2 BreedR - A statistical R-package for genetic evaluation of trees
BreedR provides frequentist and Bayesian statistical tools to build predictive models useful for breeders, quantitative genetists and forest genetic resources analysts communities. It aims to assess the genetic value of individuals under a number of situations, including spatial autocorrelation, genetic/environment interaction and competition.
3 Trees4Future training workshop were held on the use of the statistical package breedR.
- 30 June to 3 July 2015 in Jaca, Spain
- 10-11 December 2015 in Sekocin Stary, Poland.
- 14-15 March 2016 in Bucharest, Romania
The workshops were led by Facundo Muñoz from INRA (Orléans) with the help of local organizers. After the presentation (showing the functionality of the program), participants will worked on their own data, presented the results and discussed about them.
2.1 Workshop training Programme
Day 1
Introduction to Linear Mixed Models (LMMs) and breedR
- Workshop opening
- Morning Workshop (1.5 hs.)
- breedR overview:
- Case studies in common field trials
- The additive genetic model
- breedR models for spatial autocorrelation and competition
- Theoretical session (1.5 hs.)
- Statistical inference (frequentist/Bayesian; (RE)ML/MCMC)
- Linear Mixed Models
Genetic models, spatial autocorrelation and competition
- Theoretical session (1.5 hs.)
- Introduction to environment heterogeneity and competition effects
- Diagnosis of spatial and competition effects
- Autoregressive and splines spatial models
- Competition model - Examples of application
- Afternoon Workshop (3 hs.) scripts: Douglas-fir; E. globulus
- Diagnosis of spatial and competition effects
- Analysis of spatial autocorrelation
- Analysis of Competition
Day 2
- Field excursion visit natural populations of mixed Beech-Fir and Romanesque monastery San Juan de la Peña
Genotype by Environment and multi-trait models
- Theoretical session (1.5 hs.)
- Genetic correlations
- G×E analysis
- GxE Workshop (2 hs.)
- Toy examples of interaction analysis
- Case study in G×E interaction in a multi-site context
- 18.00 Afternoon workshop (1.5 hs.)
- datasets: (genotypes case-1; case-2; phenotypes case-1; case-2)
- Simulated examples with Genomic data
Day 3
WP3 thematic network on Phenotypic Plasticity
- Theoretical session (1.5 hs.)
- Phenotypic plasticity
- Analysis of phenotypic plasticity
- Theoretical session (1.5 hs.)
- Longitudinal models
- Larix longitudinal example
- Afternoon workshop (5 hs.)
- Discussion and analysis of participant’s use cases
- Black poplar case study
Day 4
- Participant’s session
- Open time for exercises
- Wrap up and conclusions
2.2 Training materials and online tool package
Download the full training package in one zip file.
2.2.1 Presentations
- BreedR Statistical methods for forest genetic resources analysis
- BreedR overview
- Environmental heterogeneity and competition effects in forest genetics trials
- Genetic correlations
- G×E analysis
- Ecovalences_generator
- G×E interaction in a multi-site context
- Simulated examples with Genomic data - introduction
- Simulated examples with Genomic data - exercise
- Basic concepts in phenotypic plasticity of forest trees
- Longitudinal models
- Larix longitudinal example
- Accounting for spatial variability in forest genetic trials using breedR: a case study with black poplar
2.2.2 Course materials
2.2.2.1 Preliminary tasks
- Install and get familiar with R via this weblink: http://famuvie.github.io/breedR/getR/
- Install the latest version of breedR via this weblink: http://famuvie.github.io/breedR/
- The BreedR tool package is available via the following weblink: http://www.trees4future.eu/tools/breedr.html
2.2.2.2 Scripts
Script A - Code BreedR
Script B - Diagnosis and spatial and competiton models in forest genetic trialsusing BreedR an example in douglas fir
Script C - Diagnosis and spatial and competiton models in forest genetic trials using BreedR and example in eucalyptus globulus
Script D - Ecovalences_generator
Script E - G×E interaction in a multi-site context
Script F - Simulated examples with Genomic data
Script G - Analysis of phenotipic plasticity
Script H - Larix longitudinal example
Script I - Accounting for spatial variability in forest genetic trials using breedR: a case study with black poplar
2.2.2.3 Datasets
Dataset a – genotype case-1
Dataset b – genotype case-2
Dataset c – phenotype case-1
Dataset d – phenotype case-2
Dataset e - Analysis of phenotipic plasticity
Dataset f - Accounting for spatial variability in forest genetic trials using breedR: a case study with black poplar
