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United States Department of Agriculture

Agricultural Research Service

Title: Maizedb - a Functional Genomics Perspective

Authors
item Schaeffer, Mary
item Coe Jr, Edward
item Fang, Zhiwei - UNIV OF MISSOURI
item Hancock, Denis - UNIV OF MISSOURI
item Sanchez-Villeda, Hector - UNIV OF MISSOURI
item Schroeder, Steve - UNIV OF MISSOURI

Submitted to: Comparative and Functional Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 13, 2002
Publication Date: April 1, 2002
Citation: Polacco, M.L., Coe Jr, E.H., Fang, Z., Hancock, D., Sanchez-Villeda, H., Schroeder, S. 2002. Maizedb - a functional genomics perspective. Comparative and Functional Genomics. V.3(2):128-131.

Interpretive Summary: Data about genes and inheritance in corn (maize) from over a century of research have been compiled and made computer-accessible for over 10 years in the Maize Genome Database (MaizeDB). The database management system of MaizeDB, in Sybase, has proven to enable access to even the most complex and challenging of today's genomics research. One of the most significant arising areas of access is in gene functions, which are increasingly being queried in experimental studies that use rapidly evolving laboratory techniques. The capabilities of MaizeDB to aid the research scientist are continuously enhanced with new tools. Three new features in the context of the comprehensive database are described: (1) up-to-the-minute tables of DNA probes that are used in genetic mapping; (2) a search tool to query whether a specified DNA base sequence has already been mapped in the genome; and (3) a graphical tool to make comparisons among different genetic maps, including across different species, e.g., rice. Because of the truly remarkable diversity for disease and insect resistance, stress responses, and productivity that exists in maize, waiting to be exploited, access to genomic knowledge will increase the efficiency by which more-desirable heritable properties can be extracted from germplasm, and the diversity can be used with increasing effectiveness. Breeders and biotechnologists are rapidly taking advantage of the knowledge and tools of this project to access information and diversity for the advancement of maize productivity and efficiency. The present work greatly enhances and facilitates the ability of plant scientists seeking to make crop improvements as well as to understand basic biological systems, to extract current and retrospective data together, and to use them effectively.

Technical Abstract: The Maize Genome Database (MaizeDB), www.agron.missouri.edu, since the early 90s has provided comprehensive access to genome-specific data grounded in genetic maps, their documentation and annotation. The database management system of MaizeDB is robust and has continuously been Sybase. This paper is an introduction to the database as a functional genomics tool and introduces new accesses to the data: (1) probe tables by bin location; (2) BLAST access to map data; and (3) cMap, a comparative map graphical tool.

Last Modified: 9/2/2014
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