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Comparative Analysis of Dof Transcription Factor Family in Maize

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Abstract

Deoxyribonucleic acid binding with one finger (Dof) family, a kind of plant-specific transcription factor family, is involved in a variety of biological processes including signal transduction, morphogenesis, and environmental stress responses. In the present study, 46 putative Dof genes were identified from maize (Zea mays subsp. mays). The predicted ZmDof genes were non-randomly distributed within their chromosomes, and segmental duplication seemed to be the prevalent mechanism for their expansion. Most of these genes lacked introns and some only possessed one intron. Here, we classified 140 Dof proteins from Arabidopsis, rice, sorghum, and maize into seven groups by means of phylogenetic analysis. In addition, many cis-elements responding to light, endosperm specific gene expression, hormone, meristem specific expression, and stress were also found in the 1,000 bps upstream sequences of promoter regions. Selection analysis also identified some significant site-specific constraints acted on most Dof paralogs. Expression profiles based on microarray data provided insights into the functional divergence of different tissues. Results by quantitative reverse transcription polymerase chain reaction analysis indicated that some ZmDofs responded to some abiotic stresses. Taken together, our study will provide some useful information for biological evolution and functional characterization of the maize Dof genes.

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Abbreviations

Dof:

DNA binding with one finger

NJ:

neighbor joining

MEME:

multiple EM for motif elicitation

TSS:

transcription start site

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Acknowledgments

This project is supported by grants from the National Science Foundation of China (No. 31100923), the National Science Foundation of Jiangsu Province (BK2011467), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and Jiangsu University “Youth Backbone Teacher Training Project” (2012–2016) to JC.

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  1. Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China

    Yuzhu Chen & Jun Cao

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  1. Yuzhu Chen
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  2. Jun Cao
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Correspondence to Jun Cao.

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Data S1

Alignment data used in this study. (TXT 129 kb)

Fig. S1

Neighbor-joining phylogenetic tree of Dof proteins in Arabidopsis, rice, sorghum, and maize. (PDF 61 kb)

Fig. S2

Distribution of the predicted positive selection sites on the secondary structure of Dof protein in group VII. The predicted positive selection sites are indicated with arrows and red bold letters. (PDF 56 kb)

Table S1

Distribution of five class’s cis-elements in the promoter regions of the 46 ZmDof genes. (XLS 39 kb)

Table S2

Primers used in this study. (DOC 31 kb)

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Chen, Y., Cao, J. Comparative Analysis of Dof Transcription Factor Family in Maize. Plant Mol Biol Rep 33, 1245–1258 (2015). https://doi.org/10.1007/s11105-014-0835-9

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