Abstract
Abstract Phosphorus (P) is an essential macronutrient required for respiration, photosynthesis/carbohydrate metabolism, redox homeostasis, signaling, and synthesis/function of nucleic acids, cellular membranes, enzymes, etc. To cope with P-deficiency, plants reprogram gene expression for necessary alterations in metabolic/signaling pathways. To attain P homeostasis, plants readjust metabolism through transcriptional, post-transcriptional, and/or post-translational machinery involving biochemical, physiological, genomic, epigenomic, proteomic, and metabolomic functions. However, the underlying molecular mechanisms/pathways/genes for P-deficiency tolerance in crop plants remain elusive. To decipher the mechanisms/pathways adopted by rice under P-starvation/deficiency stress, a pair of contrasting rice [Pusa-44 (high-yielding, P-deficiency sensitive) and its near-isogenic line (NIL)-23, P-deficiency tolerant) for Pup1 QTL] genotype was used for comparative analyses. Omics analyses of shoot and root tissues from 45-day-old plants grown hydroponically in P-sufficient (16 ppm Pi), P-deficient (4 ppm Pi) or P-starved (0 ppm Pi) medium revealed important roles of P transporters, transcription factors (TFs), Transposable elements (TEs), auxin-responsive proteins, cell wall modulation, fatty acid metabolism, and chromatin architecture/epigenetic modifications in making NIL-23 tolerant to stress. The proteins involved in photosynthesis, sucrose-/starch-/energy-metabolism, transcription factors, and phytohormone signaling were observed to be differentially expressed in NIL-23. Since only a few coding genes are located on the QTL, modulations in morpho-physio-biochemical and molecular parameters under P-starvation/deficiency stress were attributed to the regulatory functions of Pup1 through TFs, TEs, epigenetic/chromatin architectural changes, etc. introgressed in Pusa-44 genetic background. Thus, the study provides new insights into molecular/regulatory functions of Pup1 under P-starvation/deficiency stress in rice, which might be useful to improve P-use efficiency in rice for better productivity in P-deficient soils.