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Identification and characterization of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in maize

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Abstract

Eukaryotic gene expression is regulated at least by two processes, RNA interference at the post-transcriptional level and chromatin modification at the transcriptional level. Distinct small RNAs (approximately 21–24 nucleotides; sRNAs) were demonstrated to play vital roles in facilitating gene silencing. In plants, the generation of these sRNAs mainly depends on some proteins encoded by respective Dicer-like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerases (RDR) gene families. Here, we analyzed the DCL, AGO and RDR gene families in maize, including gene structure, phylogenetic relationships, protein conserved motifs and genomic localization among gene family members. A total of 5 Zmdcl, 18 Zmago and 5 Zmrdr genes were identified in maize. Phylogenetic analyses clustered each of these genes families into four subfamilies. In addition, gene chromosomal localization revealed that five pairs of Zmago genes resulted from tandem or segmental duplication, respectively. EST expression data mining revealed that these newly identified genes had temporal and spatial expression pattern. Furthermore, the transcripts of these genes were detected in the leaves by two different abiotic stress treatments using semi-quantitative RT-PCR. The data demonstrated that these genes exhibited different expression levels in stress treatments. The results of this study provided basic genomic information for these gene families and insights into the probable roles of these genes in plant growth and development. This will further provide a solid foundation for future functional genomics studies of Dicer-like, Argonaute and RDR gene families in maize.

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Acknowledgments

This study was supported by grants from the National High-Tech Research and Development Program (863 Program) (No. 2008AA10Z408) and the National Natural Science Foundation of China (No. 11075001 and No. 30771309). We wish to thank the two anonymous reviewers for their helpful comments on this manuscript. We also acknowledge Professor Beijiu Cheng for critical reading of the manuscript.

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Correspondence to Beijiu Cheng.

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Communicated by B. Li.

Y. Qian and Y. Cheng contributed equally to this work.

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Qian, Y., Cheng, Y., Cheng, X. et al. Identification and characterization of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in maize. Plant Cell Rep 30, 1347–1363 (2011). https://doi.org/10.1007/s00299-011-1046-6

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  • DOI: https://doi.org/10.1007/s00299-011-1046-6

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