

a.     Palm oil market

b.     The oil palm (Elaeis guineensis and E. oleifera)

2. Traits of interests

3. Reciprocal recurrent selection (RRS) for yield

a.     Why RRS in oil palm?

b.     Implementation of the RRS scheme

c.      Seed production

d.     Genomic RRS

4. Interspecific breeding

6. Breeding for resistance to diseases

7. Marker assisted selection for simple traits


  See this page for specific teaching sessions and (possibly more recent) associated files.


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