biologia plantarum

International journal on Plant Life established by Bohumil Němec in 1959

Biologia plantarum 57:255-261, 2013 | DOI: 10.1007/s10535-012-0270-4

Microarray-based screening of the microRNAs associated with caryopsis development in Oryza sativa

H. Liu1, D. Shen1, S. Jia1, W. Li1, J. Li1, J. Liu1, S. Han1,*, Y. Wang1,*
1 Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, P.R. China

Plant microRNAs modulate diverse developmental processes by regulating expression of their target genes. To explore potential miRNA-guided gene regulation in developing rice (Oryza sativa L.) caryopses, a miRNA microarray was used to identify miRNAs present at the different developmental stages. We found that 27 miRNAs, of which 16 were conserved miRNAs, were present in developing caryopses. High expression levels were detected for miR159, miR167, and miR530 at the morphogenesis stage and for miR169, miR435, and miR528 at the stage of accumulation of metabolites. Next, 26 target genes were predicted for seven of the detected miRNAs and the expression profiles of these miRNAs and their corresponding target genes were examined in developing caryopses. Our results suggest that the miRNAs and their target genes examined at the two distinct stages could contribute to the developmental progress of rice caryopses in concert with phytohormone signalling.

Keywords: nutrient storage; morphogenesis; rice
Subjects: microarray; microRNA; caryopsis development; rice; nutrient storage; morphogenesis; gene epression

Received: December 17, 2011; Accepted: July 3, 2012; Published: June 1, 2013  Show citation

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Liu, H., Shen, D., Jia, S., Li, W., Li, J., Liu, J., Han, S., & Wang, Y. (2013). Microarray-based screening of the microRNAs associated with caryopsis development in Oryza sativa. Biologia plantarum, 57(2), 255-261. doi: 10.1007/s10535-012-0270-4
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    References

