Natural variation in DXR expression is associated with apical hook bending under NaCl stress in Arabidopsis thaliana

Successful soil emergence requires apical hook establishment during skotomorphogenesis. Soil salinity disrupts this process, but the mechanisms linking environmental stress to hook growth remain unclear. Here, we employed a genome-wide association study (GWAS) across Arabidopsis thaliana accessions to identify a locus associated with variation in the salt-induced reduction of apical hook curvature. Fine mapping reveals genetic variation in the promoter of 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE (DXR), encoding the first committed enzyme of the plastid-localized methylerythritol phosphate (MEP) pathway. Accessions carrying an alternative promoter haplotype exhibit elevated DXR expression and a stronger hook bending under salt. Salt treatment and loss of transcriptional repressor PHYTOCHROME INTERACTING FACTOR1 (PIF1) additively increase DXR transcript levels, and pif1-2 seedlings exhibit higher apical hook angles under salt stress. This phenotype is suppressed by inhibition of DXR activity, indicating that an increased MEP pathway flux reduces salt sensitivity in pif1-2 seedlings. Across accessions, DXR expression positively correlates with hook curvature under salt stress, further strengthening the link between DXR and modulation of hook bending under salt stress. Together, these findings identify plastid metabolism as a regulatory layer linking environmental stress to altered skotmomorphogenis, and raise important questions about how etioplast-derived signals interact with growth-control networks in the dark. HighlightA genome wide association study in Arabidopsis reveals that variation in DXR expression, encoding an essential enzyme in the MEP pathway, drives salt-induced repression of apical hook formation darkness.