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Genetic adaptations to climate in Arabidopsis thaliana

Final Report Summary - CLIMATE_ADAPTATION (Genetic adaptations to climate in Arabidopsis thaliana)

A major goal in evolutionary biology is to clarify the basis of local adaptation. The limited mobility of plants may translate into particularly strong selection due to climate-mediated selection pressures.
Some of the earliest evidence for this comes from phenotypic clines with the environment. The overarching goal of this project was to identify loci and specific genetic variants that contribute to climatic adaptation in the model plant, Arabidopsis thaliana.
For the first half of the project, the focus was on generating data for the 1001 Genomes Project by preparing samples for sequencing (including samples used for estimating error rates) and processing of sequence data (alignment to the reference genome, calling SNPs and TEs and checking quality of the resulting sequence calls). During this period the host of the grant was the Gregor Mendel Institute fuer Molekulare Pflanzenbiologie. This work was aided by Viktoria Nizhynska (technician) and Alexander Platzer (Bioinformatics), who were each paid to work on the project 10hrs/week. I requested a change of host was for the For the second half of the project because by then I had a group leader position at the University of Vienna in the Department of Structural and Computational Biology. At this point, the focus of the project shifted to analysis and work towards functional validation. We also conduced sequencing to extend and test the conclusions from the publicly available data. Results from this additional sequencing is expected to result in two publications over the next year.
I met the major objective of the project by modeling the population history of the samples and using this to identify loci that are associated with climate in the sample. I found the strongest signals were with precipitation-related variables consistent with an important role for adaptation to drought tolerance across the Eurasian range of Arabidopsis thaliana. Twenty variants were significant with a conservative false discovery rate (FDR) cutoff of 5% and 4 of these resulted in a change at the amino acid level. These included 2 SNPs in CYP705A30, 1 SNP in PSD3, and 1 SNP in a tRNA/rRNA methyltransferase. The climate correlation results are especially interesting in the context of our finding that most Eurasian A. thaliana accessions represent a major post-glacial expansion of the species, while a minor subset of relicts represent very old lineages. These relicts are mainly found in Iberia and occur in locations where precipitation is lower than for non-relicts. SNPs in the genes Ethylene response factor 1 (ERF1) and Mildew-resistance 11 (ATMLO11) were associated with precipitation at the 5% FDR, and these associations were characterized by much higher derived frequencies in the relicts compared to the general population. These most significant loci and SNPs are optimal candidates for functional follow-up analyses. More detail regarding these results is available in our recent publication (doi:10.1016/j.cell.2016.05.063).
Natural variation in A. thaliana has served as an important tool. Our findings are useful for understanding the history of A. thaliana in Eurasia and the expectations for the distribution and reasons for variation in phenotypes and genetic variation across this part of the range.