    1. Adai, A., Johnson, C., Mlotshwa, S., Archer-Evans, S., Manocha, V., Vance, V., Sundaresan, V.: Computational prediction of miRNAs in Arabidopsis thaliana. - Genome Res. 15: 78-91, 2005. Go to original source...
    2. Axtell, M.J., Bowman, J.L.: Evolution of plant microRNAs and their targets. - Trends Plant Sci. 13: 343-349, 2008. Go to original source...
    3. Aya, K., Ueguchi-Tanaka, M., Kondo, M., Hamada, K., Yano, K., Nishimura, M., Matsuoka, M.: Gibberellin modulates anther development in rice via the transcriptional regulation of GAMYB. - Plant Cell 21: 1453-1472, 2009. Go to original source...
    4. Barroco, R.M., Peres, A., Droual, A.M., De Veylder, L., Nguyen, L.S.L., De Wolf, J., Mironov, V., Peerbolte, R., Beemster, G.T.S., Inze, D., Broekaert, W.F., Frankard, V.: The cyclin-dependent kinase inhibitor orysa;KRP1 plays an important role in seed development of rice. - Plant Physiol. 142: 1053-1064, 2006. Go to original source...
    5. Cartolano, M., Castillo, R., Efremova, N., Kuckenberg, M., Zethof, J., Gerats, T., Schwarz-Sommer, Z., Vandenbussche, M.: A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity. - Nat. Genet. 39: 901-905, 2007. Go to original source...
    6. Chen, C.F., Ridzon, D.A., Broomer, A.J., Zhou, Z.H., Lee, D.H., Nguyen, J.T., Barbisin, M., Xu, N.L., Mahuvakar, V.R., Andersen, M.R., Lao, K.Q., Livak, K.J., Guegler, K.J.: Real-time quantification of microRNAs by stem-loop RT-PCR. - Nucl. Acids Res. 33: e179, 2005. Go to original source...
    7. Chuck, G., Candela, H., Hake, S.: Big impacts by small RNAs in plant development. - Curr. Opin. Plant Biol. 12: 81-86, 2009. Go to original source...
    8. Gutierrez, L., Van Wuytswinkel, O., Castelain, M., Bellini, C.: Combined networks regulating seed maturation. - Trends Plant Sci. 12: 294-300, 2007. Go to original source...
    9. Hoshikawa, K.: Anthesis, fertilization and development of caryopsis. - In: Matsuo, T., Hoshikawa, K. (ed.): Science of the Rice Plant. Vol. 1: Morphology. Pp. 339-376. Food and Agriculture Policy Research Center, Tokyo 1993.
    10. Huang, S.Q., Peng, J., Qiu, C.X., Yang, Z.M.: Heavy metalregulated new microRNAs from rice. - J. Inorg. Biochem. 103: 282-287, 2009. Go to original source...
    11. Ishimaru, T., Hirose, T., Matsuda, T., Goto, A., Takahashi, K., Sasaki, H., Terao, T., Ishii, R., Ohsugi, R., Yamagishi, T.: Expression patterns of genes encoding carbohydratemetabolizing enzymes and their relationship to grain filling in rice (Oryza sativa L.): comparison of caryopses located at different positions in a panicle. - Plant Cell Physiol. 46: 620-628, 2005. Go to original source...
    12. Itoh, J., Nonomura, K., Ikeda, K., Yamaki, S., Inukai, Y., Yamagishi, H., Kitano, H., Nagato, Y.: Rice plant development: from zygote to spikelet. - Plant Cell Physiol. 46: 23-47, 2005. Go to original source...
    13. Jian, X., Zhang, L., Li, G., Wang, X., Cao, X., Fang, X., Chen, F.: Identification of novel stress-regulated microRNAs from Oryza sativa L. - Genomics 95: 47-55, 2010. Go to original source...
    14. Jones-Rhoades, M.W., Bartel, D.P.: Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. - Mol. Cell 14: 787-799, 2004. Go to original source...
    15. Jones-Rhoades, M.W., Bartel, D.P., Bartel, B.: MicroRNAs and their regulatory roles in plants. - Annu. Rev. Plant Biol. 57: 19-53, 2006. Go to original source...
    16. Kaneko, M., Inukai, Y., Ueguchi-Tanaka, M., Itoh, H., Izawa, T., Kobayashi, Y., Hattori, T., Miyao, A., Hirochika, H., Ashikari, M., Matsuoka, M.: Loss-of-function mutations of the rice GAMYB gene impair alpha-amylase expression in aleurone and flower development. - Plant Cell 16: 33-44, 2004. Go to original source...
    17. Li, T., Li, H., Zhang, Y.X., Liu, J.Y.: Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). - Nucl. Acids Res. 39: 2821-2833, 2010. Go to original source...
    18. Liu, H.H., Tian, X., Li, Y.J., Wu, C.A., Zheng, C.C.: Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. - RNA-Publ. RNA Soc. 14: 836-843, 2008. Go to original source...
    19. Liu, Q., Zhang, Y.C., Wang, C.Y., Luo, Y.C., Huang, Q.J., Chen, S.Y., Zhou, H., Qu, L.H., Chen, Y.Q.: Expression analysis of phytohormone-regulated microRNAs in rice, implying their regulation roles in plant hormone signaling. - FEBS Lett. 583: 723-728, 2009. Go to original source...
    20. Liu, Z.H., Bao, W.J., Liang, W.Q., Yin, J.Y., Zhang, D.B.: Identification of gamyb-4 and analysis of the regulatory role of GAMYB in rice anther development. - J. Integr. Plant Biol. 52: 670-678, 2010. Go to original source...
    21. Luo, Y.C., Zhou, H., Li, Y., Chen, J.Y., Yang, J.H., Chen, Y.Q., Qu, L.H.: Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development. - FEBS Lett. 580: 5111-5116, 2006. Go to original source...
    22. Nikovics, K., Blein, T., Peaucelle, A., Ishida, T., Morin, H., Aida, M., Laufs, P.: The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. - Plant Cell 18: 2929-2945, 2006. Go to original source...
