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A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members

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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.

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Abbreviations

Athb:

Arabidopsis thaliana homeobox

CNA:

CORONA

DAF:

Days after flowering

EST:

Expressed sequence tag

HB:

Homeobox

HD:

Homeodomain

HD-Zip:

Homeodomain-leucine zipper

MP:

Maximum parsimony

NJ:

Neighbour-joining

Oshox:

Oryza sativa homeobox gene

PCR:

Polymerase chain reaction

PHB:

PHABULOSA

PHV:

PHAVOLUTA

REV:

REVOLUTA

RT:

Reverse transcription

RWC:

Relative water content

Zip:

Leucine zipper

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Acknowledgments

The authors thank Elly Schrijnemakers for plant care and NIAS DNA Bank in Japan for sending EST clones. This work was supported by the EU FP5 project TF-STRESS (QLK3-2000-00328) for HJ, PE and AHM, by the SPIN-BIORIN Programme (99-BT-01) of the Royal Netherlands Academy of Arts and Sciences (KNAW) for SP and AE, by the Programme Scientific Alliance (04-PSA-BD-04) of KNAW for AA, MW and ZZ, by the EU FP6 INCO-MPC2 project CEDROME (INCO-CT-2005-015468) for XZ, LX and PBFO and by the Indonesian International Joint Research Program (RUTI) for IHS and SP.

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Author notes

  1. Adamantia Agalou

    Present address: Laboratory of Cellular Signaling and Molecular Pharmacology, Institute of Biology, National Center for Scientific Research “Demokritos”, Ag. Paraskevi, 15310, Athens, Greece

Authors and Affiliations

  1. Institute of Biology, Clusius Laboratory, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands

    Adamantia Agalou, Sigit Purwantomo, Amy Estiati, Rolf J. de Kam, Mei Wang, Annemarie H. Meijer & Pieter B. F. Ouwerkerk

  2. Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor Km. 46, Cibinong, 16911, Indonesia

    Sigit Purwantomo, Amy Estiati & Inez H. Slamet-Loedin

  3. Department of Physiological Botany, EBC, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden

    Elin Övernäs, Henrik Johannesson & Peter Engström

  4. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shi-Zhi-Shan Street, No. 1, 430070, Wuhan, China

    Xiaoyi Zhu & Lizhong Xiong

  5. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 917 Building, Datun Road, Deshenmenwai, Beijing, 100101, China

    Zhen Zhu

  6. TNO Quality of Life, Zernikedreef 9, P.O. Box 2215, 2301 CE, Leiden, The Netherlands

    Mei Wang

Authors
  1. Adamantia Agalou
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  2. Sigit Purwantomo
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  3. Elin Övernäs
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  4. Henrik Johannesson
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  5. Xiaoyi Zhu
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  6. Amy Estiati
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  7. Rolf J. de Kam
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  8. Peter Engström
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  9. Inez H. Slamet-Loedin
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  10. Zhen Zhu
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  11. Mei Wang
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  12. Lizhong Xiong
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  13. Annemarie H. Meijer
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  14. Pieter B. F. Ouwerkerk
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Corresponding author

Correspondence to Pieter B. F. Ouwerkerk.

Additional information

Adamantia Agalou and Sigit Purwantomo contributed equally to this work.

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Agalou, A., Purwantomo, S., Övernäs, E. et al. A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol Biol 66, 87–103 (2008). https://doi.org/10.1007/s11103-007-9255-7

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  • DOI: https://doi.org/10.1007/s11103-007-9255-7

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