SorghumDB 96.1:

A Genome Database for Gossypium hirsutum and related species

Bob Klein, Najeeb Siddiqi, and Russell J. Kohel

USDA ARS Southern Crops Research Laboratory, 2765 F&B Road, College Station, TX 77845

INTRODUCTION

The sorghum database that we have been working on has been available at the National Agricultural Library (NAL) since January 1995 (SorghumDB 95.1). The current version has added data and has been updated to modern program versions. Now that a base amount of information pertaining to sorghum has been deposited into the database known as SorghumDB, it is desired to attempt keeping the the information up-to-date. Presently, the SorghumDB is available over the World-Wide-Web (WWW) under the URL address:

http://probe.nalusda.gov:8300/index.html

If you have an interest in sorghum research, you may want to view the database at your leisure. If you have any comments that may be useful in the organization, structure, or information contained in the database, I have set up a WWW page for providing input into SorghumDB. The forms found at this WWW page are for contributing information about Colleagues, Research, Biochemical Pathways, Literature, and Comments which may be periodically updated to SorghumDB. The URL address for this page is:

http://algodon.tamu.edu/sorghumdb.html

I hope that this structured input of information will be useful in maintaining an up-to-date database. If you know of others that might be interested in viewing or contributing to the database, please forward this information. All comments are welcome.

Presently, SorghumDB is based on ACEDB version 4.1 (Richard Durbin and Jean Thierry-Mieg, MRC LMB Cambridge, England and CNRS, Montpellier, France, respectively). Other plant genome databases were used as models in setting up some of the data entries.

At present, SorghumDB 96.1 (12 Janurary 1996) contains:

Allele               51   Gene and Sequence
Author            16778   Authors associated with Paper entries
Clone               176   Genes and Markers
Colleague           548   Names and Addresses of Sorghum-associated People
Image                70   Pictures and Scans
Journal            2409   Journal Headings
Locus               586   Observed and Molecular Genetic Markers
Map                 118   Maps for Observed and Molecular Markers
Map_Data             11   Data for Maps
Multimap             12   Comparative Maps
Paper             15887   Sorghum-related Agricola and Direct-entry Literature
Pathology            70   Biotic and Abiotic Factors Associated with Sorghum
Pathogens            90   Sorghum Disease Pathogens
Probe               266   Information About Probes Used to Screen Germplasm
Sequence             94   Sorghum-associated Sequences from GenBank and Others
Taxonomy              6   Section of Sorghum
Trait                20   Plant Traits
Other_Locus         486

MAIN SCREEN

The Main Screen of SorghumDB displays a number of Classes by which to retrieve information from the database. Several Classes for describing databases have been devised from the many plant genomes studied. The only Classes used in SorghumDB at this time are Genus_species, Colleague, Paper, Pathology, Trait_scores, Collection, Author, Locus, Sequence, Journal, Trait_Study, Map, Polymorphism, Germplasm, Species, and Image. This screen provides the means to search for information based on the provided Classes, or by use of search tools.

COLLEAGUES

Over 1100 names of sorghum researchers have been gathered. Information has been entered from Annual Cotton Beltwide Conference attendance and related sorghum meetings. To look up a COLLEAGUE, simply use the "mouse" to select COLLEAGUE and a list of alphabetically listed names will appear; scroll down until the desired name is reached, and further contact information will appear.

Contact information may also include addresses for e-mail and facsimile contact, or other information provided to SorghumDB by the COLLEAGUE.

PAPERS

Over 7000 bibliographic references have been gathered from the National Agricultural Library Agricola listings, Annual Cotton Beltwide Conference meetings, and individual entries. Entries can be accesses by querying AUTHOR, JOURNAL, or KEYWORD searches.

All references associated with an individual AUTHOR may be viewed. Individual PAPER information provides article referencing, associated AUTHORs, ABSTRACTs, and KEYWORDs.

Further queries may make use of other cross-referenced information provided in the referenced paper. If the AUTHOR is listed in the COLLEAGUE list, further contact information may be provided.

LOCUS

Information is provided for over 60 observed genetic loci contributed from a review of Upland and Asiatic sorghum (Endrizzi et al, 1984). Where possible, assignments to known chromosomes or linkage groups are given. Proposed symbol desigantions, species origins, and mapping positions are also provided.

Relative map positions may be visualized from graphical displays of chromosomes. Maps are provided for both molecular and observed genetic markers. It is hopeful that consensus maps will be available from further genetic studies.

MAPS

The use of molecular biology methods may be useful as tools in assisting sorghum mapping efforts. Some of the 6788 restriction-fragment-length-polymorphism (RFLP) DNA markers recently published from the Paterson Laboratory at Texas A&M University (Reinisch et al, 1994) are illustrated. Information provided in a graphical interface may assist in genetic screening for polymorphism, or searching for closely linked molecular and observed genetic markers. The construction of different kinds of genetic maps (observed, RFLP, RAPD, SSR, etc...) may eventually serve in the development of overlapping consensus maps.

SEQUENCE

Nucleic acid sequences obtained from the GenBank resource contains at least 30 entries obtained from the sorghum genome. Sequences can be cross-referenced to the literature, and sequence information can be manipulated to visualize different sorts of information (open reading frames, introns, functional domains, etc...). Protein sequences may also be referenced. As more sequences of the sorghum genome become available, listings of homologies with expressed sequence tags (ESTs) may be presented to assist in gene identification.

IMAGES

Images can be useful in mapping efforts by providing visual eveidence of results that may be assessed by other research groups. In the example provided, DNA fragments generated from random-amplified-polymporphic-DNA (RAPD) polymerase chain reaction (PCR) analyses of sorghum germplasm are illustrated. Information about the DNA primers, sources, observed polymorphism, and proprosed linkages are presented. Other images that may be made available with a graphical interface are those of plant phenotypes, disease symptoms, illustrated timelines of cultivar breeding histories, Southern hybridization profiles of DNA probes, and others.

DATA COLLECTION

Separate from the SorghumDB resource, data request forms available over the Internet will help curators keep the databases current and up-to-date. Information may be entered using a similarly designed graphical interface to ease data-entry. New information, or updates may be entered regarding literature, colleagues, genetics, or other research observations. Such a format will allow speedy updates of the sorghum genome database on a regular schedule.

If you have colleague, research, or literature information that would be of value to the sorghum community, SorghumDB encourages you to fill out their information forms. Comments are also encouraged. All these forms may be accessed from the WWW SorghumDB Data Collection Site.

FUTURE DIRECTIONS

SorghumDB 4.1 was created with a base amount of information to speed its availability to the research community. Now that some SorghumDB information is available, some reformatting of data presentation is in progress. Additional information is being entered in the database including images, pathology, and molecular data. A WWW Data Collection Page has been established for SorghumDB and it is hopeful that the sorghum research community will make use of this page to make corrections, contribute information, and suggest improvments to make SorghumDB useful.

PLEASE SEND COMMENTS TO : raj@algodon.REMOVETHIStamu.edu(remove the REMOVETHIS string from the email)