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Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice

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Abstract

Most plant cells retain the capacity to differentiate into all the other cell and organ types that constitute a plant. However, genome-wide transcriptional activities underlying the process of cell differentiation are poorly understood, especially in monocot plants. Here we used a rice (Oryza sativa) cell culture system to generate somatic embryos, which were further induced into shoots and roots. The global transcriptional reorganization during the development of somatic embryos, shoots, and roots from cultured cells was studied using a rice whole genome microarray and verified by RNA blotting analysis of representative genes. Overall, only 1–3% of expressed genes were differentially regulated during each organogenesis process at the examined time point. Also metabolic pathways were minimally regulated. Thus the genes that dictating organ formation should be relatively small in number. Comparison of these three transcriptomes revealed little overlap during these three organogenesis processes. These results indicate that each organogenesis involves specific reorganization of genome expression.

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Acknowledgments

We thank Valerie J. Karplus for reading and commenting on this manuscript, and the Yale DNA microarray laboratory of the Keck Biological Resource Center for the printing of the rice 70-mer oligo microarray slides used in this study (http://info.med.yale.edu/wmkeck/dna_arrays.htm). This research was supported by grants from National Institutes of Health (GM-47850) and National Science Foundation Plant Genome Program (DBI-0325821) to XWD, and by the Ministry of Science and Technology of China special rice functional genomics program. Kun He is supported by Monsanto Fellowship of PYC center, the National Key Basic Research Program of China (2003CB715900), and the National Natural Science Foundation of China (30170232).

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Authors and Affiliations

  1. Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, 100871, China

    Ning Su, Kun He, Sulan Bai & Xing Wang Deng

  2. Department of Molecular, Cellular, and Development Biology, Yale University, Osborn Memorial Laboratories, Room 352A, 165 Prospect Street, P.O. Box 208104, New Haven, CT , 06520-8104, USA

    Ning Su, Kun He, Yuling Jiao, Junli Zhou, Lei Li, Sulan Bai, Xueyong Li & Xing Wang Deng

  3. Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing , 101300, China

    Chen Chen

  4. James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou , 310008, China

    Chen Chen

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  1. Ning Su
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  2. Kun He
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  3. Yuling Jiao
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Correspondence to Xing Wang Deng.

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Ning Su, Kun He, and Yuling Jiao have contributed equally to this work

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Su, N., He, K., Jiao, Y. et al. Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice. Plant Mol Biol 63, 337–349 (2007). https://doi.org/10.1007/s11103-006-9092-0

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