Abstract
In a rapidly changing climate, plants are facing constant challenges. As sessile organisms, their best strategy to survive and provide their offspring with a fitness advantage is adaptation to local environments. Adaptation is defined as a phenotype that maximizes the organism’s fitness in its local habitat compared to foreign phenotypes. Studying the genetic basis of past changes in plant adaptation can help us understand how plant populations are going to cope with and adapt to future climatic changes. Nevertheless, adaptation is not the only process leading to allele frequency changes in a population. Gene flow, genetic drift and demographic history, can confound with or hinder environmental adaptation, perplexing the study of its genetic basis. Taking advantage of the recent development of whole-genome sequencing techniques and of the theoretical and practical advances in evolutionary genomics, this task becomes yet at reach. In this thesis, we use the Mediterranean grass Brachypodium distachyon, a recently established model species, with a fully-sequenced and annotated genome. Using the species’ extensive diversity panel, we aimed at: i) understanding the molecular basis of its adaptation to different environments, ii) delving into the effect of structured populations on the discovery of adaptive variants using genome-wide studies and iii) investigating the flowering time differences and genetic architecture of this trait on natural populations. By doing so, we also provide the community with genomic resources that close a conspicuous sampling gap in the Balkan region. Our results show that B. distachyon’s genetic clades (populations) occupy different ecological niches, and we suggest that the species recolonized Europe and the Middle East following the last glacial maximum. Furthermore, we confirm that the level of population subdivision influences the detection of candidate variants and that local populations adapted through different strategies to the same environmental pressure. We also demonstrate that natural accessions across the species’ range display large differences regarding flowering time and vernalization requirements, using data of both an outdoor and a greenhouse experiment. Finally, we reveal that eight well-characterized flowering-time genes contribute significantly to flowering time variation and display signs of polygenic selection in the natural populations of B. distachyon. In summary, this thesis establishes B. distachyon as a model for research in ecology and evolution and pave a new avenue of research in the field of population genomics.