CornChip0-Maize Pilot GeneChip Array

To define the parameters necessary to design short oligo arrays for maize (Zea mays L.), a species with particularly high nucleotide (SNP) and insertion-deletion (indel) polymorphism frequencies, gene expression was analyzed in for four maize inbred lines using a custom Affymetrix DNA array. Statistically significant interactions between probes and maize inbreds were detected, affecting five or more probes (out of 30 probes per transcript) in the majority of cases, indicating the effect of polymorphisms on gene expresison estimates using this platform. Keywords: genotype effect Plant growth, tissue collection and RNA extractions were repeated three times (biological replication) for each of four maize lines: B73, Mo17, W23 and Wf9. Total RNA was labeled according to the Affymetrix Expression Analysis Manual, and hybridized to two CornChips (technical replicates). A total of six replicates (three biological, two technical) of each line were hybridized to the CornChips.