MaizeGDB STATUS REPORT A SUMMARY OF RECENT UPDATES AND ACTIVITIES AS WELL AS NEW INITIATIVES USDA-ARS Project No. 3625-21000-045 (Ames, IA) and Project No. 3622-21000-027 (Columbia, MO) [formerly Project No. 3622-21000-026 (Columbia, MO)] Prepared by C. Lawrence, M. Schaeffer, T. Seigfried, and D. Campbell SEPTEMBER 2006 Contact: C. Lawrence USDA-ARS and Iowa State University 1565 Agronomy Hall Ames, IA 50011 Email: [email protected] URL: http://www.lawrencelab.org 515-294-2299 (fax) 515-294-7380 Page 1 of 308 TABLE OF CONTENTS 1 – Status 3 Summary 4 Happenings over the last 2 years (NAR submission) 5 2 – History 25 Overall history of the project 26 2004 MaizeDB to MaizeGDB Steering Committee Report 27 3 – Future 35 New hires to be made 36 Guidance from National Program Staff on 2 locations 43 Concept Paper (Ames, IA) 46 Concept Paper (Columbia, MO) 47 4 – Charge 48 Annual Maize Genetics Conference Forum Report 49 2006 Maize Genetics Executive Committee Survey 52 Status of maize bioinformatics resources, prepared for MGEC 56 5 – Budget 58 Ames, IA 59 6 – POPcorn Proposal 61 7 – Publications 67 MaizeGDB in Nucleic Acids Research, 2004 68 MaizeGDB in Plant Physiology, 2005 73 Database Needs Assessment Advisory Whitepaper, 2005 77 Advisory Whitepaper overview in The Scientist, 2006 117 Morgan2McClintock Tool in Genetics, 2006 119 A QTL database strategy in Maydica, 2006 122 Plant growth stage ontology in Plant Physiology, in press 133 MaizeGDB book chapter, in press 177 MNL contributions from the MaizeGDB Team: 207 Volume 77, 2003 207 Volume 78, 2004 251 Volume 79, 2005 264 Volume 80, 2006 266 8 – Press Releases 292 Nature Genetics, 2003 293 ISU Biotechnology Update, 2005 294 USDA-ARS Online, 2005 296 Agricultural Research Magazine, 2006 297 ISU College of Agriculture Website, 2006 (Outreach) 299 9 – Questions 305 10 – Appendix 307 Letter to allow travel in federal vehicles 308 Page 2 of 308 Status-1 Page 3 of 308 Summary Since the dissolution of the MaizeGDB Steering Committee just after their last meeting in August of 2004, the MaizeGDB team has sought to steadily improve the interfaces and data available at MaizeGDB and also improve our own internal procedures so that we are prepared for future growth. Outlined in the following submission to Nucleic Acids Research are improvements and changes in five broad areas: • Data Improvements include a stable and organized pipeline for the incorporation of public sequence data into MaizeGDB and the regular acquisition of data from community sources, including the founding of an Editorial Board to collect relevant papers for community reading. • Public Interface Improvements include new map displays, incremental improvements including faster and more accurate general searching and relevant search result pages, and the Morgan2McClintock tool which allows researchers to convert genetic maps into cytological maps and vice-versa. • Curation Tool Improvements include the development and deployment of a module for the inclusion of QTL experiments, the development and deployment of “professional” curation tools at the University of Illinois by Marty Sachs’ team, and incremental improvements. • Maize Community Support includes extensive support of the Maize Genetics Conference, including having two members of the MaizeGDB team serving as ex officio members of the conference planning committee, support of the Executive Committee including public surveys and elections, increased interactions with other groups – especially Gramene and the Maize Sequencing Project, and facilitation of community contacts. • Standard Operating Procedures outlines our procedures for data storage, redundancy, and security. Page 4 of 308 Nucleic Acids Research MaizeGDB's new data types, resources, and activities For Peer Review Journal: Nucleic Acids Research Manuscript ID: draft Manuscript Type: 6 Database Issue Key Words: maize, database, bioinformatics, website, zea Page 5 of 308 Page 1 of 19 Nucleic Acids Research Lawrence et al. 1 1 2 3 4 5 MaizeGDB's new data types, resources, 6 7 8 9 and activities 10 11 12 13 14 15 1,2,* 3 16 Carolyn J. Lawrence , Mary L. Schaeffer , Trent E. 17 18 1 For Peer1 Review 4 19 Seigfried , Darwin A. Campbell , and Lisa C. Harper 20 21 1 22 USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA 50011-3260, USA 23 2 24 Department of Agronomy and Department of Genetics, Development and Cell Biology, 25 26 Iowa State University, Ames, IA 50011-3260, USA 27 28 3 29 USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, University of 30 31 Missouri, Columbia, MO 65211, USA 32 33 and 34 35 4 36 Department of Molecular and Cell Biology, University of California, Berkeley, CA 