| Rice stem functions in the transportation of water, minerals and organic compounds, and is essential for the yield and quality of rice. We constructed cDNA library for rice stems at the stage of 4-5 leaves, and conducted EST sequencing and bioinformatical analysis for better understanding of gene expression pattern and stem-specific genes. Some highly-expressed genes were isolated in rice stem cDNA library, and nine cDNA probes were used for hybridization with RNA array containing 755 rice bio-phenotypes to test whether these genes were stem-specific or not. The main results were as follow:1. 4704 clones were randomly selected from rice stem cDNA library and sequenced from 3'-end by MegaBace 1000, 3652 of which produced readable sequences, and 2683 effective ESTs were isolated by bioinformatical analysis. Among them, 2485 high quality ESTs with poly (A)+ at 3 end were further analyzed, while additional 2630 ESTs have been registered in dbEST (http://www.ncbi.nlm.nih.gov/dbEST).2. 1903 unique genes were identified by redundancy analysis with DNA user software from 2485 3'-ESTs. The expression abundance of the 1903 unique genes was different in rice stem. 1591(83.6%) of them were low expression abundance genes, 282 (14.8%) of them were moderate expression abundance genes, and only 30 (1.6%) of them were high expression abundance genes in which the highest one consisting of 21 ESTs. The results indicated that most genes in rice stem were low or moderate expression abundance genes.3. 1903 ESTs were blasted with rice database of NCBI and the uni-gene database of rice stem were constructed. On the basis of database searches, 1066 (56.0%) were novel genes that had no homology in public database, 353 (18.5%) were known genes with function annotation or putative function annotation, 593 (31.2%) were genes with the information of location, and another 109 (5.7%) were genes with information of function and location. The results indicated that most genes in rice stem were unknown genes which express specifically in stem.4. Genes with function annotation or putative function annotation were assigned to 11 functional gene classes by the means of function classification in Arabidopsis. They are genes related to protein synthesis and destination (PRO, 21.6%), metabolism (MET, 17.3%), energy (ENG, 13.5%), cell rescue, defense, cell death and ageing (RES, 12.9%), cellular communication/signal transduction (COM,8.3%), transcription (SCR, 7.6% ), cellular biogenesis and organization (BIO, 5.5%), cell growth, cell division and DNA synthesis (GRO, 1.3%), transport facilitation and mechanism (TRA, 4.3%) and development (DEV, 0.1%) and miscellaneous: unclassified or unknown gene (MIS, 7.6%);5. 20 genes with high expression abundance and function annotation were identified in our study. Among them, light harvesting chlorophyll a/b-binding protein had the highest expression abundance, with the expression frequency of 21, while EF-1 alpha and abscisic acid and stress -inducible protein was the second, with the expression frequency of 14. Some other genes, including proline rich protein (PRP), alpha-tubulin, lipid transfer protein (LTP), high mobility group protein (HMG) and phenylalanine ammonia-lyase (PAL) were also identified.6. RNA array analysis showed that co-regulation existed in the expression among high mobility group protein, elongation factor-1 alpha and catalase. The expression of high mobility group protein changed little in all the bio-phenotypes and it seemed to be house-keeping gene. The expression profiles of lipid transfer protein and proline-rich protein were similar. Chlorophyll a/b-binding protein was highly expressed in leaves and induced by light, and it seemed to be a gene related to photosynthesis. Studies of gene expression in rice leaf, stem and root showed that tubulin was highly express both in stem and root, indicating that root fibrosis and stem lignification share the same chemical process. Abscisic acid-an...
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