MaizeGDB: A Very Short Overview of a Database Resource for Biological Information on Zea mays Jack M. Gardiner ASPB 2010

MaizeGDB 101 MaizeGDB strives to: –Serve as a central repository for public maize information –Disseminate the data in a user friendly manner that creates intuitive biological connections –Encourage community involvement in the evolution of the data and user interface MaizeGDB was established in 1991 by USDA-ARS.

Basic Utility of MaizeGDB -Top of of Each Page- Each page at MaizeGDB offers a set of consistent tools for users, from searching to access to popular pages… These tools are found along the top of each page.

Basic Utility of MaizeGDB -Bottom of Each Page- Search bar (duplicate) Feedback is key to getting what you want and helping us deliver a usable resource!

What Data Types are Available from MaizeGDB? MaizeGDB includes a number of data types, all available from the front page. Genome Browser Data types available: –Probes (BACs, overgos, SSRs, etc.) –Gene Products –Locus/Loci –Maps –Metabolic Pathways –People/Organizations –Phenotypes –QTL –References –Sequences –Stocks –Variations

Spotlight on Three Resources Available from MaizeGDB Phenotypes –An overview of the depth and breadth of what’s available Popcorn –One stop resource for maize sequences Maize Genome Browser –How to access

Phenotype Data at MaizeGDB Sources –The MGCSC Maize Genetics Cooperation Stock Center, Illinois USA, Marty Sachs, Director –High-throughput projects –Mutants of Maize, eds MG Neuffer, EH Coe, SR Wessler (1997) –Images - Community, MG Neuffer collection –Literature

How Many Phenotypes are in MaizeGDB? > 800 genes in MaizeGDB with a designated phenotype < 250 with some description in Mutants of Maize. Most unsequenced with only approximate chromosome location known a new peer reviewed, on line community resource seeks to capture new and existing maize phenotypes via community curationwww.maizegenereview.org

POPCorn PrOject Portal for Corn PopCorn: –Provides a searchable database of 92 maize projects and resources –Allow searching of multiple projects with a single sequence query –Provides behind-the-scenes tools to enable projects to transition their data to MaizeGDB –Funded by NSF DBI

POPCorn Two Options for Sequence Searches

Accessing the Maize Genome Sequence through MaizeGDB

MaizeGDB Tutorials

A Very Brief Overview of Maize Genome Sequencing Projects Mo17 Genome –Sequenced at the DOE Joint Genome Institute –65 Million total 454 shotgun reads 16 million reads with < 1/3 repeat content Aligned to the B73 Sequence at Palomero Toluqueño Genome –Sequenced at CINVESTAV Irapuato, Mexico –Ancient Mexican popcorn landrace provides diversity comparison with B73 genome sequence

A Very Brief Overview of Maize Genome Sequencing Projects B73 Genome –Sequenced by the Maize Genome Sequencing Consortium –Funded by the NSF, DOE, and USDA and completed 2008 –Sequencing of ~16,600 BACs at 6X coverage was based on a well developed integrated genetic and physical map Current Status of the B73 Genome –Version 2 of the pseudomolecules released in March 2010 –A tremendous resource but many sequence contigs within BACs remain unordered. This presents annotation challenges. –Version 2 of the annotation to be released by the MGSC in summer 2010

Works in Progress at MaizeGDB SNPs –Working to bring in a large SNP dataset(s) and present on the maize genome browser Gene Expression Data –Working to bring a large NimbleGen microarray data set across 60 maize tissues Truman State University Collaboration on Undergraduate-Driven Community Annotation –Focus is on genes involved in Shoot Apical Meristem development.

MaizeGDB Team MaizeGDB Core Team –Carolyn Lawrence-Director –Darwin Campbell-DBA –Carson Andorf-Bioinformatics –Tanner Sen-Computational Biology –Ethy Cannon-Software Dev –Mary Schaeffer-Curator –Jack Gardiner-Curator –Lisa Harper-Curator Working Group Volker Brendel Mike Freeling Anne-Francoise Lamblin Thomas Lubberstedt Owen Hoekenga Karen McGinnis Lukas Mueller Mihai Pop (Chair) Marty Sachs Pat Schnable Anne Sylvester Doreen Ware

Contact at ASPB 2010 Will be at Plant Genome Resources Outreach Booth –Saturday 11:00 to 2:00 –Sunday 11:00 to 1:45 –Monday 10:00 to 1:45 –Tuesday 11:00 to 1:00 me at for a