title: A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members.
abstract: The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.
authors.affiliation: Institute of Biology, Clusius Laboratory, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.
authors.forename: Adamantia
authors.initials: A
authors.lastname: Agalou
authors.forename: Sigit
authors.initials: S
authors.lastname: Purwantomo
authors.forename: Elin
authors.initials: E
authors.lastname: Overnäs
authors.forename: Henrik
authors.initials: H
authors.lastname: Johannesson
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Zhu
authors.forename: Amy
authors.initials: A
authors.lastname: Estiati
authors.forename: Rolf J
authors.initials: RJ
authors.lastname: de Kam
authors.forename: Peter
authors.initials: P
authors.lastname: Engström
authors.forename: Inez H
authors.initials: IH
authors.lastname: Slamet-Loedin
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhu
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.forename: Lizhong
authors.initials: L
authors.lastname: Xiong
authors.forename: Annemarie H
authors.initials: AH
authors.lastname: Meijer
authors.forename: Pieter B F
authors.initials: PB
authors.lastname: Ouwerkerk
mesh_terms: D002874:Chromosome Mapping; D004190:Disasters; D020224:Expressed Sequence Tags; D005801:Genes, Homeobox; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction