Genetic variation associated with plastic and homeostatic growth responses to drought in Arabidopsis

Natural genetic variation influences plant responses to environmental stressors. However, the extent to which such variation underlies plastic versus homeostatic response phenotypes has been little studied. We quantified the extent of drought-induced changes in leaf area in a set of Iberian Arabidopsis accessions and then performed association studies correlating variation in this phenotype with genomic and transcriptomic variation. Drought-induced plastic reductions in relative leaf area typified accessions originating from productive environments. In contrast, in relative leaf area typified accessions originating from unproductive environments. Genome-Wide Association Studies (GWAS), Transcriptome Wide Association Studies (TWAS), and expression GWAS (eGWAS) highlighted the importance of auxin-related processes and, in particular, the potential role of the SMALL AUXIN UP RNA 26 (SAUR26) gene in conferring leaf area plasticity. Homeostatic responses in relative leaf area were associated with a diverse gene set and positively associated with a higher intrinsic water use efficiency (WUEi) as confirmed in a TWAS metanalysis of previously published δ13C measurements. We have identified not only candidate plasticity genes but also candidate homeostasis genes controlling leaf area. Our results demonstrate the value of a combined GWAS, TWAS, and eGWAS approach to identify mechanisms underlying phenotypic responses to stress.