Genetic diversity contribution to errors in short oligonucleotide microarray analysis

doi:10.1111/j.1467-7652.2006.00198.x

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Wiley InterScience

Plant Biotechnology Journal

Volume 4 Issue 5, Pages 489 - 498

Published Online: 15 Jun 2006

Plant Biotechnology Journal is published by Wiley-Blackwell in association with the Society for Experimental Biology (SEB) and the Association of Applied Biologists (AAB).

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Genetic diversity contribution to errors in short oligonucleotide microarray analysis

Matias Kirst ^1,*^,†, Rico Caldo ² , Paula Casati ^3,‡, Gene Tanimoto ⁴ , Virginia Walbot ³ , Roger P. Wise ^2,5 and Edward S. Buckler ^1,6

¹ Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853-2703, USA
² Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
³ Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
⁴ Affymetrix, Inc., Santa Clara, CA 95051, USA
⁵ USDA-ARS, Corn Insects and Crop Genetics Research, Iowa State University, Ames, IA 50011, USA
⁶ USDA-ARS, Plant, Soil, and Nutrition Research Unit, Cornell University, Ithaca, NY 14853, USA

* Correspondence (fax +1 352 846 1277; e-mail: mkirst@ufl.edu)

† Present address: School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, FL 32611, USA

‡ Present address: Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI), Suipacha 531, 2000 Rosario, Argentina

KEYWORDS

Affymetrix • genetic diversity • maize • microarray • type I error

ABSTRACT

DNA arrays based on short oligonucleotide (≤ 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.

Received 26 January 2006; revised 17 April 2006; accepted 20 April 2006

DIGITAL OBJECT IDENTIFIER (DOI)

10.1111/j.1467-7652.2006.00198.x About DOI