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Global transcriptome profile of rice root in response to essential macronutrient deficiency.

ABSTRACT: Deficiency of the three essential macronutrients, nitrogen, phosphorus and potassium, leads to large reduction in crop growth and yield. To characterize the molecular genetic basis of adaptation to macronutrient deprivation, we performed microarray analysis of rice root at 6 and 24 h after nitrogen, phosphorus and potassium deficiency treatments. The transcriptome response to nitrogen depletion occurred more rapidly than corresponding responses to phosphorus and potassium deprivation. We identified several genes important for response and adaptation to each nutrient deficiency. Furthermore, we found that signaling via reactive oxygen species is a common feature in response to macronutrient deficiency and signaling via jasmonic acid is associated with potassium depletion response. These results will facilitate deeper understanding of nutrient utilization of plants.

SUBMITTER: Takehisa H

PROVIDER: S-EPMC3907390 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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Global transcriptome profile of rice root in response to essential macronutrient deficiency.

Takehisa Hinako H Sato Yutaka Y Antonio Baltazar A BA Nagamura Yoshiaki Y

Plant signaling & behavior 20130419 6

Deficiency of the three essential macronutrients, nitrogen, phosphorus and potassium, leads to large reduction in crop growth and yield. To characterize the molecular genetic basis of adaptation to macronutrient deprivation, we performed microarray analysis of rice root at 6 and 24 h after nitrogen, phosphorus and potassium deficiency treatments. The transcriptome response to nitrogen depletion occurred more rapidly than corresponding responses to phosphorus and potassium deprivation. We identif ...[more]

PMID: 23603969

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Project description:BackgroundMacronutrients are pivotal elements for proper plant growth and development. Although extensive gene expression profiling revealed a large number of genes differentially expressed under various nutrient deprivation, characterization of these genes has never been fully explored especially in rice. Coexpression network analysis is a useful tool to elucidate the functional relationships of genes based on common expression. Therefore, we performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions. Moreover, we conducted a large scale coexpression analysis by integrating the data with previously generated gene expression profiles of organs and tissues at different developmental stages to obtain a global view of gene networks associated with plant response to nutrient deficiency.ResultsWe statistically identified 5400 differentially expressed genes under the nutrient deficiency treatments. Subsequent coexpression analysis resulted in the extraction of 6 modules (groups of highly interconnected genes) with distinct gene expression signatures. Three of these modules comprise mostly of downregulated genes under N deficiency associated with distinct functions such as development of immature organs, protein biosynthesis and photosynthesis in chloroplast of green tissues, and fundamental cellular processes in all organs and tissues. Furthermore, we identified one module containing upregulated genes under N and K deficiency conditions, and a number of genes encoding protein kinase, kinase-like domain containing protein and nutrient transporters. This module might be particularly involved in adaptation to nutrient deficiency via phosphorylation-mediated signal transduction and/or post-transcriptional regulation.ConclusionsOur study demonstrated that large scale coexpression analysis is an efficient approach in characterizing the nutrient response genes based on biological functions and could provide new insights in understanding plant response to nutrient deficiency.

Project description:BackgroundPotassium (K+) is an important nutrient ion in plant cells and plays crucial roles in many plant physiological and developmental processes. In the natural environment, K+ deficiency is a common abiotic stress that inhibits plant growth and reduces crop productivity. Several microarray studies have been conducted on genome-wide gene expression profiles of rice during its responses to various stresses. However, little is known about the transcriptional changes in rice genes under low-K+ conditions.ResultsWe analyzed the transcriptomic profiles of rice roots in response to low-K+ stress. The roots of rice seedlings with or without low-K+ treatment were harvested after 6 h, and 3 and 5 d, and used for microarray analysis. The microarray data showed that many genes (2,896) were up-regulated or down-regulated more than 1.2-fold during low-K+ treatment. GO analysis indicated that the genes showing transcriptional changes were mainly in the following categories: metabolic process, membrane, cation binding, kinase activity, transport, and so on. We conducted a comparative analysis of transcriptomic changes between Arabidopsis and rice under low-K+ stress. Generally, the genes showing changes in transcription in rice and Arabidopsis in response to low-K+ stress displayed similar GO distribution patterns. However, there were more genes related to stress responses and development in Arabidopsis than in rice. Many auxin-related genes responded to K+ deficiency in rice, whereas jasmonic acid-related enzymes may play more important roles in K+ nutrient signaling in Arabidopsis.ConclusionsAccording to the microarray data, fewer rice genes showed transcriptional changes in response to K+ deficiency than to phosphorus (P) or nitrogen (N) deficiency. Thus, transcriptional regulation is probably more important in responses to low-P and -N stress than to low-K+ stress. However, many genes in some categories (protein kinase and ion transporter families) were markedly up-regulated, suggesting that they play important roles during K+ deficiency. Comparative analysis of transcriptomic changes between Arabidopsis and rice showed that monocots and dicots share many similar mechanisms in response to K+ deficiency, despite some differences. Further research is required to clarify the differences in transcriptional regulation between monocots and dicots.

Dataset Information

Global transcriptome profile of rice root in response to essential macronutrient deficiency.

Publications

Global transcriptome profile of rice root in response to essential macronutrient deficiency.

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