What traits were phenotyped to study GxG interactions ?

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Table of contents

Introduction
I. Importance of plant-plant interactions
I.A. General overview
I.B. The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions
I.C Towards unifying evolutionary ecology and genomics to understand genotype-by-genotype
interactions within wild plant species
I.D. Prevailing questions in the study of intraspecific interactions?
II. Arabidopsis thaliana as a model species to unravel the adaptive genetic and molecular bases of plant-plant interactions?
II.A. General characteristics
II.B. Genetic and genomic resources and tools available for Arabidopsis thaliana
II.C. A model for studying natural variation of plant-plant interactions?
III. How to identify the genetic basis of adaptation?
III.A. Genome wide association (GWA) mapping
III.B. Genome-Environment Association (GEA)
IV. Outline of the thesis
V. References
Chapter 1 Establishing a genomic map of local adaptive cooperation in Arabidopsis thaliana
I. Introduction
II. Objective
III. Materials and methods
III.A. Biological material
III.B. Experimental design
III.C. Phenotypic trait measurement
III.D. Statistical analysis of natural variation of positive interactions
III.E. GWA mapping using a Bayesian hierarchical model
III.F. Testing for signatures of local adaptation
III.G. Estimating putative ecological drivers of positive interactions
IV. Results
IV.A. Natural genetic variation of positive GxG interactions
IV.B. Genetic bases of positive GxG interactions and their adaptive status
IV.C. Selective ecological drivers of positive GxG interactions
IV.D. Genetic bases of local adaptive cooperation in 52 local populations
V. Discussion and perspectives
V.A. Natural genetic variation of intraspecific positive interactions
V.B. Genetic bases of local adaptive positive interactions
V.C. Selective ecological drivers of intraspecific positive interactions
V.D. Candidate genes underlying the identified QTLs: pre-eminence of functions related to
metabolism
VI. References
VII. Supplementary information
Chapter 2 Investigating positive GxG interactions at the genomic level in a local population of Arabidopsis thaliana
I. Introduction
II. Objective
III. Materials and methods
III.A. Biological material
III.B. Experimental design
III.C. Phenotypic trait measurement
III.D. Statistical analysis of natural variation of positive interactions
III.E. GWA mapping combined with a local score analysis
III.F. Estimating genetic relationships underlying the ‘super overyielding’ strategy
IV. Results
IV.A. Natural genetic variation of GxG interactions within a local population
IV.B. Genetic architecture of positive GxG interactions
IV.C. Investigating relationships between cooperators at the genomic level
IV.D. Genetic bases associated with the ‘super overyielding’ strategy
V. Discussion and perspectives
V.A. The occurrence of a ‘super overyielding’ strategy in the local TOU-A population
V.B. The ‘super overyielding’ strategy observed in the TOU-A population may be driven by compatibility genes
V.C. Candidate genes underlying the ‘super overyielding’ strategy
VI. References
VII. Supplementary information
General discussion and perspectives
I. Introduction
II. Natural genetic variation of intraspecific positive interactions at different geographic scales
III. Biotic factors as the main selective drivers of positive interactions?
IV. What are the molecular determinants of cooperative plant-plant interactions?
V. References
VI. Supplementary information