Published in Probe Volume 5(2): April-June 1995
Clare Nelson, Database Curator
Department of Plant Breeding and Biometry
Cornell University
SolGenes, along with GrainGenes and RiceGenes, is one of the three plant genome databases based on the ACeDB software and funded by the Plant Genome Project. All three are under development at Cornell University.
The scope of SolGenes is the solanaceous crop species - to date including tomato
(Lycopersicon spp.) potato (Solanum spp.), pepper (Capsicum spp.), and their wild relatives. Genomic research data from other Solanum species (such as S. melongena, eggplant) and other genera in the family (Datura, Petunia, and Nicotiana for example) are not yet featured but are also welcome.
The core of SolGenes consists of genetic maps of the various species, stored and displayed in ways that allow for ready cross-referencing. Currently, available are tomato, potato, and pepper RFLP maps constructed at Cornell, as well as a tomato morphological map assembled by S.D. Tanksley with many refinements on chromosomes 3 and 6 added by M. Koornneef and colleagues. We are adding potato maps from C. Gebhardt (Max-Planck-Institut) and Dutch colleagues, and new pepper maps from M. Kyle at Cornell and from French researchers. Since all these maps share at least some probes, their availability in a singledatabase should ease the construction of useful consensus maps for these crop species.
Also available is a recently updated list of more than 3,000 tomato germplasm stocks (mutants, chromosome testers, etc.) with passport information, maintained at the Tomato Genetic Resources Center (TGRC) in Davis, CA, by R. Chetelat. Work in generating images of these plants and loading them into the database is in progress. Recently, a set of 50 L. pennellii single-segment introgressions into a L. esculentum background was constructed by Y. Eshed and characterized with some 350 RFLP and isozyme markers. These lines are available from the TGRC, and the marker data defining the introgressed regions were contributed to SolGenes. ACeDB databases are equipped with routines to display chromosomal regions, and these work nicely for the introgressed segments.
These entries are connected and cross-referenced by a background of literature citations (130), a colleague directory (541), and catalogs of probes (1,000), loci (2,000), and restriction enzymes (340). Lacking are physical-mapping data, and we will be seeking YAC and BAC information, primer sequences, probe sequences, and related information. Increasingly relevant are gene-mapping and variety-discrimination studies with molecular markers, and we have (and seek) sources of such data for all three major species.
Also of interest is the increasing application of molecular information to breeding, and results in this area will be incorporated; that is, field studies or marker-assisted selection results.
Another kind of information that might be welcome to breeders and researchers is moregermplasm catalogs. We will not try to incorporate existing catalogs, but where germplasm databases are already accessible, SolGenes might be able to direct users to them.
The entire database may be obtained via anonymous ftp from probe.nalusda.gov:pub/solgenes, if you wish to set it up on a local (typically Unix-based) computer. There is a Macintosh version of ACeDB called MacAce, but to date no one (me, in other words) has compiled the SolGenes data into it. You can access SolGenes via a text interface through either of these gopher servers:
nightshade.cit.cornell.edu port 71
probe.nalusda.gov port 7006
The URL for access to SolGenes via the World Wide Web is: http://probe.nalusda.gov:8300
The text-based ways of accessing the database do not take full advantage of the graphical displays available with a version running locally, though all the data, including images in TIFF format, are still available. An X-window emulator program, however, running on your local PC or Macintosh (MacX, for example) will give you, via remote logon, the full range of graphical displays built into ACeDB databases.
If you would like to contribute information to SolGenes, we would like to hear from you. Data need not be in a special format; our group can do most of the preparation. We also invite suggestions for sources of data and suggestions about data types that would be of useto you, as well as ways in which you would prefer to view or search the database. ACeDB databases, while they have some underlying structure, leave a curator free to adapt data interconnections to users' preferences.
A mailing list of interested users is maintained and messages may be posted by any subscriber to the rest of the group via e-mail to solfolk@nightshade.cit.cornell.edu. To be placed on or taken off this list, send an e-mail message to me at the address above or to cnelson@nightshade.cit.cornell.edu.
Several scientists in the United States and Europe have agreed to serve on an informal steering committee for SolGenes. They will provide consultation about the direction of development and assist as liaisons with other workers in the solanaceous crops who might want to use and/or contribute data to the database. Please feel free to communicate with them in this capacity. The current steering committee consists of:
Potato
Herman van Eck, Wageningen University, Netherlands
herman.vaneck@users.pv.wau.nl
David Douches, Michigan State University 517-355-6887
Robert Hanneman, Jr., University of Wisconsin rehannem@facstaff.wisc.edu
Pepper
Molly Kyle, Cornell University mmk9@cornell.edu
Paul Bosland, New Mexico State University pbosland@NMSU.edu
Tomato
Pim Lindhout, Wageningen University, Netherlands
Pim.Lindhout@USERS.PV.WAU.NL
Roger Chetelat, UC Davis, California chetelat@vegmail.ucdavis.edu
Martin Ganal, Gatersleben, Germany Martin Ganal, Inst. fnr Pflanzengenetik u.
Kulturpflanzenforschung
Gatersleben, Germany
FAX: 49-39482-280