Transcriptional profiling of wheat caryopsis development using cDNA microarrays

Debbie L. Laudencia-Chingcuanco, Boryana Stamova, Frank M. You, Gerard R. Lazo, Diane M. Beckles, Olin D. Anderson

Research output: Contribution to journalArticle

63 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)651-668
Number of pages18
JournalPlant Molecular Biology
Volume63
Issue number5
DOIs
StatePublished - Mar 1 2007

Fingerprint

Oligonucleotide Array Sequence Analysis
Triticum
wheat
fruits
Genes
genes
Molecular Sequence Annotation
Desiccation
Endosperm
Cluster Analysis
Analysis of Variance
endosperm
Carbohydrates
Gene Expression
protein synthesis
analysis of variance
developmental stages
carbohydrates
gene expression
Proteins

Keywords

  • ANOVA
  • Caryopsis
  • cDNA
  • Development
  • Endosperm
  • Microarray
  • Profiling
  • Transcriptome
  • Wheat

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

Cite this

Laudencia-Chingcuanco, D. L., Stamova, B., You, F. M., Lazo, G. R., Beckles, D. M., & Anderson, O. D. (2007). Transcriptional profiling of wheat caryopsis development using cDNA microarrays. Plant Molecular Biology, 63(5), 651-668. https://doi.org/10.1007/s11103-006-9114-y

Transcriptional profiling of wheat caryopsis development using cDNA microarrays. / Laudencia-Chingcuanco, Debbie L.; Stamova, Boryana; You, Frank M.; Lazo, Gerard R.; Beckles, Diane M.; Anderson, Olin D.

In: Plant Molecular Biology, Vol. 63, No. 5, 01.03.2007, p. 651-668.

Research output: Contribution to journalArticle

Laudencia-Chingcuanco, DL, Stamova, B, You, FM, Lazo, GR, Beckles, DM & Anderson, OD 2007, 'Transcriptional profiling of wheat caryopsis development using cDNA microarrays', Plant Molecular Biology, vol. 63, no. 5, pp. 651-668. https://doi.org/10.1007/s11103-006-9114-y
Laudencia-Chingcuanco, Debbie L. ; Stamova, Boryana ; You, Frank M. ; Lazo, Gerard R. ; Beckles, Diane M. ; Anderson, Olin D. / Transcriptional profiling of wheat caryopsis development using cDNA microarrays. In: Plant Molecular Biology. 2007 ; Vol. 63, No. 5. pp. 651-668.
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