V. MAIZE GENOME DATABASE

www.maizegdb.org

Reverse Genetics: TILLING, Ac and Ds Toolkits, RNAi

Integration of the Maize TILLING Project's mutant information into MaizeGDB has been modeled, and will soon be available. Please visit http://genome.purdue.edu/maizetilling for projected release dates.

Information about stocks available from the Stock Center representing Ds or Ac tags from Hugo Dooner's and Tom Brutnell's projects is regularly updated. RNAi transgenic stocks available at the Stock Center are incorporated, using information provided by the Maize Chromatin Project and linked to targeted genes and constructs within MaizeGDB; links are also provided to the Chromatin Consortium database (http://www.chromdb.org). Query on the Stock page http://www.maizegdb.org/stock.php for stocks of type="Toolkit" and the focus linkage group of interest to retrieve the Ac and Ds insertion set; query for stocks of type="ChromDB" will retrieve RNAi stocks.

Sequences

Updated raw and assembled sequence sets are loaded into MaizeGDB on the first Tuesday of each month from a dataset prepared by Volker Brendel�s PlantGDB project group (Dong et al., Plant Physiol. 139:610-618, 2005). The sequence set includes all maize sequences available at GenBank as well as PlantGDB's transcript contigs which are called PUTs (for "PlantGDB-assembled Unique Transcript Fragment") and GSS contigs (called GSStucs for "Genome Survey Sequence tentatively unique contigs"). For access to the most up-to-date sequence sets, visit PlantGDB (http://www.plantgdb.org) where the sequence set is updated daily. To gain access to sequences and their related data (e.g., map positions, probe information, etc.) visit MaizeGDB. Note that reciprocal linkages between both sites are present at both sites, enabling ease of navigation no matter where you start your sequence search.

Genetic Maps

The updated community IBM map (cIBM 2005) based on the IBM-94 mapping population includes some 1930 loci, where 580 now serve as the framework in the MapMaker computation, compared to 250 framework loci in previous versions of the cIBM maps. This framework was developed in collaboration with Ed Coe and is based on the framework used by Georgia Davis for quantitative trait mappings. Most of the new loci were incorporated from the Genoplante EST-based RFLP mapping (see also maps IBM GNP2004; Falque et al., Genetics 170:1957-1966, 2005). Other loci were mapped from data released by the Maize Chromatin Project (Karen Cone); the Maize Mapping Project (Mike McMullen); and the Ac Mutagensis Project (Tom Brutnell). The cIBM maps may be viewed, along with supporting data including map scores, probe details, etc., at MaizeGDB.

The new neighbors map (IBM2 neighbors 2005) now includes some 35,000 probed sites, most of which are related to public ESTs. In addition to the previously included genetic maps, this consensus map computation incorporates order information from several new maps,including Pat Schnable's IDP maps; RFLP maps from Genoplante (Falque et al., 2005); the Cornell University (CU) maps; the MITEs maps; and frame work loci on the Genetic 2005 maps, which encompass the UMC 98 RFLP maps in order to permit incorporation into neighbors. In addition, this build includes any locus ordered onto anchored BAC contigs in the maize FPC product (http://www.arizona.genome.edu). Only loci identified by at least 2 hits by a probe are included (see maps IBM2 FPC0507); probes represented include overgos, RFLPs, and SSRs. The IBM2 FPC0507 maps were built in collaboration with Mike McMullen as a part of the Maize Diversity Project.

Plant Ontology Curation

The Plant Ontology Consortium (http://www.plantontology.org) has developed over the past few years a logical structure for describing plant anatomy, development and growth. While the initial emphasis has been on 3 plants: Arabidopsis, rice, and maize, support for several other angiosperm crop plants is now included. At MaizeGDB, anatomical aspects of phenotypes have been associated with Plant Ontology accessions and the phenotype-inferred associations to loci, stocks and alleles have been supplied to the Plant Ontology database (http://www.plantontology.org. Curation tools for annotation of other types of gene expression are under development to add to associations inferred by mutant or trait phenotype.

Community Curation at MaizeGDB

A quantitative trait experiment module has added to the curation tool suite at MaizeGDB (Schaeffer et al., in preparation). This module builds on the earlier tools used at MaizeDB (Byrne et al., J. Agric. Genomics 1:1-11, 1995) and adds many automated and quality control features. For example, much of the nomenclature of objects (maps, QTL, alleles, and panels of stocks) are now auto-computed from symbols assigned to the trait and parental germplasm. Similar to the case for previous community curation tools, the record may be updated by the contributor up until the time it is considered ready for the monthly release. Changes made to data that have been released should be made by communicating with a staff curator. We encourage persons with publications in press to submit their data to MaizeGDB, beginning with the contact form provided on each page at MaizeGDB. Refer to http://www.maizegdb.org/data_contribution.php for more information about data submission to MaizeGDB.

How You Can Help MaizeGDB to Succeed

As you know, MaizeGDB is a �model organism database� and is the community of maize researchers� repository for genomic and genetic data pertaining to our favorite plant, Zea mays ssp. mays. At the Community Forum session during the Maize Genetics Conference this past year, the statement that MaizeGDB needs to evolve into a more TAIR-like resource (see http://www.arabidopsis.org) was made, and a desire for the community database to improve was communicated by many attendees, both during and after that session (minutes from the Community Forum can be accessed at http://www.maizegdb.org/maize_meeting/2006/ and in this MNL, pp. 111-113). Subsequently, the Maize Genetics Executive Committee surveyed the community to find out what issues were of the most importance to the community of maize geneticists. The survey�s full report can be accessed at http://www.maizegdb.org/SurveyResults06.doc and in this MNL, pp. 114-117. The top three �General Community Needs� identified were:

1. High quality maize genome sequence annotation.

2. Improved maize reverse genetics resources that allow investigators to move from sequence to seed.

3. An improved maize database that allows investigators to move seamlessly between multiple genomic datasets and expression analysis.

Improving the MaizeGDB addresses needs one and two, and the desire for an improved database is stated per se as need three. Help us to meet your needs by voicing this concern! To find out how to help, read "Plant Biology Database s: A Needs Assessment", an advisory whitepaper to the NSF and USDA, which can be accessed at http://www.maizegdb.org/PDBNeeds.pdf, and contact us directly at [email protected]. For an abbreviated version of the Advisory Whitepaper�s recommendations, see Stein et al. (The Scientist 20(4):24-25, 2006).

Acknowledgements

We thank MaizeGDB's interface developer and bioinformatics engineer Trent Seigfried and database administrator Darwin Campbell for supporting the curation efforts described here. We are grateful for assistance from the MaizeGDB Working Group: Volker Brendel, Ed Buckler, Karen Cone, Mike Freeling, Owen Hoekenga, Lukas Mueller, Marty Sachs, Pat Schnable, Tom Slezak, Anne Sylvester, and Doreen Ware. We thank the MaizeGDB Editorial Board for recommending, on a monthly basis, noteworthy primary literature. This Board currently includes: Tom Brutnell, Surinder Chopra, Karen McGinnis, Wojtek Pawlowski and Jianming Yu.

Submitted by:

Mary Schaeffer (Polacco)

Carolyn J. Lawrence