The developmental dynamics of the maize leaf transcriptome

Pinghua Li, Boyce Thompson Institute for Plant Research
Lalit Ponnala, Cornell University
Neeru Gandotra, Yale University
Lin Wang, Boyce Thompson Institute for Plant Research
Yaqing Si, Iowa State University
S. Lori Tausta, Yale University
Tesfamichael H. Kebrom, Boyce Thompson Institute for Plant Research
Nicholas Provart, University of Toronto
Rohan Patel, University of Toronto
Christopher R. Myers, Cornell University
Edwin J. Reidel, Cornell University
Robert Turgeon, Cornell University
Peng Liu, Iowa State University
Qi Sun, Cornell University
Timothy Nelson, Yale University
Thomas P. Brutnell, Boyce Thompson Institute for Plant Research


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 C 4 photosynthetic development toward the tip. This dataset will serve as the foundation for a systems biology approach to the understanding of photosynthetic development. © 2010 Nature America, Inc. All rights reserved.