Pup1 QTL-Mediated Tissue-Specific Differential Expression of Transcription Factors Help Mitigate Deleterious Effects of Phosphorus-Starvation in Rice (Oryza sativa L.)

Phosphorus (P) deficiency is one of the abiotic stresses limiting crop growth and productivity. Plants endure low-P stress by regulating gene-networks through controlling biochemical, physiological processes, and modifying growth/development of plant. Transcription factor (TF)-mediated regulation of gene networks is crucial for responses of plant to abiotic stresses. TFs being early stress-responsive proteins regulate the expression of late stress-responsive genes as part of adaptive responses to environmental stresses. The present study focuses on comparative expression analysis of TFs in two contrasting rice [Pusa-44 (P-deficiency-sensitive) and its near isogenic line (NIL)-23 for Phosphorus uptake 1 (Pup1) QTL (P-deficiency-tolerant)] genotypes. Total of 56 TF families comprising of 1727 TF genes were differentially expressed in root and shoot of the contrasting rice genotypes grown under P-starvation stress. The TF families represented by > 100 members of TFs (including bHLH, ERF, NAC, MYB, FAR1, and WRKY families) differentially expressed and 49 gene ontology (GO) terms significantly over-represented in NIL-23 (compared to that in Pusa-44) under stress indicate the regulatory role of Pup1 QTL under P-starvation stress in rice. While upregulated expression of TFs in root played primary role in P acquisition, upregulation of TFs (e.g., NAC, ERF, bHLH, MYB, WRKY) in shoot complemented in managing with stress. Molecular functions of TFs supported morpho-physio-biochemical traits (e.g., stress signalling, root architecture, P acquisition) in imparting better P-starvation/deficiency tolerance to NIL-23. However, the plants of NIL-23 remained feeble in the vegetative stage and could not enter into the reproductive phase under P-starvation stress. Some of these TFs might serve as candidate gene(s) for genetic manipulation to improve phosphorus-use efficiency in rice cultivars.