Skip to main content

Using cis-regulatory mutations to highlight polygenic adaptation in natural plant systems

Periodic Reporting for period 3 - AdaptoSCOPE (Using cis-regulatory mutations to highlight polygenic adaptation in natural plant systems)

Reporting period: 2018-09-01 to 2020-02-29

This project will use the genome-wide distribution of cis-regulatory variants to discover the molecular pathways that are optimized during adaptation via accumulation of small effect mutations. Current approaches include scans for outlier genes with strong population genetics signatures of selection, or large effect QTL associating with fitness. They can only reveal a small subset of the molecular changes recruited along adaptive paths. The goal of this project is to demonstrate that novel aspects of the molecular basis of Darwinian adaptation can be discovered if the polygenic basis of adaptation is taken into account. The distribution of small effect mutations will be used to make inferences on the adaptive evolution of the gene regulatory network of divergent populations in each of the two closely related species, A. thaliana and A. lyrata, which are both found at diverse latitudes and show sign of local adaptation to climatic differences. Mutations affecting cis-regulation will be identified in leaves of plants exposed to various temperature regimes triggering phenotypic responses of adaptive relevance. Their distribution in clusters of co-expressed genes will be quantified. The phylogeographic differences in the distribution of the mutations will be used to disentangle neutral from adaptive clusters of co-expressed genes in each of the two species. This project will identify the molecular pathways subjected collectively to natural selection. It will further examine whether local adaptation occurs by convergent evolution of molecular systems in plants. This approach has the potential to find broad applications in ecology and agriculture.
The goal of this project is to demonstrate that novel aspects of the molecular basis of Darwinian adaptation can be discovered if the polygenic basis of adaptation is taken into account. This project will use the genome-wide distribution of cis-regulatory variants to discover the molecular pathways that are optimized during adaptation via accumulation of small effect mutations.
Five specific objectives were defined:
1. Identify temperature perturbation regimes that trigger a regionally adaptive developmental response in A. thaliana and A. lyrata.
2. Identify regulatory modules involved in regional adaptation in Europe in A. thaliana and A. lyrata by the genomic mapping of cis-regulatory variants revealed in F1 individuals.
3. Test whether local adaptation in plant populations proceeds via convergent modifications of regulatory pathways.
4. Validate the functional relevance of traits controlled by regulatory modules with an excess of cis-regulatory mutations for plant growth and fitness in A. thaliana
5. Improve our understanding of plant promoters by comparing the genomic properties of cis-regulatory variance in A. thaliana and A. lyrata

Objective 1 is completed and a proof-of-principle for objective 2 has been published in 2016.
Objective 2 is half-way through, material has been collected and will be sequenced in 2018 and at the beginning of 2019
Objective 3 is half-way through. We have conducted a population genetics analysis to detect signatures of selection. These analysis reveal that there is parallel evolution between A. lyrata and A. thaliana. A manuscript is in preparation. In 2019 we will examine whether cis-regulatory evolution also follows a parallel evolutionary pattern
Objective 4 is not yet completed. We are running field experiment to evaluate fitness variation across genotypes
Objective 5 is being tackled with interspecific data at the moment. We hope to be able to run validation experiment in 2019.
The project is progressing well. We anticipate that 3 additional manuscripts will be published in 2018: Glander et al. 2018, Göbel et al. 2018 are already accepted in Genome Biology and Evolution. Dittberner et al. is being revised by Molecular Ecology. Three additional manuscript are in preparation which we hope to submit before the end of the year : He et al. , Wieters et al. and Takou et al. For now, most of these publications were paid by remaining funds from other projects, which explains why there is at this stage no money invested in dissemination. We expect this will change this year.