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Award Abstract #0638770

Functional Analyses of Genes Involved in Meristem Organization and Leaf Initiation

NSF Org:    IOS Division Of Integrative Organismal Sys    
Initial Amendment Date:    July 13, 2006   
Latest Amendment Date:     September 4, 2007    
Award Number:    0638770   
Award Instrument:     Continuing grant   
Program Manager:    Diane Jofuku Okamuro IOS Division Of Integrative Organismal Sys BIO Direct For Biological Sciences   
Start Date:     January 1, 2006   
End Date:    August 31, 2008 (Estimated)   
Awarded Amount to Date:     $1,979,543.00    
Investigator(s):    Michael Scanlon mjs298@cornell.edu (Principal Investigator)    
Sponsor:     Cornell Univ - State: AWDS MADE PRIOR MAY 2010 373 Pine Tree Road Ithica, NY 14850-2488 (607)255-5014    
NSF Program(s):    PLANT GENOME RESEARCH PROJECT    
Program Reference Code(s):     9109, 9184, BIOT    
Program Element Code(s):    1329    

ABSTRACT

All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, marked by tissue zonation and cell layering. The structure of plant SAMs is correlated with their function, such that new leaves are initiated from the peripheral zone of the SAM and the central zone replenishes new meristematic cells that are lost during organogenesis. Establishment and maintenance of these structurally and functionally distinct zones of the SAM is achieved by differential expression patterns and interactions of thousands of plant genes. Breakthrough technologies have emerged that enable the identification and analysis of genes required for meristem function in maize. Laser dissection microscopy (LCM) is a powerful technique that permits the isolation of RNA from specific cell types within fixed plant tissues immobilized on slides. RNA collected from 1,000-10,000 cells is sufficient for use in microarray analyses of gene expression, which permit the simultaneous examination of expression profiles of 15,000 to 30,000 genes. The relatively large size of the maize vegetative meristem, approximately 250 meristematic cells are recruited into the incipient maize leaf, renders this plant especially tractable for this experimental system. The laser-capture microdissection/microarray technique will be used to capture cells from specific domains of the maize meristem and newly formed leaf primordia for use in comparative analyses of global gene expression. The differential expression patterns of candidate genes will be verified by more traditional analyses (RT-PCR, RNA gel blot hybridization and in situ hybridization) of transcript accumulation in maize tissues. These experiments will microdissect gene expression patterns in meristems and leaf primordia, and will provide novel insight into mechanisms of plant development.

This research project will generate the following set of deliverables:

1. LCM will be optimized and improved for use on maize SAMs. Information will be available on a project web site at ISU and in publications.

2. Microarray profiles of global gene expression in the SAM will be deposited in public web sites, maizeGDB.

3. An EST collection from meristem-enriched cDNA library will be developed beginning in the second year of the project, depending on need. If developed, all EST sequences will be deposited in Genbank and in maizeGDB.

4. Sequence generated by students mining for maize equivalents to already known genes from other plants will be sent directly to Genbank and maizeGDB.

Outreach and training will be enhanced in three ways:

1. Undergraduate students from Truman State University will engage in cutting edge genomics research.

2. PI Scanlon will deliver guest lectures at local high schools with predominantly minority enrollment.

3. The University of Georgia and the CSHL Dolan DNA Learning Center (DNALC) will train teachers from underrepresented minority high schools and university settings in plant genomics and bioinformatics.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Jon Beck, Brent Buckner, Olga Nikolova,* and Diane Janick-Buckner. 2007. "Using interdisciplinary bioinformatics undergraduate research to recruit and retain computer science students.," SIGCSE Bulletin, v.39, 2007, p. 358. Nogueira F, Madi S, Juarez M, Timmermans MCP. "Two small regulatory RNAs establish opposing fates of a developmental axis," Genes and Development, v.21, 2007, p. 750. Emrich SJ, Barbazuk WB, Li L, Schnable PS. "Gene discovery and annotation using LCM-454 transcriptome sequencing.," Genome Research, v.17, 2007, p. 69. Henderson D, Zhang X, Brooks L, and Scanlon MJ. "RAGGED SEEDLING2 is required for expression of KANADI2 and REVOLUTA homologues in the maize shoot apex," Genesis, v.44, 2006, p. 372-382. Nettleton D. "A discussion of statistical methods for design and analysis of microarray experiments for plant scientists," Plant Cell, v.18, 2006, p. 2112. Henderson D, Zhang X, Brooks L, and Scanlon MJ. "RAGGED SEEDLING2 is required for expression of KANADI2 and REVOLUTA homologues in the," Genesis, v.44, 2006, p. 372-382. Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MC, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon MJ, Schnable PS.. "Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).," Plant Journal, v.52, 2007, p. 391-404. Zhang X, Madi S, Borsuk L, Nettleton D, Elshire RJ, Buckner B, Janick-Buckner D, Beck J, Timmermans M, Schnable PS, Scanlon MJ.. ") Laser microdissection of narrow sheath mutant maize uncovers novel gene expression in the shoot apical meristem.," PLoS Genet, v.3, 2007, p. 1040. Emrich SJ, Barbazuk WB, Li L, Schnable PS.. "Gene discovery and annotation using LCM-454 transcriptome sequencing.," Genome Res, v.17, 2007, p. 69. Buckner B, Beck J, Browning K*, Fritz A*, Grantham L*, Hoxha E*, Kamvar Z*, Lough A*, Nikolova O*, Schnable PS, Scanlon MJ, Janick-Buckner D. "Involving undergraduates in the annotation and analysis of global gene expression studies: creation of a maize shoot apical meristem expression database," Genetics, v.176, 2007, p. 741.
Beck J, Buckner B, Nikolova O*, Janick-Buckner D.. "Using interdisciplinary bioinformatics undergraduate research to recruit and retain computer science students.," SIGCSE Bull, v.39, 2007, p. 358.

Nogueira FT, Madi S, Chitwood DH, Juarez MT, Timmermans MC.. "Two small regulatory RNAs establish opposing fates of a developmental axis.," Genes Dev, v.21, 2007, p. 750.

Buckner B, Swaggart KA*, Wong CC*, Smith HA*, Aurand KM*, Scanlon MJ, Schnable PS, Janick-Buckner D. "Expression and Nucleotide Diversity of the Maize RIK Gene," J. Hered, v.99, 2008, p. 407.

Xiaolan Zhang, Joshua Strable, Ryan N. Douglas, Kazuhiro Ohtsu, Sarah Hargreaves, Douglas Eudy, Marja C. P. Timmermans, Dan Nettleton, Brent Buckner, Diane Janick-Buckner, Patrick S. Schnable, and Michael J. Scanlon. "Laser microdissection identifies a novel maize gene required for leaf pattern formation.," PNAS, 2009.

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