Poster: Genomic & proteomic resources

Abs # 901: Results from the Affymetrix Maize Pilot Array

Presenter:	Williams, Alan J, alan_williams@affymetrix.com
Authors	Walbot, Virginia  (B)   Roger, Wise  (C)   Edward, Buckler  (D)   Caldo, Rico  (C)   Hanna, David  (A)   McLean, Lianne  (A)   Tanimoto, Gene  (A)   Williams, Alan J (A)
Affiliations:	(A): Affymetrix, Inc. (B): Department Biological Sciences, Stanford University (C): Department of Plant Pathology, Iowa State University (D): Institute for Genomic Diversity, Cornell University

A pilot study was conducted to evaluate design criteria and analytical methods (particularly signal estimators) for gene expression monitoring in a selection of maize inbreds (B73, W23) and exotic land races using the Affymetrix probe array technology. The key issue was whether eleven 25-mer probe pairs could measure transcript levels robustly despite the exceptionally high polymorphism in maize genes. As a first step in understanding how polymorphisms impact data collection, a maize pilot array containing 8,396 sets of 30 probe pairs was used. Content for the array was generated using the standard Affymetrix cDNA cluster design pipeline [1]. Content on the array is equally divided between probe designs based on all public cDNA sequences (zm1 design) and probe sets restricted to the B73 inbred (zm3 design). Most probe sets were selected from a subset of elements in Maize Gene Discovery spotted cDNA microarray experiments [2]. 43 probe sets target Glutathione S-transferases to evaluate resolution of gene expression patterns within gene families with both closely and distantly related members. The results of this pilot will be used in the design of a larger, comprehensive maize gene expression monitoring array. This larger design will be carried out under the Affymetrix Consortia Design Program [3].

[1] http://www.affymetrix.com/ support/ technical/ technotes/ hgu133_design_technote.pdf
[2] Casati, P. and V. Walbot. 2003. Gene expression profiling in response to ultraviolet radiation in Zea mays genotypes with varying amounts of flavonoids. Plant Physiology 132: 1739-1754.
[3] http://www.corporate-ir.net/ ireye/ ir_site.zhtml?ticker=AFFX&script=410&layout=-6&item_id=483499