Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE)

Serial analysis of gene expression (SAGE) was applied for profiling express ed genes in rice seedlings. In the SAGE method, a 9-11 bp fragment (tag) re presents each transcript, and frequency of a tag in the sample directly ref lects the abundance of the respective mRNA. We studied 10 122 tags derived from 5921 expressed genes in rice (Oryza sativa L.) seedlings, among which only 1367 genes (23.1%) matched the rice cDNA or EST sequences in the DNA d atabase. SAGE showed that most of the highly expressed genes in rice seedli ngs belong to the category of housekeeping genes (genes encoding ribosomal proteins or proteins responsible for metabolism and cell structure). Unexpe ctedly, the most highly expressed gene in rice seedlings was a metallothion ein (MT) gene, and together with three other messages for MT, it accounts f or 2.7% of total gene expression. To our knowledge, this is the first quant itative study of global gene expression in a higher plant. We further appli ed the SAGE technique to identify differentially expressed genes between an aerobically treated and untreated rice seedlings. Additionally, we show tha t a longer cDNA fragment can be easily recovered by PCR using the SAGE tag sequence as a primer, thereby facilitating the analysis of unknown genes id entified by tag sequence in SAGE. In combination with micro-array analysis, SAGE should serve as a highly efficient tool for the identification and is olation of differentially expressed genes in plants.