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Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice

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Abstract

NAM, ATAF, and CUC (NAC) transcription factors comprise a large plant-specific gene family and a few members of this family have been characterized for their roles in plant growth, development, and stress tolerance. In this study, systematic sequence analysis revealed 140 putative NAC or NAC-like genes (ONAC) in rice. Phylogenetic analysis suggested that NAC family can be divided into five groups (I–V). Among them, all the published development-related genes fell into group I, and all the published stress-related NAC genes fell into the group III (namely stress-responsive NAC genes, SNAC). Distinct compositions of the putative motifs were revealed on the basis of NAC protein sequences in rice. Most members contained a complete NAC DNA-binding domain and a variable transcriptional regulation domain. Sequence analysis, together with the organization of putative motifs, indicated distinct structures and potential diverse functions of NAC family in rice. Yeast one-hybrid analysis confirmed that 12 NAC proteins representing different motif compositions can bind the NAC core DNA-binding site. Real-time polymerase chain reaction (PCR) analysis revealed 12 genes with different tissue-specific (such as callus, root, stamen, or immature endosperm) expression patterns, suggesting that these genes may play crucial regulatory roles during growth and development of rice. The expression levels of this family were also checked under various abiotic stresses including drought, salinity, and low temperature. A preliminary check based on our microarray data suggested that more than 40 genes of this family were responsive to drought and/or salt stresses. Among them, 20 genes were further investigated for their stress responsiveness in detail by real-time PCR analysis. Most of these stress-responsive genes belonged to the group III (SNAC). Considering the fact that a very limited number of genes of the NAC family have been characterized, our data provide a very useful reference for functional analysis of this family in rice.

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Abbreviations

NAC:

NAM, ATAF, and CUC transcription factor

PCR:

Polymerase chain reaction

MEME:

Multiple EM for motif elicitation

Y1H:

Yeast one-hybrid

ERD1:

Early responsive to drought 1

ABA:

Abscisic acid

GA:

Gibberellin

SA:

Salicylic acid

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Acknowledgments

This work was supported by grants from the National Natural Science Foundation of China, the National Program on the Development of Basic Research, the National Program on High Technology Development, and the EU FP6 INCO-MPC2 project CEDROME (INCOCT-2005-015468).

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070, Wuhan, China

    Yujie Fang, Jun You, Kabin Xie, Weibo Xie & Lizhong Xiong

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  1. Yujie Fang
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  2. Jun You
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  5. Lizhong Xiong
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Correspondence to Lizhong Xiong.

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Communicated by K. Shirasu.

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Fang, Y., You, J., Xie, K. et al. Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Genet Genomics 280, 547–563 (2008). https://doi.org/10.1007/s00438-008-0386-6

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  • DOI: https://doi.org/10.1007/s00438-008-0386-6

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