Darkness Attenuates the Early Transcriptional Response to Phosphate Deficiency in Soybean Roots

Phosphate (Pi) deficiency induces responses that enhance Pi uptake and utilization. Light may influence these responses through photosynthetic carbon supply and signaling. We examined how light affects the early root transcriptional response to Pi deficiency in hydroponically grown soybean. Plants were exposed to phosphate-sufficient (+P) or phosphate-deficient (−P) conditions for 30 h under a light/dark cycle or continuous darkness. Root transcriptomes were analyzed using Oxford Nanopore cDNA sequencing. Principal component analysis (PCA) showed that transcriptomes separated mainly by light, with weaker separation by Pi status. Under light, Pi deficiency induced a broad response involving Pi transport, signaling, transcriptional regulation, lipid remodeling, and metabolism. In darkness, relatively few genes were upregulated under Pi deficiency. This limited response was not caused by a loss of transcriptional responsiveness, because thousands of genes were upregulated by darkness itself. Comparison of fold changes revealed that darkness attenuated, rather than reversed, the −P response. Interaction-ranked gene set enrichment analysis (GSEA) showed that the weaker response in darkness extended across signaling, metabolic, and transport pathways. Light-signaling genes responded strongly to darkness but showed little phosphate-dependent regulation. Root sucrose levels were lower in darkness, consistent with reduced carbon availability as a possible contributor to the attenuated Pi-deficiency response.