Abstract
Low phosphate (Pi) availability is an important limiting factor affecting soybean production. However, the underlying molecular mechanisms responsible for low Pi stress response and tolerance remain largely unknown, especially for the early signaling events under low Pi stress. Here, a genome-wide transcriptomic analysis in soybean leaves treated with a short-term Pi-deprivation (24 h) was performed through high-throughput RNA sequencing (RNA-seq) technology. A total of 533 loci were found to be differentially expressed in response to Pi deprivation, including 36 mis-annotated loci and 32 novel loci. Among the differentially expressed genes (DEGs), 303 were induced and 230 were repressed by Pi deprivation. To validate the reliability of the RNA-seq data, 18 DEGs were randomly selected and analyzed by quantitative RT-PCR (reverse transcription polymerase chain reaction), which exhibited similar fold changes with RNA-seq. Enrichment analyses showed that 29 GO (Gene Ontology) terms and 8 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were significantly enriched in the up-regulated DEGs and 25 GO terms and 16 KEGG pathways were significantly enriched in the down-regulated DEGs. Some DEGs potentially involved in Pi sensing and signaling were up-regulated by short-term Pi deprivation, including five SPX-containing genes. Some DEGs possibly associated with water and nutrient uptake, hormonal and calcium signaling, protein phosphorylation and dephosphorylation and cell wall modification were affected at the early stage of Pi deprivation. The cis-elements of PHO (phosphatase) element, PHO-like element and P responsive element were present more frequently in promoter regions of up-regulated DEGs compared to that of randomly-selected genes in the soybean genome. Our transcriptomic data showed an intricate network containing transporters, transcription factors, kinases and phosphatases, hormone and calcium signaling components is involved in plant responses to early Pi deprivation.
Highlights
As a non-substitutable macronutrient, phosphorus (P) is essential for plant growth and development by being part of fundamental bio-molecules and participating in various cellular activities
In Arabidopsis, the MYB-CC (MYB-coiled–coil) transcription factor PHR1 and its close homologs PHR1-LIKE 1 (PHL1) and PHL2 are considered to be the central signaling components controlling transcriptional and metabolic responses to variations in Pi supply [10,11,12]; SPX-MFS (SPX-Major Facilitator Superfamily) protein VPT1 (Vacuolar Phosphate Transporter 1, named PHT5;1) is regarded to mediate vacuolar Pi sequestration, which is critical for plant acclimation to varying Pi availability in the environment [13,14,15]; microRNAs are important players in controlling Pi transport by regulating the expression levels of some key components in Pi signaling networks, such as PHO2 and NLA (Nitrogen Limitation Adaptation) [16,17,18]
Numerous genes were shown to be responsive to Pi deprivation, including genes involved in Pi acquisition and recycling, hormonal signaling and transcriptional regulation
Summary
As a non-substitutable macronutrient, phosphorus (P) is essential for plant growth and development by being part of fundamental bio-molecules and participating in various cellular activities. In order to improve Pi acquisition and use efficiency of crop plants, many studies have been conducted to understand the physiological, biochemical and molecular mechanisms of plant adaptation and tolerance to low Pi stress [3,4,5,6]. Transcriptomic analyses by microarray and recently developed high-throughput sequencing methods provide a useful tool for holistic understanding of the transcriptional responses under Pi deficiency in the post-genome era. Numerous genes were shown to be responsive to Pi deprivation, including genes involved in Pi acquisition and recycling, hormonal signaling and transcriptional regulation. These findings support previous physiological and biochemical studies [28,29]. The DEGs and signaling components identified here represent new candidates for understanding the molecular mechanisms of early Pi stress responses in leaves and the improvement of Pi stress tolerance in soybean
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