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Transcriptional profiling of wheat caryopsis development using cDNA microarrays

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Abstract

The expression of 7,835 genes in developing wheat caryopses was analyzed using cDNA arrays. Using a mixed model analysis of variance (ANOVA) method, 29% (2,237) of the genes on the array were identified to be differentially expressed at the 6 different time-points examined, which covers the developmental stages from coenocytic endosperm to physiological maturity. Comparison of genes differentially expressed between two time-points revealed a dynamic transcript accumulation profile with major re-programming events that occur at 3–7, 7–14 and 21–28 DPA. A k-means clustering algorithm grouped the differentially expressed genes into 10 clusters, revealing co-expression of genes involved in the same pathway such as carbohydrate and protein synthesis or preparation for desiccation. Functional annotation of genes that show peak expression at specific time-points correlated with the developmental events associated with the respective stages. Results provide information on the temporal expression during caryopsis development for a significant number of differentially expressed genes with unknown function.

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Acknowledgements

We would like to thank Adaku Ude, Sarah Vela and Joseph Pham for their excellent technical assistance and Dr. Grace Chen, Dr. Michael Gitt, Dr. Kent McCue and Dr. Craig Parker for the critical reading of the manuscript. We apologize to those whose works we have not cited owing to restrictions in the length of this article. The USDA-ARS CRIS Project 5325-21000-011 funded this work.

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  1. Genomics and Gene Discovery, USDA-ARS-WRRC, 800 Buchanan Street, Albany, CA, 94710, USA

    Debbie L. Laudencia-Chingcuanco, Gerard R. Lazo & Olin D. Anderson

  2. Genetic Resources Conservation Program, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA

    Boryana S. Stamova

  3. Plant Sciences Department, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA

    Frank M. You & Diane M. Beckles

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  1. Debbie L. Laudencia-Chingcuanco
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Correspondence to Debbie L. Laudencia-Chingcuanco.

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Boryana S. Stamova share first co-authorship

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Laudencia-Chingcuanco, D.L., Stamova, B.S., You, F.M. et al. Transcriptional profiling of wheat caryopsis development using cDNA microarrays. Plant Mol Biol 63, 651–668 (2007). https://doi.org/10.1007/s11103-006-9114-y

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