    23. Olsen, O.A.: Nuclear endosperm development in cereals and Arabidopsis thaliana. - Plant Cell 16: S214-S227, 2004. Go to original source...
    24. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., Bartel, D.P.: MicroRNAs in plants. - Genes Dev. 16: 1616-1626, 2002. Go to original source...
    25. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., Bartel, D.P.: Prediction of plant microRNA targets. - Cell 110: 513-520, 2002. Go to original source...
    26. She, K.C., Kusano, H., Koizumi, K., Yamakawa, H., Hakata, M., Imamura, T., Fukuda, M., Naito, N., Tsurumaki, Y., Yaeshima, M., Tsuge, T., Matsumoto, K., Kudoh, M., Itoh, E., Kikuchi, S., Kishimoto, N., Yazaki, J., Ando, T., Yano, M., Aoyama, T., Sasaki, T., Satoh, H., Shimada, H.: A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. - Plant Cell 22: 3280-3294, 2010. Go to original source...
    27. Song, X.J., Huang, W., Shi, M., Zhu, M.Z., Lin, H.X.: A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. - Nat. Genet. 39: 623-630, 2007. Go to original source...
    28. Sunkar, R., Girke, T., Jain, P.K., Zhu, J.K.: Cloning and characterization of MicroRNAs from rice. - Plant Cell 17: 1397-1411, 2005. Go to original source...
    29. Sunkar, R., Zhou, X.F., Zheng, Y., Zhang, W.X., Zhu, J.K.: Identification of novel and candidate miRNAs in rice by high throughput sequencing. - BMC Plant Biol. 8: 25, 2008. Go to original source...
    30. Sunkar, R., Zhu, J.K.: Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. - Plant Cell 16: 2001-2019, 2004. Go to original source...
    31. Thomson, J.M., Parker, J., Perou, C.M., Hammond, S.M.: A custom microarray platform for analysis of microRNA gene expression. - Natur. Methods 1: 47-53, 2004. Go to original source...
    32. Tsuji, H., Aya, K., Ueguchi-Tanaka, M., Shimada, Y., Nakazono, M., Watanabe, R., Nishizawa, N.K., Gomi, K., Shimada, A., Kitano, H., Ashikari, M., Matsuoka, M.: GAMYB controls different sets of genes and is differentially regulated by microRNA in aleurone cells and anthers. - Plant J. 47: 427-444, 2006. Go to original source...
    33. Tusher, V.G., Tibshirani, R., Chu, G.: Significance analysis of microarrays applied to the ionizing radiation response. - Proc. nat. Acad. Sci. USA 98: 5116-5121, 2001. Go to original source...
    34. Wang, D.K., Pei, K.M., Fu, Y.P., Sun, Z.X., Li, S.J., Liu, H.Q., Tang, K., Han, B., Tao, Y.Z.: Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). - Gene 394: 13-24, 2007. Go to original source...
    35. Wang, E., Wang, J., Zhu, X.D., Hao, W., Wang, L.Y., Li, Q., Zhang, L.X., He, W., Lu, B.R., Lin, H.X., Ma, H., Zhang, G.Q., He, Z.H.: Control of rice grain-filling and yield by a gene with a potential signature of domestication. - Nat. Genet. 40: 1370-1374, 2008. Go to original source...
    36. Wang, J.F., Zhou, H., Chen, Y.Q., Luo, Q.J., Qu, L.H.: Identification of 20 microRNAs from Oryza sativa. - Nucl. Acids Res. 32: 1688-1695, 2004. Go to original source...
    37. Weng, J.F., Gu, S.H., Wan, X.Y., Gao, H., Guo, T., Su, N., Lei, C.L., Zhang, X., Cheng, Z.J., Guo, X.P., Wang, J.L., Jiang, L., Zhai, H.Q., Wan, J.M.: Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. - Cell Res. 18: 1199-1209, 2008. Go to original source...
    38. Xue, L.J., Zhang, J.J., Xue, H.W.: Characterization and expression profiles of miRNAs in rice seeds. - Nucl. Acids Res. 37: 916-930, 2009. Go to original source...
    39. Yang, J.H., Han, S.J., Yoon, E.K., Lee, W.S.: Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells. - Nucl. Acids Res. 34: 1892-1899, 2006. Go to original source...
    40. Yang, T.W., Xue, L.G., An, L.Z.: Functional diversity of miRNA in plants. - Plant Sci. 172: 423-432, 2007. Go to original source...
    41. Young, T.E., Gallie, D.R., DeMason, D.A.: Ethylene-mediated programmed cell death during maize endosperm development of wild-type and shrunken2 genotypes. - Plant Physiol. 115: 737-751, 1997. Go to original source...
    42. Zhang, Y.J.: miRU: an automated plant miRNA target prediction server. - Nucl. Acids Res. 33: W701-W704, 2005. Go to original source...
    43. Zhao, B.T., Liang, R.Q., Ge, L.F., Li, W., Xiao, H.S., Lin, H.X., Ruan, K.C., Jin, Y.X.: Identification of drought-induced microRNAs in rice. - Biochem. biophys. Res. Commun. 354: 585-590, 2007. Go to original source...
    44. Zhao, B.T., Ge, L.F., Liang, R.Q., Li, W., Ruan, K.C., Lin, H.X., Jin, Y.X.: Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. - BMC mol. Biol. 10: 29, 2009. Go to original source...
    45. Zhou, X.J., Li, J., Cheng, W., Liu, H., Li, M.M., Zhang, Y.A., Li, W.B., Han, S.C., Wang, Y.D.: Gene structure analysis of rice ADP-ribosylation factors (OsARFs) and their mRNA expression in developing rice plants. - Plant mol. Biol. Rep. 28: 692-703, 2010. Go to original source...
    46. Zhu, Q.H., Spriggs, A., Matthew, L., Fan, L.J., Kennedy, G., Gubler, F., Helliwell, C.: A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. - Genome Res. 18: 1456-1465, 2008. Go to original source...

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