Published in Probe Volume 1(3-4): Fall-Winter 1991
Dr. Ed Coe, Research Geneticist
Plant Genetics Research Unit
USDA Agricultural Research Service
and University of Missouri, Columbia
Corn's significant role in U.S. agricultural productivity is grounded in its innate physiological efficiency, enhanced during this century by breeding for increased productivity, responsiveness to intensive culture, and resistance to pests and stresses.
Less known to the public are its remarkable genetic diversity, the crop's open-book robustness of genetic traits such as kernel variants segregating on an ear of several hundred progeny, and scientists' fascination with its genetic phenomena right from the beginnings of genetic analysis. For example, in addition to his well-known work with peas in the mid-1800's, botanist Gregor Mendel examined segregations in maize. In 1901, German scientist Carl Correns published an extensive monograph on inheritance in maize.
It is little wonder, from this long history of genetic studies, that there are some 670 characterized genes (of which 440 determine "naked eye" polymorphisms; 230 define protein or enzyme polymorphisms). In addition, there are 540 mapped genes; 6,000 mutants awaiting analysis; 1,300 molecular (RFLP) markers in five partly merged maps; 100 cloned sequences of known function; 30 cytologically defined polymorphisms; 880 reciprocal translocations; 84 translocations with the supernumerary B chromosome; and each of 10 trisomics and monosomics.
Maize Database Project
A primary goal of USDA's Plant Genome Research Program is to develop a database system that will contain plant genome information for four agricultural species--soybean, wheat, loblolly pine, and maize.
The intent of the maize database project, currently underway, is to systematize and evaluate maize genetic information, ensure its accuracy, and structure it in a readily accessible database prototype along with data from other crops. A questionnaire sent to maize geneticists last January sought help in defining the essential components and structure of the database; and elicited suggestions, creative ideas, offers of data, and offers of participation in the effort.
Advisory Group Meets
An advisory group of 18 scientists met in St. Louis last April to begin planning the prototype effort. Providing guidance and database expertise for the group were industry-affiliated members (who have had experience with large relational databases), Mary Berlyn (who co-developed the E. coli database at Yale University), and Douglas Bigwood (the NAL database manager for USDA's plant genome database project).
The group assigned subcommittees in the areas of Nomenclature and Standards, User Needs and Quality Control, Clone Banks, Quantitative Characters and Descriptors, Germplasm Characterization, Prototype Development, and other high-priority data compilation and collection. (See the shaded box for a list of subcommittees and their respective chairpersons.)
One or more group members have visited database project locations of other species, including Yale University (E. coli), the Livermore National Laboratory (human), the Welch Library at Johns Hopkins University (human GDB), the University of Missouri and Washington University (nematodes), Agrigenetics (maize), and the Lawrence Berkeley Laboratory (human).
Project Assignments
Prototype development and implementation are being executed by Letovsky Associates through a research agreement with Stan Letovsky, which includes Yale University's Mary Berlyn as a project cooperator. Initial drafts of the structure, form specifications, and entity relationships have been developed and will soon be provided in revised form.
Priority characterization of germplasm is being carried out for 100 inbred lines across 26 isozymes and 100 RFLP probes by Biogenetic Services, through a research agreement with Alex Kahler. The isozyme analyses have been completed. Reproduction of most of the specific pedigrees has been completed at the University of Missouri. The characterized strains will be deposited in the appropriate ARS germplasm collection.
Scientists Mary Polacco and Marty Sachs, affiliated with the project at Missouri on a half-time basis, are participating in developing the database structure, user needs, quality control, and vocabularies. Mary also is evaluating methods of systematic access and interconnection of genic and mapping data from the literature. Marty is carrying on acquisition and mapping of functionally defined clones, and mapping of reciprocal translocations. The computer specialist on staff at the University of Missouri is geneticist Denis Hancock.
Maize Subcommittees and Chairpersons
Nomenclature and Standards: Oliver Nelson, University of Wisconsin, Phone 608-262-3344, Fax 608-262-2976, nelsonoe@wiscmacc
User Needs and Quality Control: Ed Coe, USDA-ARS, University of Missouri, Phone 314-882-2768, Fax 314-875-5359 agrocoe@umcvmb
Clone Banks: Shiaoman Chao, University of Missouri, Phone 314- 882-3698, FAX 314-875-5359; and Tim Helentjaris, University of Arizona, Phone 602-621-8746, Fax 602-621-7186 helnjars@arizrvax
Quantitative Characters and Descriptors: Jim Coors, University of Wisconsin, Phone 608-262-7959, Fax 608-262-5217
Germplasm Characterization: Charles Stuber, USDA-ARS, North Carolina State University, Phone 919-737-2289, Fax 919-515-3355
Cytogenetic Data Compilation: Dave Weber, Illinois State University, Phone 309-438-2685, Fax 309-438-3722
Stock Center Cataloging: Al Kriz, University of Illinois, Phone 217-244-6308, Fax 217-333-9817
RFLP Mapping, Pooling of Data: Tim Helentjaris, University of
Arizona (Phone number listed above); and Ben Burr, Brookhaven
National Laboratory, Phone 516-282-3396, Fax 516-282-3407,
burr@bnluxl.bnl.gov
Chloroplast: Steve Rodermel, Iowa State University, Phone 515-
294-7172
Mitochondrion: Christiane Fauron, University of Utah, Phone 801- 581-5192