BackgroundLong, robust hypocotyls are important for facilitating greenhouse transplant production. Use of far-red light at the end of the day (end-of-day far-red, EOD-FR) is known to affect hypocotyl elongation. Auxin is an important regulator of plant growth and development, but its role and mechanism in EOD-FR-mediated hypocotyl elongation remain unclear. Here we combined transcriptome sequencing and metabolite profiling of pumpkin hypocotyls with related physiological experiments to provide insight into the mechanisms by which auxin affects the response to EOD-FR. ResultsAfter EOD-FR treatment, the length of pumpkin Hypocotyl and the IAA level of plant Hypocotyl were significantly promoted. When NPA was applied, the Hypocotyl elongation mediated by EOD-FR and the increase of IAA content were counteracted.At the same time, through the observation of Hypocotyl sections, we found that hypocotyl cells expanded significantly after EOD-FR treatment.After EOD-FR treatment, 2801 DEGs, were identified in hypocotyl, of which 31 DEGs related to auxin synthesis, transport and signal transduction and 25 cell wall protein genes were identified.Through the detection of metabolic group, it was found that the levels of tryptophan and indole in plant increased after EOD-FR treatment.All these indicate that auxin plays an essential role in EOD-FR-mediated hypocotyl elongation.ConclusionsWe identified a large number of differentially expressed genes related to auxin synthesis, transport, and downstream response. We speculate that auxin is essential for pumpkin hypocotyl elongation mediated by EOD-FR, and that the synthesis of free IAA may be performed by the tryptophan-dependent TAA-YUC pathway. This study improves our understanding of auxin’s role in EOD-FR-mediated hypocotyl elongation.