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The developmental dynamics of the maize leaf transcriptome

Nature Genetics volume 42, pages 1060–1067 (2010)Cite this article

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Abstract

We have analyzed the maize leaf transcriptome using Illumina sequencing. We mapped more than 120 million reads to define gene structure and alternative splicing events and to quantify transcript abundance along a leaf developmental gradient and in mature bundle sheath and mesophyll cells. We detected differential mRNA processing events for most maize genes. We found that 64% and 21% of genes were differentially expressed along the developmental gradient and between bundle sheath and mesophyll cells, respectively. We implemented Gbrowse, an electronic fluorescent pictograph browser, and created a two-cell biochemical pathway viewer to visualize datasets. Cluster analysis of the data revealed a dynamic transcriptome, with transcripts for primary cell wall and basic cellular metabolism at the leaf base transitioning to transcripts for secondary cell wall biosynthesis and C4 photosynthetic development toward the tip. This dataset will serve as the foundation for a systems biology approach to the understanding of photosynthetic development.

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Figure 1: Defining developmental and physiological characters along a B73 seedling leaf.
Figure 2: RNA-seq analysis of B73 leaf transcriptome.
Figure 3: Alternative splicing of GRMZM2G147687.
Figure 4: Dynamic progression of leaf transcriptome.
Figure 5: Dynamics of transcription factor accumulation profiles.
Figure 6: eFP browser view of expression changes over leaf development.

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Acknowledgements

This work was supported by grants from the National Science Foundation (IOS-0701736 to R.T., P.L., Q.S., T.N. and T.P.B.). C.R.M. acknowledges support from a grant to the International Rice Research Institute from the Bill and Melinda Gates Foundation and T.P.B. acknowledges support from the iPlant Collaborative for development of the eFP browser.

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Author notes

  1. Pinghua Li and Lalit Ponnala: These authors contributed equally to this work.

Authors and Affiliations

  1. Boyce Thompson Institute, Cornell University, Ithaca, New York, USA

    Pinghua Li, Lin Wang, Tesfamichael H Kebrom & Thomas P Brutnell

  2. Computational Biology Service Unit, Cornell University, Ithaca, New York, USA

    Lalit Ponnala, Christopher R Myers & Qi Sun

  3. Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA

    Neeru Gandotra, S Lori Tausta & Timothy Nelson

  4. Department of Statistics and Statistical Laboratory, Iowa State University, Ames, Iowa, USA

    Yaqing Si & Peng Liu

  5. Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada

    Nicholas Provart & Rohan Patel

  6. Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada

    Nicholas Provart & Rohan Patel

  7. Department of Plant Biology, Cornell University, Ithaca, New York, USA

    Edwin J Reidel, Robert Turgeon & Thomas P Brutnell

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Contributions

T.P.B., T.N. and R.T. designed the experiments. P. Li, L.P., N.G., E.J.R. and T.H.K. optimized and performed the experiments. Q.S., L.P., P. Liu, P. Li, L.W., Y.S., R.P., T.P.B., N.P., N.G., S.L.T. and C.R.M. performed data analysis. P. Li, L.P., T.N., N.G., S.L.T. and T.P.B. wrote the manuscript.

Corresponding author

Correspondence to Thomas P Brutnell.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Table 1, Supplementary Figures 1–13 and Supplementary Note (PDF 8744 kb)

Supplementary Table 2

Verification of RNA-seq results by qRT-PCR. (XLS 35 kb)

Supplementary Table 3

List of the K-means clusters. (XLS 4141 kb)

Supplementary Table 4

List of genes exhibiting differential expression between bundle sheath and mesophyll cells. (XLS 1078 kb)

Supplementary Table 5

Correlation between RNA-seq and proteomics data in the bundle sheath and mesophyll cells. (XLS 268 kb)

Supplementary Table 6

List of C4 genes and their expression changes along developmental zones. (XLS 41 kb)

Supplementary Table 7

List of differentially expressed transcription factors in the developmental zones and bundle sheath and mesophyll cells. (XLS 725 kb)

Supplemenatry Table 8

List of gene ID?s and RPKM estimates for Supplementary Figs. 8-12. (XLS 52 kb)

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Li, P., Ponnala, L., Gandotra, N. et al. The developmental dynamics of the maize leaf transcriptome. Nat Genet 42, 1060–1067 (2010). https://doi.org/10.1038/ng.703

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