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Open Access Highly Accessed Research article

A cross-species transcriptomics approach to identify genes involved in leaf development

Nathaniel Robert Street1, Andreas Sjödin1, Max Bylesjö2, Petter Gustafsson1, Johan Trygg2 and Stefan Jansson1*

Author Affiliations

1 Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden

2 Research Group for Chemometrics, Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden

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BMC Genomics 2008, 9:589  doi:10.1186/1471-2164-9-589

Published: 5 December 2008

Abstract

Background

We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.

Results

Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.

Conclusion

This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.