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


CONCLUSIONS
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.
Street
Nathaniel Robert
NR
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden. nathaniel.street@plantphys.umu.se
Sjödin
Andreas
A
Bylesjö
Max
M
Gustafsson
Petter
P
Trygg
Johan
J
Jansson
Stefan
S
D017360:Arabidopsis / Q000235:genetics; D016000:Cluster Analysis; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D020411:Oligonucleotide Array Sequence Analysis; D018515:Plant Leaves / Q000235:genetics*; D032107:Populus / Q000235:genetics*; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics
D014157:Transcription Factors