Natural variation links seedling hypocotyl growth with water loss in Arabidopsis

SUMMARY Plants integrate environmental and internal cues such as light and sugar availability to coordinate growth and water‐use strategies. While hypocotyl elongation is widely used to study photo‐ and thermo‐morphogenesis, its connection to whole‐plant physiological traits remains unclear. Here, we uncover a negative correlation between hypocotyl length in young Arabidopsis thaliana seedlings and water loss in mature plants. Genome‐wide association mapping across diverse natural accessions identified two genes, HEAT SHOCK TRANSCRIPTION FACTOR A2 ( HSFA2 ) and a 2‐oxoglutarate‐dependent dioxygenase‐like ( 2OGD ‐ like ), that affect hypocotyl elongation. Both genes are preferentially expressed in guard cells and are associated with reduced hypocotyl growth and increased stomatal conductance. Loss‐of‐function mutants displayed elongated hypocotyls and reduced gas exchange, whereas inducible and guard cell‐specific expression of HSFA2 suppressed hypocotyl elongation and promoted stomatal opening. Guard cell transcriptomics and ChIP‐seq analyses further revealed that HSFA2 directly targets genes involved in sugar signaling, light responses, and actin reorganization, including SCAR3 , a component of the WAVE‐ARP2/3 complex required for stomatal dynamics. Together, these findings establish a functional link between seedling growth and stomatal performance, expand the role of HSFA2 beyond heat responses, and position hypocotyl growth as a predictive platform for assessing plant water‐use traits.