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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Healthy Processed Foods Research » Research » Publications at this Location » Publication #129959
Title: DIGITAL FRUIT RIPENING: DATAMINING IN THE TIGR TOMATO GENE INDEX

Author
item Bartley, Glenn
item Ishida, Betty

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2001
Publication Date: 6/1/2002
Citation: Bartley, G.E., Ishida, B.K. 2002. Digital fruit ripening: data mining in the tigr tomato gene index. Plant Molecular Biology Reporter 20: 115-130.

Interpretive Summary: Many sequences of genes are now contained databases available to the public. These databases can form the foundation for research in the future. Extracting useful information from these databases is of utility to all forms of genetic, biochemical and molecular biological research. We are interested in improving the nutrition of the tomato through the understanding of fundamentals of the molecular biological and biochemical processes occurring during the development of the tomato fruit. The TIGR Tomato Gene Index has been of great use to in determining new areas of molecular analysis for this research. We have mined this database for useful genes and information. In this paper, we report a number of genes previously not observed, that are possibly involved in the development of the tomato fruit. This new information may lead to a new and improved tomato and point out some of the benefits of biotechnology.

Technical Abstract: Many sequences of genes are now contained in databases available to the public. These databases can form the foundation for research in the future. Extracting useful information from these databases is of utility to all forms of genetic, biochemical and molecular biological research. We are interested in improving the nutrition of the tomato through understanding of the fundamentals of the molecular biological and biochemical processes occurring during the development of the tomato fruit. The TIGR Tomato Gene Index has been of great use to our laboratory in determining new areas of molecular analysis for this research. We have mined this database for possible useful genes by using the nucleic acid and protein sequence searching software BLAST, and by comparison of gene expression information contained within the database. In this paper, we report a number of genes previously not observed, that are possibly involved in the development of the tomato fruit. Transcripts for MADS Box genes, zinc finger genes, homeobox genes, and polycomb genes are among the transcripts that show up-regulation during tomato fruit ripening in our study. This paper will help expand the current knowledge of fruit development and provide some starting points for molecular research of tomato ripening.