IX. MaizeDB: MAIZE GENOME DATABASE

CONTEXT: The USDA Plant Genome Initiative includes design and implementation of a database and network system for genetic data, analysis of data, and linked access to sequences, clones, biosynthetic pathways, and the like, across species boundaries. In addition to research grants through the Competitive Grants Program , the Initiative supports database development through the Agricultural Research Service. The Plant Genome Database was derived by "Prototype Developers" working first on maize, soybean, wheat, forest trees, and Arabidopsis, and is now being followed with other species. The structure is inclusive of higher plant data and is focused at the National Agricultural Library (NAL).

PRODUCTS AND PROSELYTIZING: The Gene List, Stock List, and Zealand 94 this year were derived by output from MaizeDB. Demonstrations of MaizeDB have been given at recent Maize Genetics Conferences, Plant Genome I and II, Corn Breeders School, North Central Corn Breeding Conf., Amer. Soc. Plant Phys., Arabidopsis Int. Conf., Int. Genetics Cong., and the Amer. Seed Trade Assoc. (COOPERATORS NOTE: the most enthusiastic interest in MaizeDB was at the Plant Phys. and the Arabidopsis meetings). Development and advancement has been greatly aided by comments and responses from the 1992 and 1993 demonstrations, and by experience with the implementation before and after the demos.

CONTENT: MaizeDB now includes much more information. Extensive descriptions of mutant genes have been provided to Gerry Neuffer by Cooperators, and these continue to be enhanced with new information; extensive stock information (especially inbred lines and their parentage); maps from new sources; latest map scores for the BNL RI populations and others; probe data; gene products; GenBank identifications; current literature references, and others. Requests to Cooperators for explicit mapping data are being made as needed. The database design for representing QTL data is approaching a testing phase. Phenotype and trait information is progressing toward a structured, systematic form. Rate of progress, and the breadth and depth of the database, will depend on your encouragement and on the continuity and extent of resources for the work in the future.

WHAT CAN I DO? Systematically presented data, including consistent use of terms and symbols in consistent, partitioned form, are particularly valuable for database entry. As you are describing a new variant, for example, try to identify the stage(s), body part(s), condition(s), expression, and characteristics as fully and precisely as possible. If a clone is derived and is used in mapping or in other work, assign a unique, unambiguous name to the clone and maintain that name (when needed, cite synonyms that have been used in other published work with it). Avoid terming two objects (mutants, genes, probes, clones) the same if they may turn out to be different. We will be happy to provide to you a template for systematic representation of probes and the parameters needed for molecular-marker mapping, for your use in your lab or to accompany data to be incorporated in MaizeDB.

WHERE DO I GET IT? MaizeDB can be accessed as described in the following two pages. These are simple and convenient means by which to look up and extract information. The MaizeDB Group asks for your help and input. We especially ask for your corrections, suggestions and ideas as they arise from using the database.

The MaizeDB Working Group is Ed Coe, Mary Berlyn, Pat Byrne, Georgia Davis, Denis Hancock, Stan Letovsky, Mary Polacco, and Marty Sachs.
 
 

Ye Nomenclature Standards are for all Cooperators, including thyself. Ere thee name a gene, consider ye Criteria, refer to ye Standards, and consult MaizeDB. Else.

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors

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