This workshop is organised with funds from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement n° 284181 (“Trees4Future”)

June 30 – July 3 2015

Jaca, Spain

Preliminary tasks

Participants are expected to bring their laptops and have the following tasks done, if necessary, before the workshop

• Install and get familiar with R
• Install the latest version of breedR
• Join our discussion group
• Bring your datasets and prepare your questions

Provisional program

last updated March 18, 2015

Day 1: Tuesday June 30

Introduction to Linear Mixed Models (LMMs) and breedR

Participants are expected to arrive in the course of the morning.

09.00 Workshop opening (slides)

09.30 Morning Workshop (1.5 hs.) Facundo Muñoz (INRA Orléans)

• slides · code
• breedR overview:
  • Case studies in common field trials
  • The additive genetic model
  • breedR models for spatial autocorrelation and competition

11.00 Theoretical session (1.5 hs.) Luis Varona (U. de Zaragoza)

• Statistical inference (frequentist/Bayesian; (RE)ML/MCMC)
• Linear Mixed Models

Genetic models, spatial autocorrelation and competition

14.00 Theoretical session (1.5 hs.) Eduardo Cappa (INTA Buenos Aires)

• slides
• Introduction to environment heterogeneity and competition effects
• Diagnosis of spatial and competition effects
• Autoregressive and splines spatial models
• Competition model
• Examples of application

16.00 Afternoon Workshop (3 hs.) Facundo Muñoz (INRA Orléans); Eduardo Cappa (INTA Buenos Aires)

• scripts: Douglas-fir; E. globulus
• Diagnosis of spatial and competition effects
• Analysis of spatial autocorrelation
• Analysis of Competition

Day 2: Wednesday July 1st

09.00 Field excursion visit natural populations of mixed Beech-Fir and Romanesque monastery San Juan de la Peña

Genotype by Environment and multi-trait models

14.00 Theoretical session (1.5 hs.) Leopoldo Sánchez (INRA Orleans)

• Genetic correlations (slides)
• G×E analysis (slides)

16.00 GxE Workshop (2 hs.)

• Toy examples of interaction analysis (slides; script)
• Case study in G×E interaction in a multi-site context (slides; script)

18.00 Afternoon workshop (1.5 hs.)

• datasets: (genotypes case-1; case-2; phenotypes case-1; case-2)
• Simulated examples with Genomic data (slides-intro; excercise; script)

Day 3: Thursday July 2

WP3 thematic network on Phenotypic Plasticity

09.00 Theoretical session (1.5 hs.) José Climent (CIFOR-INIA)

• Phenotypic plasticity (slides)
• Analysis of phenotipic plasticity (dataset; script)

11.00 Theoretical session (1.5 hs.)

• Longitudinal models (slides)
• Larix longitudinal example (slides; script)

14.00 Afternoon workshop (5 hs.)

• Discussion and analysis of participant’s use cases
  • Mesfin case study (slides; script; dataset)

Day 4: Friday July 3

09.00 Participant’s session

• Open time for excercises

12.30 Wrap up and conclusons

Further possible contents

• Genfored as a data base (E. Notivol)
• Possible extensions of breedR (A. Legarra)