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MaizeGDB: The Maize Genetics and Genomics Database

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Plant Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1374))

Abstract

MaizeGDB is the community database for biological information about the crop plant Zea mays. Genomic, genetic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes stored at MaizeGDB. At the project’s website (http://www.maizegdb.org) are custom interfaces enabling researchers to browse data and to seek out specific information matching explicit search criteria. In addition, pre-compiled reports are made available for particular types of data and bulletin boards are provided to facilitate communication and coordination among members of the community of maize geneticists.

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References

  1. Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V (2004) MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Res 32:D393–D397

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  2. Polacco M, Coe E (1999) In: Letovsky SI (ed) Bioinformatics: databases and systems. Kluwer Academic Publishers, Norwell, MA, pp 151–162

    Google Scholar 

  3. Polacco M, Coe E, Fang Z, Hancock D, Sanchez-Villeda H, Schroeder S (2002) MaizeDB—a functional genomics perspective. Comp Funct Genomics 3(2):128–131

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Dong Q, Roy L, Freeling M, Walbot V, Brendel V (2003) ZmDB, an integrated database for maize genome research. Nucleic Acids Res 31:244–247

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME, Duvick J, Brendel VP, Cannon E, Campbell DA, Lawrence CJ (2009) MaizeGDB becomes ‘sequence-centric’. Database. doi:10.1093/database/bap020

    PubMed Central  PubMed  Google Scholar 

  6. Lawrence CJ, Harper LC, Schaeffer ML, Sen TZ, Seigfried TE, Campbell DA (2008) MaizeGDB: the maize model organism database for basic, translational, and applied research. Int J Plant Genomics. doi:10.1155/2008/496957

    PubMed Central  PubMed  Google Scholar 

  7. Lawrence CJ, Schaeffer ML, Seigfried TE, Campbell DA, Harper LC (2007) MaizeGDB’s new data types, resources and activities. Nucleic Acids Res 35(Database issue):D895–D900

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Lawrence CJ, Seigfried TE, Brendel V (2005) The maize genetics and genomics database: the community resource for access to diverse maize data. Plant Physiol 138:55–58

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res 11:1425–1433

    Article  Google Scholar 

  10. Bruskiewich R, Coe E, Jaiswal P, McCouch S, Polacco M, Stein L, Vincent L, Ware D (2002) The plant ontologytm consortium and plant ontologies. Comp Funct Genomics 3:137–142

    Article  Google Scholar 

  11. Cannon EK, Birkett SM, Braun BL, Kodavali S, Jennewein DM, Yilmaz A, Antonescu V, Antonescu C, Harper LC, Gardiner JM, Schaeffer ML, Campbell DA, Andorf CM, Andorf D, Lisch D, Koch KE, McCarty DR, Quackenbush J, Grotewold E, Lushbough CM, Sen TZ, Lawrence CJ (2011) POPcorn: an online resource providing access to distributed and diverse maize project data. Int J Plant Genomics. doi:10.1155/2011/923035

    Google Scholar 

  12. Andorf CM, Lawrence CJ, Harper LC, Schaeffer ML, Campbell DA, Sen TZ (2010) The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps. Bioinformatics. doi:10.1093/bioinformatics/btp556

    PubMed  Google Scholar 

  13. Monacoa MK, Senbc TZ, Dharmawardhanad PD, Rena L, Schaefferbe M, Naithanif S, Amarasinghed V, Thomasona J, Harperbg L, Gardinerch J, Cannonc EKS, Lawrencebc CJ, Wareab D, Jaiswal P (2013) Maize metabolic network construction and transcriptome analysis. Plant Genome. doi:10.3835/plantgenome2012.09.0025

    Google Scholar 

  14. Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D’Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D (2013) Gramene 2013: comparative plant genomics resources. Nucleic Acids Res. doi:10.1093/nar/gkt1110

    Google Scholar 

  15. Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ (2007) An “electronic fluorescent pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS One 2(8), e718

    Article  PubMed Central  PubMed  Google Scholar 

  16. Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37(6):914–939

    Article  CAS  PubMed  Google Scholar 

  17. Laurie DA, Bennett MD (1985) Nuclear DNA content in the genera Zea and Sorghum—intergenic, interspecific and intraspecific variation. Heredity 55:307–313

    Article  Google Scholar 

  18. Gardiner JM, Coe EH, Melia-Hancock S, Hoisington DA, Chao S (1993) Development of a core RFLP map in maize using an immortalized F2 population. Genetics 134(3):917–930

    PubMed Central  CAS  PubMed  Google Scholar 

  19. Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Sen TZ, Lawrence CJ (2011) MaizeGDB: curation and outreach go hand-in-hand. Database (Oxford). doi:10.1093/database/bar022

    Google Scholar 

  20. Harper LC, Schaeffer ML, Thistle J, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Braun BL, Birkett SM, Lawrence CJ, Sen TZ (2011) The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video. Database (Oxford). doi:10.1093/database/bar016

    PubMed Central  Google Scholar 

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Acknowledgments

The author would like to thank Darwin Campbell for his work in maintaining the MaizeGDB database; Mary Schaeffer, Ed Coe, and Marty Sachs for their curatorial work; and Ethalinda Cannon, Bremen Braun, Scott Burket, John Portwood, and Jackie Richter for their technical support. This work was supported by the USDA-ARS, and the National Corn Growers Association.

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Correspondence to Lisa Harper .

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Harper, L., Gardiner, J., Andorf, C., Lawrence, C.J. (2016). MaizeGDB: The Maize Genetics and Genomics Database. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3167-5_9

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  • DOI: https://doi.org/10.1007/978-1-4939-3167-5_9

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3166-8

  • Online ISBN: 978-1-4939-3167-5

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