Phosphorus (P) is an essential macronutrient for plant growth and development; however, soil P available for plant absorption is often limited, putting constraints over agricultural sustainability. Understanding the physiological and molecular responses to P deficiency can help design strategies for diagnosis and mitigation of P deficiency in crop plants. The advent of the next-generation sequencing technologies has made it possible to characterize genome-wide molecular responses to P deficiency in plants. However, such research efforts are very limited for woody crops. In this study, RNA-seq was used to investigate P starvation-induced transcriptomic changes in roots of a frequently used citrus rootstock, Poncirus trifoliata (L.) Raf. A total of 1,135 genes showed differential expression in response to P deficiency. The transcriptomic data were further validated by real-time quantitative RT-PCR. Interestingly, at least one or more P-responsive cis-elements (P1BS) were found in the promoter regions of 76 differentially expressed genes. Functional annotation revealed that the predicted proteins of 117 of the differentially expressed genes were assigned to the categories of transporters, transcription factors or components involved in plant hormone signal regulation, suggesting that these genes may play important roles in response to P starvation. A comparative analysis of the citrus- and Arabidopsis-responsive transcripts under P deficiency also identified 174 commonly regulated genes, including those involved in P metabolism. Taken together, our transcriptomic data revealed changes of genome-wide gene expression in responses to P starvation in Poncirus, which should provide a solid basis for future identification and characterization of key genes involved in nutritional stress response in citrus rootstocks.
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