Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

A GeneChip® For Citrus.

Timothy J Close¹ , Steve Wanamaker¹ , Matthew Lyon¹ , Gangwu Mei² , Chris Davies² , Mikeal L Roose¹

¹  Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521-0124, USA

²  Affymetrix Inc., 6550 Vallejo Street, Emeryville, CA, 94608, USA

A GeneChip® containing 960,444 total 25-mer oligos in an 11 micron format has been produced for citrus research. About 2/3 of the content was designed for gene expression analysis using 30,264 probe sets, each composed of 22 paired perfect match and mismatch oligos. Most of the remaining 1/3 was designed to genotype 3,219 genes using 5,023 SNPs identified in ESTs from Citrus sinensis and other citrus species. Each SNP is represented by 56 oligos. Content for the citrus GeneChip® was selected from assemblies of 166,244 EST and GenBank nr cDNA sequences. Interpretation of data from this GeneChip® is supported by gene function annotations and interactive graphical user interfaces in the HarvEST:Citrus software (harvest.ucr.edu) and through Affymetrix NetAFFX (http://www.affymetrix.com/analysis/index.affx). These resources operate in part by linking to additional information available from National Center for Biotechnology Information, The Institute for Genomic Research and UniProt. The citrus GeneChip® also includes tiling on 35-base centers of one region of the Poncirus trifoliata genome containing a citrus tristeza virus resistance locus, as well as probe sets for detection of several viruses, viroids, Xylella fastidiosa and commonly used transgenes. This work was supported by the California Citrus Research Board, UC Discovery Grant Program, the Agricultural Experiment Station and the Affymetrix GeneChip® Consortia Program.