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Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage

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Abstract

Microspore production using endogenous developmental programs has not been well studied. The main limitation is the difficulty in identifying genes preferentially expressed in pollen grains at early stages. To overcome this limitation, we collected transcriptome data from anthers and microspore/pollen and performed meta-expression analysis. Subsequently, we identified 410 genes showing preferential expression patterns in early developing pollen samples of both japonica and indica cultivars. The expression patterns of these genes are distinguishable from genes showing pollen mother cell or tapetum-preferred expression patterns. Gene Ontology enrichment and MapMan analyses indicated that microspores in rice are closely linked with protein degradation, nucleotide metabolism, and DNA biosynthesis and regulation, while the pollen mother cell or tapetum are strongly associated with cell wall metabolism, lipid metabolism, secondary metabolism, and RNA biosynthesis and regulation. We also generated transgenic lines under the control of the promoters of eight microspore-preferred genes and confirmed the preferred expression patterns in plants using the GUS reporting system. Furthermore, cis-regulatory element analysis revealed that pollen specific elements such as POLLEN1LELAT52, and 5659BOXLELAT5659 were commonly identified in the promoter regions of eight rice genes with more frequency than estimation. Our study will provide new sights on early pollen development in rice, a model crop plant.

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Acknowledgments

We appreciate the support of Dr. Pamela Ronald and Dr. Peijian Cao in developing the meta-expression profiling database for rice. This work was supported by the Next-Generation BioGreen21 Program of the Rural Development Administration in the Republic of Korea (PJ01100401 to KHJ and PJ01194201 to SKP), and by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education, Science and Technology (NRF-2013R1A1A2006040 to KHJ).

Author contributions

T.D.N., S.M., S.K.P., G.A., M.S.S., J.T.S., and K.H.J. designed the research. T.D.N., S.M., A.K.N.C., V.N.T.N., Y.S.G., and S.A.O. performed experiments. T.D.N. and S.M. analyzed data. T.D.N., S.M., S.A.O., S.K.P., and K.H.J. wrote the manuscript.

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    Authors and Affiliations

    1. School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea

      Tien Dung Nguyen, Jong Tae Song, Sung Aeong Oh & Soon Ki Park

    2. Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea

      Sunok Moon, Van Ngoc Tuyet Nguyen, Yunsil Gho, Anil Kumar Nalini Chandran, Gynheung An & Ki-Hong Jung

    3. Department of Molecular Biology, Sejong University, Seoul, 143-747, Republic of Korea

      Moon-Soo Soh

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    2. Sunok Moon
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    3. Van Ngoc Tuyet Nguyen
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    5. Anil Kumar Nalini Chandran
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    7. Jong Tae Song
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    8. Gynheung An
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    9. Sung Aeong Oh
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    10. Soon Ki Park
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    11. Ki-Hong Jung
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    Corresponding authors

    Correspondence to Soon Ki Park or Ki-Hong Jung.

    Additional information

    Tien Dung Nguyen and Sunok Moon have contributed equally to this work.

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    Nguyen, T.D., Moon, S., Nguyen, V.N.T. et al. Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage. Plant Mol Biol 92, 71–88 (2016). https://doi.org/10.1007/s11103-016-0496-1

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    • DOI: https://doi.org/10.1007/s11103-016-0496-1

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