Analysis of the root-hair morphogenesis transcriptome reveals the molecular identity of six genes with roles in root-hair development in Arabidopsis

Root-hair morphogenesis is a model for studying the genetic regulation of plant cell development, and double-mutant analyses have revealed a complex genetic network underlying the development of this type of cell. Therefore, to increase knowledge of gene expression in root hairs and to identify new genes involved in root-hair morphogenesis, the transcriptomes of the root-hair differentiation zone of wild-type (WT) plants and a tip-growth defective root-hair mutant, rhd2-1, were compared using Affymetrix ATH1 GeneChips((R)). A set of 606 genes with significantly greater expression in WT plants defines the 'root-hair morphogenesis transcriptome'. Compared with the whole genome, this set is highly enriched in genes known to be involved in root-hair morphogenesis. The additional gene families and functional groups enriched in the root-hair morphogenesis transcriptome are cell wall enzymes, hydroxyproline-rich glycoproteins (extensins) and arabinogalactan proteins, peroxidases, receptor-like kinases and proteins with predicted glycosylphosphatidylinositol (GPI) anchors. To discover new root-hair genes, 159 T-DNA insertion lines identified from the root-hair morphogenesis transcriptome were screened for defects in root-hair morphogenesis. This identified knockout mutations in six genes (RHM1-RHM6) that affected root-hair morphogenesis and that had not previously been identified at the molecular level: At2g03720 (similar to Escherichia coli universal stress protein); At3g54870 (armadillo-repeat containing kinesin-related protein); At4g18640 (leucine-rich repeat receptor-like kinase subfamily VI); At4g26690 (glycerophosphoryl diester phosphodiesterase-like GPI-anchored protein); At5g49270 (COBL9 GPI-anchored protein) and At5g65090 (inositol-1,4,5 triphosphate 5-phosphatase-like protein). The mutants were transcript null, their root-hair phenotypes were characterized and complementation testing with uncloned root-hair genes was performed. The results suggest a role for GPI-anchored proteins and lipid rafts in root-hair tip growth because two of these genes (At4g26690 and At5g49270) encode predicted GPI-anchored proteins likely to be associated with lipid rafts, and several other genes previously shown to be required for root-hair development also encode proteins associated with sterol-rich lipid rafts.