Transcriptome analysis of rice root responses to potassium deficiency

BACKGROUND: Potassium (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. RESULTS: We 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. CONCLUSIONS: According 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.