Published in Probe Volume 2(2): Summer 1992
Olin Anderson
Research Geneticist
USDA, Agricultural Research Service
Western Regional Research Center
Albany, CA
Efforts are underway to assemble a wheat prototype database, a goal of the U.S. Department of Agriculture's (USDA) Plant Genome Program. The database will be maintained at the Agricultural Research Service's (ARS) Western Regional Research Center in Albany, CA. Coordinator for the project is ARS Researcher Olin Anderson.
The primary goals of the project are to establish the hardware and software systems to construct and maintain a wheat database and to coordinate the loading of all available and useful data. The initial priority is to accumulate genome mapping and probe/clone/library information. Additional data areas will include information on wheat germplasm, including pedigrees, and data on wheat genetics and traits.
Design and Implementation
The wheat database prototype is being designed and implemented in cooperation with the Computer Science Division of the Lawrence Berkeley Laboratory. John McCarthy (Phone: 510-486-5307) is the principal contact. The prototype will operate on a Sun workstation at Albany (plus mass storage devices) operating as a server. Access will initially be limited to designated users who are able to connect to INTERNET. The updated database will periodically be copied to the master plant database being organized at USDA's National Agricultural Library. The master database is intended as the resource for general public access.
The Albany site will also provide molecular biological support to mapping and map utilization. Persons involved in the project are establishing a repository of probes and clone libraries of the Triticeae, with initial emphasis on wheat. The repository, to be supervised by Susan Altenbach, will serve as both permanent storage and at least initial distribution of probes and libraries. Plans are to exchange probes and duplicate the repository at other sites world wide. Also to be explored is the development of additional molecular biological resources for Triticeae research; that is, the construction and utilization of improved and novel recombinant libraries, and mapping technology support.
Data Coordinators
Participants in the project have identified some specific areas that require data assembly and organization, and, as a result, have selected subject-area coordinators. Many areas are overlapping and will require input from several areas of expertise. As the need becomes apparent, "subcommittees" will form around broad topics. The following is a list of the coordinators and subject areas:
Cytology:
Bikram Gill, Department of Plant
Pathology, Kansas State University,
Throckmorton Hall,
Manhattan, KS 66506
Tel: 913-532-6176, FAX 913-532-5692
Database Assembly,
and Maintenance:
Olin Anderson, USDA, ARS, WRRC,
800 Buchanan Street, Albany, CA 94710
Tel: 510-559-5773, FAX 510-559-5777
Genetics, Nomenclature:
Gary Hart, Department of Soil & Crop
Sciences, Texas A&M University,
College Station, TX 77843
Tel: 409-845-8293, FAX 409-845-0456
Genetic Stcks:
Perry Gustafson, USDA, ARS, Department
of Agronomy, University of Missouri,
Columbia, MO 65211
Tel: 314-882-7318 FAX 314-875-5359
Germplasm:
Ken Kephart, 214 Waters Hall,
University of Missouri,
Columbia, MO 65211
Tel: 314-882-2001, FAX 314-884-4317
Pathology:
David Porter, USDA, ARS, Oklahoma
State University,Stillwater, OK 74075
Tel: 405-624-4212, FAX 405-372-1398
Probe/Library Repository;
Susan Altenbach, USDA, ARS, WRRC,
800 Buchanan St., Albany, CA 94710
altenbach @ sun-dq.pw.usda.gov
Tel: 510-559-5716, FAX 510-559-5777
Proteins; Gel Patterns, Wheat Quality:
Bob Graybosch, USDA, ARS, Department
of Agronomy, 322 Keim Hall,
University of Nebraska, Lincoln, NE
Tel: 402-472-1563, FAX 402-437-5234
Triticeae Mapping Initiative
To facilitate the gathering of mapping data, the database personnel are working closely with the International Triticeae Mapping Initiative (ITMI) organization. ITMI is an international group with the purpose of facilitating the mapping and dissemination of resulting data of important members of the grass tribe Triticeae, which includes wheat, rye, barley, ancestral species, and related wild grasses. Dr. Calvin Qualset (Chairman, Department of Agronomy & Range Science, University of California, Davis) is ITMI coordinator. (See Probe Spring 1992.)
