Transcriptome analysis of a near-isogenic line and its recurrent parent reveals the role of Pup1 QTL in phosphorus deficiency tolerance of rice at tillering stage

Phosphorus (P) is essential for cellular processes like respiration, photosynthesis, biosynthesis of membrane phospholipids, etc. To cope with P deficiency stress, plants adopt reprograming of the expression of genes involved in different metabolic/signaling pathways for survival, growth, and development. Plants use transcriptional, post-transcriptional, and/or post-translational machinery to achieve P homeostasis. Several transcription factors (TFs), miRNAs, and P transporters play important roles in P deficiency tolerance; however, the underlying mechanisms responsible for P deficiency tolerance remain poorly understood. Studies on P starvation/deficiency responses in plants at early (seedling) stage of growth have been reported but only a few of them focused on molecular responses of the plant at advanced (tillering or reproductive) stage of growth. To decipher the strategies adopted by rice at tillering stage under P deficiency stress, a pair of contrasting genotypes [Pusa-44 (a high-yielding, P deficiency sensitive cultivar) and its near-isogenic line (NIL-23, P deficiency tolerant) for Pup1 QTL] was used for morphophysiological, biochemical, and molecular analyses. Comparative analyses of shoot and root tissues from 45-day-old plants grown hydroponically under P sufficient (16 ppm) or P deficient (4 ppm) medium confirmed some of the known morphophysiological responses. Moreover, RNA-seq analysis revealed the important roles of phosphate transporters, TFs, auxin-responsive proteins, modulation in the cell wall, fatty acid metabolism, and chromatin architecture/epigenetic modifications in providing P deficiency tolerance to NIL-23, which were brought in due to the introgression of the Pup1 QTL in Pusa-44. This study provides insights into the molecular functions of Pup1 for P deficiency tolerance, which might be utilized to improve P-use efficiency of rice for better productivity in P deficient soils. KEY MESSAGE: Introgression of Pup1 QTL in high-yielding rice cultivar modulates mainly phosphate transporters, TFs, auxin-responsive proteins, cell wall structure, fatty acid metabolism, and chromatin architecture/epigenetic modifications at tillering stage of growth under phosphorus deficiency stress.