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MicroRNA profiles and their control of male gametophyte development in rice

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Abstract

Plant microRNAs (miRNAs) act as negative regulators of gene expression by slicing target transcripts or inhibiting translation. A number of miRNAs play important roles in development. In order to investigate the potential function of miRNAs during male gametogenesis in rice, we obtained both gene and small RNA expression profiles by combining microarray and high-throughput sequencing technologies. From the microarray datasets, 2,925 male gametophyte-specific genes were identified, including 107 transcription factors and three significant Argonaute genes (AGO12, AGO13, and AGO17). From the sRNA-Seq datasets, 104 unique miRNAs (miRus) were identified, including 47 known miRus and 57 novel miRus; interestingly, most of the new miRus are pollen-specific and not conserved among species. Furthermore, an interactive network of miRNA-target was constructed based on the two datasets. By employing enrichment analysis, the miRNA-regulated targets were found to be involved in both the up and down pathways, but predominantly in the down pathways, including 37 GO biological processes and 32 KEGG pathways. These findings indicate that miRNAs play a broad regulatory role during male gametophyte development in rice.

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Abbreviations

miRNA:

MicroRNA

miRus:

Unique miRNAs

AGO:

Argonaute

TGS:

Transcriptional gene silencing

PTGS:

Posttranscriptional gene silencing

UMP/Pa:

Uninucleate microspores

BCP/Pb:

Bicellular pollen

TCP/Pc:

Tricellular pollen

RDR:

RNA-dependent RNA polymerases

DCL:

Dicer-like protein

siRNA:

Small interfering RNA

GO:

Gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

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Acknowledgments

This paper is supported by National Natural Science Foundation of China (No. 31070276).

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  1. Key Lab of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, China

    Hua Peng, Jun Chun, Tao-bo Ai, Yong-ao Tong, Rong Zhang, Ming-ming Zhao, Fang Chen & Sheng-hua Wang

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  1. Hua Peng
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  2. Jun Chun
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  3. Tao-bo Ai
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Correspondence to Sheng-hua Wang.

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Hua Peng, Jun Chun, Tao-bo Ai, and Yong-ao Tong contributed equally to this work.

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Peng, H., Chun, J., Ai, Tb. et al. MicroRNA profiles and their control of male gametophyte development in rice. Plant Mol Biol 80, 85–102 (2012). https://doi.org/10.1007/s11103-012-9898-x

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