Multiple independent MGR5 alleles contribute to a clinal pattern in leaf magnesium across the distribution of Arabidopsis thaliana

Magnesium (Mg) is a crucial element in plants, particularly for photosynthesis. Mg homeostasis is influenced by environmental and genetic factors, and our understanding of its variation in natural populations remains incomplete. We examine the variation in leaf Mg accumulation across the distribution of Arabidopsis thaliana, and we investigate the environmental and genetic factors associated with Mg levels. Using genome-wide association studies in both the widespread Eurasian population and a local-scale population in Cape Verde, we identify genetic factors associated with variation in leaf Mg. We validate our main results, including effect size estimates, using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) mutagenesis. Our findings reveal a significant association between leaf Mg and latitude of origin. In Eurasia, we find a signal at the nutrient-response regulator, RAPTOR1A, and across the species range, we find that multiple alleles of the Mg transporter, MAGNESIUM RELEASE 5 (MGR5), underlie variation in leaf Mg and contribute to the observed latitudinal cline. Overall, our results indicate that the spatial distribution of leaf Mg in A. thaliana is affected by climatic and genetic factors, resulting in a latitudinal cline. Further, they show an example of allelic heterogeneity, in which multiple alleles at a single locus contribute to a trait and the formation of a phenotypic cline.