Identification of genes enriched in rice roots of the local nitrate treatment and their expression patterns in split-root treatment.

To identify nitrate-induced genes in rice roots, a nitrate-induced root subtracted library was constructed using the suppression subtractive hybridization (SSH) method and a split-root experiment. Based on forward and reverse screening, 37 known genes and 55 novel genes were identified to be up-regulated in nitrate-supplied side roots. The known genes are involved in nitrogen (N) uptake and assimilation, sugar transport and organic acid metabolism, signal transduction, protein synthesis and degradation, plant resistance, hormone metabolism and cell division. Most of these genes were stronger up-regulated in nitrate-supplied than in nitrate-deficient side roots, which suggests that nitrate may regulate expression of these genes. Expression pattern analysis also revealed that a fast cycle of assimilated N metabolites occurred between root and shoot. Transcriptions of some nitrate-induced genes were also up-regulated in nitrate-deficient side roots, which indicates that nitrate and/or in coordinating with N metabolites from shoots, regulate the transcription of many genes. The enhancement of carbon (C) source partition, the expressions of genes for signal transduction and transcription regulation, auxin transport and ethylene synthesis, and cyclin-dependent kinases may be responsible for the stimulated lateral root growth by nitrate.