Natural genetic variation shapes root system responses to phytohormones in Arabidopsis

Plants adjust their architecture by modulating organ growth. This ability is largely dependent on phytohormones. While responses to phytohormones have been studied extensively, it remains unclear to which extent and how these responses are modulated in non-reference strains. Here, we assess variation of root traits upon treatment with auxin, cytokinin and abscisic acid (ABA) in 192 Arabidopsis accessions. We identify common response patterns, uncover the extent of their modulation by specific genotypes, and find that the Col-0 reference accession is not a good representative of the species in this regard. We conduct genome-wide association studies and identify 114 significant associations, most of them relating to ABA treatment. The numerous ABA candidate genes are not enriched for known ABA-associated genes, indicating that we largely uncovered unknown players. Overall, our study provides a comprehensive view of the diversity of hormone responses in the Arabidopsis thaliana species, and shows that variation of genes that are yet mostly not associated with such a role to determine natural variation of the response to phytohormones.