Functional Annotation of Rice Expressed Sequence Tag Induced by Important Disease and Pest

• Main Authors: Yi-Chia Chiu, 邱怡嘉
• Other Authors: Hsiu-Ying Lu
• Format: Others
• Language: zh-TW
• Published: 2006
• Online Access: http://ndltd.ncl.edu.tw/handle/6z25qv

碩士 === 朝陽科技大學 === 生物技術研究所 === 94 === Abstract Rice (Oryza sativa L.) is the most important crop in the world. Brown planthopper is the major pest so is the rice blast disease the most serious problem. Expressed sequence tag (EST) is the fragment of cDNA sequence. Therefore, direct studies of EST is helpful to obtain the gene expression information. In order to know the functional mechanisms of the resistant gene which cause the brown planthopper and rice blast, this study firstly accessed rice EST sequences induced by brown planthopper from NCBI-dbEST database (with the total amounts as 188), and compared the gene expression difference between the resistant and sensitive varieties of rice. An analytic procedure of rice EST functional annotation was established as: Firstly, using unique sequences of high quality from removing redundancy after clustering and assembling by CAP3 software to homology search TC(tentative consensus sequence) database of TIGR (The Institute of Genomic Research), then linking to the functional catalogs of GO (Gene Ontology) and MIPS (Munich Information Center for Protein Sequences) from tentative annotation of the selected TC sequences, and finally calculating the statistics of gene functional representation. Based on this procedure, an automated system of functional annotation was developed. All programs of this system were written in perl language under local Linux platform. The automated system was implemented in the huge amount of rice ESTs induced by M. grisea (with the total amounts as 84,705) to investigate the gene expression differences among different varieties, tissues and developmental stages of rice. The results showed that (1) based on GO functional category, biological process was the dominant gene function of rice ESTs induced by brown planthopper. According to minute classification of MIPS functional category system, the genes of resistant rice variety expressed richer metabolism function than that of sensitive rice variety. The resistant rice variety switched on the functions related to cell rescue/defense and virulence, transcription, and cell growth/morphogenesis, but sensitive variety did not. (2) When rice ESTs induced by M. grisea were mixtures of sequences with different varieties, tissues or developmental stages, it appeared diversity of gene expression from those of rice ESTs from single source. The genes of wild rice expressed richer metabolism function than those of Indian rice and Japanese rice. The findings of this study will help clarify the mechanisms of rice genes resistant to disease and pest.