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ORIGINAL RESEARCH

Analysis of Gene Expression during Brassica Seed Germination Using a Cross-Species Microarray Platform

^a Torrey Mesa Research Institute, Syngenta Research and Technology, 3115 Merryfield Row, San Diego, CA 92121
^b Dep. of Crop Sciences, Univ. of Illinois, 334 NSRC, 1101 W. Peabody Blvd., Urbana, IL 61801
^c Syngenta Biotechnology, 3054 Cornwallis Rd., Research Triangle Park, NC 27709
^d Syngenta Seeds B.V., Westeinde 62, Enkhuizen, the Netherlands

^* Corresponding author (mhudson{at}uiuc.edu).

We have developed an approach to facilitate the use of model organism microarrays in related, nonmodel organisms. We demonstrate the method by using Arabidopsis oligonucleotide microarrays to analyze gene expression in Brassica. Probes with low hybridization signals to Brassica genomic DNA were excluded from the transcriptional analysis of an Arabidopsis microarray at the software level, forming a virtual Brassica microarray. We then performed an experiment on transcriptional responses during seed germination in Brassica using 17 886 homologous probesets of the virtual array where Brassica mRNA hybridization was detected. We subjected seed to hydration or priming (a step to improve germination vigor) and subsequent heating and drying treatments (steps to prolong shelf life of dried seed). Exploration of the microarray results indicated two likely expression patterns shared by many genes. One class of transcripts was strongly, globally, and irreversibly downregulated by priming, while other transcripts were induced, but often reversibly. Legacy seed-storage protein messages were in the first class, and many protein synthesis components and some resource mobilization enzymes were in the second. We were able to validate our results by confirming transcriptional responses using reverse transcription polymerase chain reaction (RT–PCR).

Abbreviations: EDTA, ethylenediaminetetraacetic acid • FDR, false discovery rate • MES, 2-N-morpholino-ethane-sulfonic acid • MOID, match-only integral distribution • RH, relative humidity • PCR, polymerase chain reaction • RT–PCR, reverse transcription polymerase chain reaction • SAM, Statistical Analysis of Microarrays • SAPE, Streptavidin Phycoerythrin