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

Phosphate (P_i) deficiency induces responses that enhance P_i 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 P_i 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 P_i status. Under light, P_i deficiency induced a broad response involving P_i transport, signaling, transcriptional regulation, lipid remodeling, and metabolism. In darkness, relatively few genes were upregulated under P_i 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 P_i-deficiency response.