37 38 94720, USA 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 * To whom correspondence should be addressed. Tel: +1 515 294 7380; Fax: +1 515 294 56 57 2299; Email: [email protected] 58 59 60 Page 6 of 308 Nucleic Acids Research Page 2 of 19 Lawrence et al. 2 1 2 3 4 ABSTRACT 5 6 MaizeGDB is the Maize Genetics and Genomics Database. Available at MaizeGDB are 7 8 9 diverse data that support maize research including maps, gene product information, loci 10 11 and their various alleles, phenotypes (both naturally occurring and as a result of directed 12 13 mutagenesis), stocks, sequences, molecular markers, references, and contact information 14 15 16 for maize researchers worldwide. Also available through MaizeGDB are various 17 18 community support serviceFor bulletin Peer boards including Review the Editorial Board’s list of high- 19 20 impact papers, information about the Annual Maize Genetics Conference, and the Jobs 21 22 23 board where employment opportunities are posted. Reported here are data updates, 24 25 improvements to interfaces, and changes to standard operating procedures that have been 26 27 made during the past two years. MaizeGDB is freely available and can be accessed online 28 29 30 at http://www.maizegdb.org. 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Page 7 of 308 Page 3 of 19 Nucleic Acids Research Lawrence et al. 3 1 2 3 4 INTRODUCTION 5 6 Maize (Zea mays ssp. mays) has long been the number one production crop in the United 7 8 9 States, and in 2001 it also became number one in the world. Because maize is 10 11 economically important and also serves as a model organism for genetics research, it is 12 13 one of the most highly researched organisms in existence. The maize genome has an 14 15 16 especially high level of DNA sequence polymorphism and extended regions of non- 17 18 homology between inbredFor lines (1,2) Peer, hence the diversityReview represented by the maize gene 19 20 pool is unparalleled in both a phenotypic and molecular sense. This provides a unique 21 22 23 vehicle to explore questions in evolution, domestication, development, trait expression, 24 25 functional allelic diversity, and the interrelated processes that shape such events and their 26 27 outcomes. 28 29 30 The application of new technologies and bioinformatic tools coupled with 31 32 thorough phenotypic evaluation for useful traits and molecular characterization of diverse 33 34 35 maize germplasm offers the potential for significant discovery via translational genomics. 36 37 The goal of turning the identification and evaluation of functional and evolutionarily 38 39 important allelic variation into a comprehensive genomics activity is dependent on being 40 41 42 able to associate diverse information in a seamless manner. MaizeGDB is the community 43 44 resource charged with developing informatic solutions for storing, displaying, and linking 45 46 comprehensive maize data so that they are made easily accessible to researchers 47 48 49 worldwide. Described here are updates and improvements to MaizeGDB that have been 50 51 made over the course of the past two years. 52 53 54 55 56 57 58 59 60 Page 8 of 308 Nucleic Acids Research Page 4 of 19 Lawrence et al. 4 1 2 3 4 NEW DATA TYPES 5 6 Since the initial announcement in 2004 that MaizeGDB was up and running (3), the 7 8 9 database has expanded to include new data types such as TILLING data (4; 10 11 http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=mtp*), cytological maps 12 13 with associated images (e.g., http://www.maizegdb.org/cgi- 14 15 16 bin/displaymaprecord.cgi?id=892372), and the maize Recombination Nodule maps (5,6; 17 18 http://www.maizegdb.org/RNmaps.php)For Peer. All new dataReview types are made available alongside 19 20 related information and are accessible through mechanisms that seamlessly integrate with 21 22 23 the site’s existing functionalities. An example of how the new Recombination Nodule map 24 25 data can be used to speed up experiments that utilize the maize translocation stocks 26 27 follows. 28 29 30 A researcher wants to determine whether the gene product of her new mutant gof1, 31 32 which maps to 3L within 1 cM of tub6, acts cell autonomously using a mosaic analysis. 33 34 35 Since there are no suitable cell autonomous markers known to be proximal to gof1, she 36 37 decides to use an A-A translocation to bring gof1+ distal to a cell autonomous marker on 38 39 another chromosome. To do this, she needs to find a translocation stock with a breakpoint 40 41 42 on 3L proximal to her gene of interest, and a breakpoint on another chromosome that is 43 44 distal to a gene that can be used as a cell autonomous marker.