Phosphorus starvation-induced alternative splicing landscape of rice confirms the regulatory function of Pup1 QTL

Low phosphorus (P) use efficiency of rice, in spite of sufficient P present in soil (mainly as insoluble complex), and excessive use of phosphatic fertilizers by farmers may cause several issues including higher cost of cultivation and environmental pollution. Alternative splicing of pre-mRNA is one of the strategies for transcriptome/proteome diversity that help plants to optimize acquisition and mobilization of P. Comparative analysis of rice [Pusa-44 and its Near-Isogenic Line (NIL)-23] grown hydroponically under contrasting conditions (16 ppm and 0 ppm) until vegetative stage deciphered stress-induced alternative splicing regulated through Pup1 QTL. The modulation in alternative splicing in root and shoot of rice under stress can be attributed to the regulatory function of Pup1. In addition to a considerable increase in the number of genes showing up-regulated expression, ∼20 genes demonstrated differential expression as well as alternative splicing (with a decrease in root but increase in shoot) in NIL-23under stress. Increase in alternative splicing of transcripts for 'iron-regulated bHLH transcription factor', 'regulation of P homeostasis' in roots while 'serine hydroxymethyltransferase' and 'iron-regulated bHLH transcription factor' in shoot, particularly those associated with P homeostasis/P-starvation stress-responsive signaling pathway, were recorded in the case of NIL-23 under stress. Genes/transcripts, particularly those associated with biological process in roots, showing reversed (increased vs. decreased) level of splicing in NIL-23 (compared to that in its parent) on P-starvation confirmed regulatory role of the QTL. Better understanding of splicing event/gene/transcript and its regulation might provide novel strategies to modulate gene expression for nutrient homeostasis and enhancing stress resilience in crop plants.