Abstract
Light quality, particularly the red-to-far-red (R:FR) ratio, regulates plant architecture, but how red-to-far-red (R:FR) spectral mixtures modulate rice (Oryza sativa L.) seedling height remains unclear. We exposed rice seedlings to a series of six R:FR mixtures (R0–R100; defined on a photon-flux basis) and measured agronomic traits, stem cell length, hormone contents, and transcriptomes. Plant height showed a triphasic response: R20 (20% red/80% far-red; R:FR = 0.25) strongly promoted elongation, R80 (80% red/20% far-red; R:FR = 4.00) suppressed it, and R100 (100% red) induced an apparent compensatory rebound. Across the R0–R80 treatments, IAA content was positively associated with plant height and stem cell length, whereas ABA showed an inverse trend; GA3 changed only slightly. RNA-seq of XZX45 seedlings identified 1533 DEGs between R20 and R80 (711 up-regulated and 822 down-regulated in R80 relative to R20; |log2 fold change| ≥ 1, adjusted p ≤ 0.05), enriched in cell wall organization, plant hormone signal transduction, and fatty acid elongation. Exploratory WGCNA identified a blue module negatively correlated with plant height, with OsNUC1 as a candidate hub gene; its module-level association was directionally reproducible but statistically inconclusive at n = 6. These findings suggest that R:FR spectral composition may modulate rice seedling height through auxin/ABA-associated pathways and candidate genes; part of the height response may also reflect the treatment-associated differences in photosynthetically active photon supply, so a sole effect of spectral composition is not established. These results provide a basis for light-quality management in controlled-environment seedling production.