Phosphate starvation induces root cell-type-specific transcriptional responses and alternative splicing

Phosphate (Pi) is an essential nutrient for plant growth, and understanding how Arabidopsis thaliana root cells respond to Pi deficiency is crucial to decipher whole plant responses. We perform high-resolution transcriptomic profiling across five distinct root cell types, identifying differentially expressed genes (DEGs) and differential alternative splicing (DAS) events that define cell-type-specific Pi-responsive regulatory layers. We identify over 7000 DEGs and 733 DAS that act largely independently and are cell-type-specific, affecting distinct loci and biological pathways. Transcription factors such as LHY, REV7 and MYB88, linked to circadian rhythms, stomatal regulation and ABA perception, acquire novel functions under Pi starvation. We show that the splicing factor SR45, previously associated with iron homeostasis, regulates Pi allocation. The sr45-1 mutant displays increased root-to-shoot Pi ratio and reduced biomass. A substantial number of Pi-responsive DAS transcripts are SR45 bound, indicating that SR45 operates as a regulatory hub for Pi transport and homeostasis. This cell-type-resolved dataset provides a detailed molecular map of Pi deficiency responses and highlights the importance of post-transcriptional regulation in shaping root adaptive strategies. Transcriptional regulation and alternative splicing emerge as coordinated mechanisms orchestrating plant adaptation to Pi starvation.