A systemic view of phosphate starvation-responsive genes in rice roots to enhance phosphate use efficiency in rice

Abstract

Phosphate (Pi) is one of the major nutrients for crop growth and yield. Although several studies have revealed a global view of Pi starvation responses in rice, the detailed features were not well-addressed. To identify differentially expressed genes associated with phosphate starvation on a genome scale, we analyzed transcriptome data of roots from 2-week old seedlings that were grown on Pi-sufficient or -deficient media for 7 and 21 days. Using publicly available RNA-sequencing data, we subsequently identified 820 up-regulated genes in roots under Pi starvation. Gene ontology enrichment analysis of these genes indicated that secondary metabolic processes are most significantly enriched under Pi starvation, and Pi transport and defense to biotic stress also play significant roles in response against Pi deficiency. Functional classification analysis using MapMan emphasizes the significance of transcription factors, such as MYB, WRKY, and bHLH, various transporters, and genes in secondary metabolic processes. Use of promoter trap lines or transgenic plants expressing the GUS reporter gene under the control of Pi starvation-inducible gene promoters confirmed the meta-expression patterns of two genes stimulated by Pi starvation, suggesting novel promoters for enhancing Pi use efficiency. In addition to the identification of two novel promoters for Pi starvation response, cis-regulatory elements for the regulation of Pi starvation are suggested. Overall, our study provides a global view of Pi starvation response based on transcriptome data and novel tools for improving PUE and Pi uptake in rice, a model crop plant.