title: Genetic diversity contribution to errors in short oligonucleotide microarray analysis.
abstract: DNA arrays based on short oligonucleotide (< or = 25-mer) probes are being developed for many species, and are being applied to quantify transcript abundance variation in species with high genetic diversity. To define the parameters necessary to design short oligo arrays for maize (Zea mays L.), a species with particularly high nucleotide (single nucleotide polymorphism, SNP) and insertion-deletion (indel) polymorphism frequencies, we analysed gene expression estimates generated for four maize inbred lines using a custom Affymetrix DNA array, and identified biases associated with high levels of polymorphism between lines. 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. SNPs and indels were identified by re-sequencing; they are the primary source of probe-by-line interactions, affecting probeset level estimates and reducing the power of detecting transcript level variation between maize inbreds. This analysis identified 36,196 probes in 5118 probesets containing markers that may be used for genotyping in natural and segregating populations for association gene analysis and genetic mapping.
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853-2703, USA. mkirst@ufl.edu
authors.forename: Matias
authors.initials: M
authors.lastname: Kirst
authors.forename: Rico
authors.initials: R
authors.lastname: Caldo
authors.forename: Paula
authors.initials: P
authors.lastname: Casati
authors.forename: Gene
authors.initials: G
authors.lastname: Tanimoto
authors.forename: Virginia
authors.initials: V
authors.lastname: Walbot
authors.forename: Roger P
authors.initials: RP
authors.lastname: Wise
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
mesh_terms: D001483:Base Sequence; D015342:DNA Probes; D020869:Gene Expression Profiling; D017343:Genes, Plant; D005838:Genotype; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D011110:Polymorphism, Genetic; D012689:Sequence Homology, Nucleic Acid; D003313:Zea mays / Q000235:genetics
chemical_list: D015342:DNA Probes