Integrated transcriptome and proteome analysis of near-isogenic line provides insights on regulatory function of Pup1 QTL in rice under phosphorus-starvation stress

Phosphorus, essential for growth/productivity of plants, is acquired through roots in the form of inorganic phosphate (Pi). The molecular mechanism of low Pi tolerance in plants is still not fully understood. Functions of Pup1 QTL in Pi-deficiency tolerance in rice are sparsely understood. To decipher the molecular functions of qPup1 in Pi-homeostasis in rice, integrated transcriptome-proteome analysis of contrasting rice genotypes grown under Pi-starvation stress was performed. Our integrated analysis identified 4614 transcripts and 107 proteins differentially expressed in roots of NIL-23 (Pi-deficiency tolerant, harboring qPup1), whereas 8555 transcripts and 687 proteins were differentially expressed in shoots of NIL-23 under Pi-starvation stress. The integrated analysis indicated 146 transcripts/proteins expressed in shoots, while 18 transcripts/proteins expressed in roots of NIL-23, which might be responsible for making it stress resilient. The genes/proteins for TFs, P metabolism, starch/sucrose metabolism, and RNA-mediated post-transcriptional regulation play important roles in Pi-starvation in rice. Functional annotation of differentially transcribed genes/expressed proteins indicated transcription factors, phosphorus/starch/sucrose metabolism, and RNA-mediated post-transcriptional regulation to be important players in Pi-starvation resilience of NIL-23. Up-regulated expression of genes/proteins under stress due to introgression of qPup1 deciphered regulatory functions of the QTL and the genes/proteins involved. These might help developing rice cultivar with improved P acquisition/use-efficiency for better performance in P-deficient soils. •Integrated transcriptome−proteome analysis revealed regulatory role of Pup1 QTL under P-starvation stress in rice.•Our analysis indicated 146 transcripts/proteins co-expressed in shoot, while 18 in root of NIL-23 making it stress-resilient.•Expression of genes/proteins for TFs, Pi/sugar metabolism, and post-transcriptional regulation played important roles.•Up-regulation of genes/proteins due to Pup1 QTL, particularly in leaf, plays important roles in stress tolerance.