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Stomata control gas exchanges between the plant and the atmosphere. How natural variation in stomata size and density contributes to resolve trade‐offs between carbon uptake and water loss in response to local climatic variation is not yet understood. We developed an automated confocal microscopy approach to characterize natural genetic variation in stomatal patterning in 330 fully sequenced  Arabidopsis thaliana  accessions collected throughout the European range of the species. We compared this to variation in water‐use efficiency, measured as carbon isotope discrimination (δ 13 C). We detect substantial genetic variation for stomata size and density segregating within  Arabidopsis thaliana . A positive correlation between stomata size and δ 13 C further suggests that this variation has consequences on water‐use efficiency. Genome wide association analyses indicate a complex genetic architecture underlying not only variation in stomatal patterning but also to its covariation with carbon uptake parameters. Yet, we report two novel QTL affecting δ 13 C independently of stomatal patterning. This suggests that, in  A. thaliana , both morphological and physiological variants contribute to genetic variance in water‐use efficiency. Patterns of regional differentiation and covariation with climatic parameters indicate that natural selection has contributed to shape some of this variation, especially in Southern Sweden, where water availability is more limited in spring relative to summer. These conditions are expected to favour the evolution of drought avoidance mechanisms over drought escape strategies.

Natural variation in stomata size contributes to the local adaptation of water‐use efficiency in Arabidopsis thaliana