Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation
Article first published online: 4 APR 2005
The Plant Journal
Volume 42, Issue 5, pages 618–640, June 2005
How to Cite
Ehlting, J., Mattheus, N., Aeschliman, D. S., Li, E., Hamberger, B., Cullis, I. F., Zhuang, J., Kaneda, M., Mansfield, S. D., Samuels, L., Ritland, K., Ellis, B. E., Bohlmann, J. and Douglas, C. J. (2005), Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation. The Plant Journal, 42: 618–640. doi: 10.1111/j.1365-313X.2005.02403.x
- Issue published online: 4 APR 2005
- Article first published online: 4 APR 2005
- Received 24 November 2004; revised 14 February 2005; accepted 15 February 2005.
- transcription factors;
- lignin biosynthesis;
- phenylpropanoid metabolism;
- shikimate pathway;
- longmer microarray
Different stages of vascular and interfascicular fiber differentiation can be identified along the axis of bolting stems in Arabidopsis. To gain insights into the metabolic, developmental, and regulatory events that control this pattern, we applied global transcript profiling employing an Arabidopsis full-genome longmer microarray. More than 5000 genes were differentially expressed, among which more than 3000 changed more than twofold, and were placed into eight expression clusters based on polynomial regression models. Within these, 182 upregulated transcription factors represent candidate regulators of fiber development. A subset of these candidates has been associated with fiber development and/or secondary wall formation and lignification in the literature, making them targets for functional studies and comparative genomic analyses with woody plants. Analysis of differentially expressed phenylpropanoid genes identified a set known to be involved in lignin biosynthesis. These were used to anchor co-expression analyses that allowed us to identify candidate genes encoding proteins involved in monolignol transport and monolignol dehydrogenation and polymerization. Similar analyses revealed candidate genes encoding enzymes that catalyze missing links in the shikimate pathway, namely arogenate dehydrogenase and prephenate aminotransferase.