Auxin is required for the long coleoptile trait in japonica rice under submergence

• Rice coleoptile elongation under submergence guarantees fast seedling establishment in the field. We investigated the role of auxin in influencing the capacity of rice to produce a long coleoptile under water. • In order to explore the complexity of auxin’s role in coleoptile elongation, we used gene expression analysis, confocal microscopy of an auxin-responsive fluorescent reporter, gas chromatography coupled to tandem mass spectrometry (GC–MS/MS), and T-DNA insertional mutants of an auxin transport protein. • We show that a higher auxin availability in the coleoptile correlates with the final coleoptile length under submergence. We also identified the auxin influx carrier AUX1 as a component influencing this trait under submergence. The coleoptile tip is involved in the final length of rice varieties harbouring a long coleoptile. • Our experimental results indicate that auxin biosynthesis and transport underlies the differential elongation between short and long coleoptile-harbouring japonica rice varieties.