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In order to investigate the overall characteristics of the transcript profiles associated with these puzzling biological effects. We used the Agilent Rice Oligo Microarray to learn the molecular mechanism in rice responding to ion implantation. The analysis of the genechip array shows that there were 982 transcripts expressed differentially (fold change >; 2 and P value <; 0.05) including 429 up-regulated transcripts and 553 down-regulated transcripts under the dose3 6x1017N+/cm2. Gene ontology analysis of the microarray data indicates that the up-regulated genes are belonged to five molecular functions, including three cellular component and one metabolic process (oxidation reduction), and the down regulated genes are belonged to ten molecular functions, nineteen biological process, but no cellular component. Significantly, the gene ontology analysis of the microarray data strongly suggests that the up-regulated retroelements transcripts and oxidoreductase activity genes, down-regulated recombinases, many down-regulated transcription factors involve in the response to the ion beam implantation for their expression changes. This gene ontology analysis might help to reveal the low-energy ion implantation regulation on many biological processes and metabolism pathways.