Mapping Coordinators
Wheat, rye, and barley, along with many wild relatives, are
syntenic--they possess homologous linkage groups with similar
linear arrangements of the same genes. To facilitate the
collation of data produced by different laboratories in different
countries, seven members of ITMI have agreed to serve as
coordinators for the seven linkage groups.
Group 1
Rudi Appels, CSIRO, GPO Box 1600,
Canberra, Australia 2601
Tel: 61 62 464496, FAX 61 62 465000
Group 2
Peter Sharp, Plant Breeding Institute
Cobbitty Road, Cobbitty, NSW 2570, Australia
Tel: 61 46 512600, FAX 61 46 512578
Group 3
Mark Sorrells, Department of Plant
Breeding and Biometry, Cornell
University, Ithaca, New York 14853
Tel: 607-255-1665, FAX 607-255-6683
David Hoisington, Molecular Biology
Lab, CIMMYT, Lisboa 27, Colonia Juarez,
Apdo, Postal 6641 06600 Mexico DF, Mexico
Tel: 52 5 761 3311 FAX 52 5 954 1069
Group 4
Jan Dvorak, Department of Agronomy
& Range Science, University of
California-Davis, California 95616
Tel: 916-752-6549 FAX 916-752-4361
Group 5
Bikram Gill (address previously listed)
Group 6
Gary Hart (address previously listed)
Group 7
Michael Gale, Cambridge Laboratory,
Colney Lane, Norwich, Norfolk
NR4 7UJ, United Kingdom
Tel: 44 603 52571 FAX 44 603 502270
Rye and Barley
Rye is a critical part of wheat breeding programs because of the importance of rye genes that are desirable to cross into wheat. Perry Gustafson, ARS, University of Missouri, is coordinating the rye genome map. Similarly, information on barley is of critical interest to wheat researchers. The input of barley data is being coordinated by Andris Kleinhofs at Washington State University.
Barley:
Andris Kleinhofs, Dept. of Crop
and Soil Sciences, Washington State
University, Pullman, WA 99164
Tel: 509-335-4389 FAX 509-335-3475
Rye:
Perry Gustafson (address previously listed)
Ancestral Genomes
Since the wild ancestral genomes of wheat and wild grasses amenable to breeding into wheat are critical sources of potential new genes for traits such as yield and pest and stress resistance, the databases will also contain results of mapping programs from these genomes as the data becomes available. Currently two of the ancestral genomes are being actively mapped:
A-genome
Rudi Appels & Mark Sorrells
D-genome
Bikram Gill & Rudi Appels
Cooperative Agreements
Contracts are in force or are now being arranged for data assembly and input into the databases. A contract to ITMI (Cal Qualset) is assisting in mapping coordination by ITMI and resource development with Jan Dvorak (UC Davis) and Gary Hart (Texas A&M). Mark Sorrells and Steven Tanksley (Cornell) have support for a programmer position for data input and for the development of software routines, along with the necessary hardware to serve as a major site of data input. Cornell will also assist the Barley Mapping Group in data input. Bikram Gill (Kansas State) will be overseeing the assembly of wheat cytogenetic data for the database. Wheat nomenclature and genetics will be contributed by Gary Hart (Texas A&M).
Data on North American wheat cultivars was already being cataloged by Ken Kephart (Missouri). He will coordinate germplasm information with other databases such as the Germplasm Information Network (GRIN) with the USDA Small Grains Repository at Aberdeen, ID, and CIMMYT in Mexico City. Also at Missouri is Perry Gustafson who will coordinate and input data on genetic stocks. Future cooperative agreements may be arranged for other areas such as pathology and wheat storage proteins. David Porter (Oklahoma State) is assembling examples of data on pathology and pests to assess for database design and input. Grain proteins are a major contributor to quality traits in wheat. Examples are being organized by Bob Graybosch at Nebraska.