Cis-regulatory diversity and adaptive divergence in the Arabidopsis genus

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This project proposes to examine cis-regulatory changes between Arabidopsis species at a genome-wide level. Relative allele expression ratios will be examined genome-wide in interspecific hybrids generated by crosses between A. thaliana and its two closest relatives, A. lyrata and A. halleri. Ratios will be examined in leaves of plants submitted to drought, cold and heavy metals and compared to ratios observed in leaves of control non challenged plants. Preliminary work has highlighted associations between epigenetic and expression differences. The epigenetic profiling of the parental genomes will therefore be performed in order to ascertain the mutational source of cis-regulatory change. The goal of this project is triple: first we want to describe the extent of cis-regulatory changes that have occurred since speciation in the Arabidopsis genus. Second, we want to estimate the number of cis-regulatory changes that are specific to an environmental cue whose ecological relevance differs between the two sister species A. lyrata and A. halleri. Third, the experiment is designed cis-regulatory changes derived in either the A. lyrata or the A. halleri lineage can be identified. Sets of co-regulated genes displaying an excess of cis-regulatory change will pinpoint gene ensembles underpinning adaptive phenotypic divergence. Experiments are planned to validate this method. If validated, it can have important implications in non-model species, in particular crops.