Plant Molecular Biology

, Volume 63, Issue 3, pp 337–349 | Cite as

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

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


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.


Rice Oligo chip Development Organogenesis Transcriptome 



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 ( 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).

Supplementary material


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Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Ning Su
    • 1
    • 2
  • Kun He
    • 1
    • 2
  • Yuling Jiao
    • 2
  • Chen Chen
    • 3
    • 4
  • Junli Zhou
    • 2
  • Lei Li
    • 2
  • Sulan Bai
    • 1
    • 2
  • Xueyong Li
    • 2
  • Xing Wang Deng
    • 1
    • 2
  1. 1.Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life SciencesPeking UniversityBeijingChina
  2. 2.Department of Molecular, Cellular, and Development BiologyYale UniversityNew HavenUSA
  3. 3.Beijing Institute of Genomics of Chinese Academy of SciencesBeijing Genomics InstituteBeijing China
  4. 4.James D. Watson Institute of Genome SciencesZhejiang UniversityHangzhou China

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