Plant Physiology Preview
Published on June 17, 2005; 10.1104/pp.104.057638
Received January 26, 2005
Returned for revision March 15, 2005
Accepted March 21, 2005
The Maize Root Transcriptome by Serial Analysis of Gene Expression
V. Poroyko , L.G. Hejlek , W.G. Spollen , G.K. Springer , H.T. Nguyen , R.E. Sharp , and H.J. Bohnert *
Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
Division of Plant Sciences, Plant Sciences Unit, University of Missouri, Columbia, Missouri 65211-7145
Department of Computer Science, University of Missouri, Columbia, Missouri 65211-7145
Department of Plant Biology, University of Illinois, Urbana, Illinois 61801; Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
* Corresponding author; email: bohnerth{at}life.uiuc.edu.
Serial Analysis of Gene Expression was used to define number and relative abundance of transcripts in the root tip of well-watered maize seedlings (Zea mays cv FR697). In total, 161,320 tags represented a minimum of 14,850 genes, based on at least two tags detected per transcript. The root transcriptome has been sampled to an estimated copy number of approximately five transcripts per cell. An extrapolation from the data and testing of single-tag identifiers by reverse transcription-PCR indicated that the maize root transcriptome should amount to at least 22,000 expressed genes. Frequency ranged from low copy number (2-5, 68.8%) to highly abundant transcripts (100 1,200; 1%). Quantitative reverse transcription-PCR for selected transcripts indicated high correlation with tag frequency. Computational analysis compared this set with known maize transcripts and other root transcriptome models. Among the 14,850 tags, 7,010 (47%) were found for which no maize cDNA or gene model existed. Comparing the maize root transcriptome with that in other plants indicated that highly expressed transcripts differed substantially; less than 5% of the most abundant transcripts were shared between maize and Arabidopsis (Arabidopsis thaliana). Transcript categories highlight functions of the maize root tip. Significant variation in abundance characterizes transcripts derived from isoforms of individual enzymes in biochemical pathways.
This article has been cited by other articles:
|
|
|
|
 
R. Tuberosa, S. Salvi, S. Giuliani, M. C. Sanguineti, M. Bellotti, S. Conti, and P. Landi
Genome-wide Approaches to Investigate and Improve Maize Response to Drought
Crop Sci.,
December 18, 2007;
47(Supplement_3):
S-120 - S-141.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Gowda, R.-C. Venu, H. Li, C. Jantasuriyarat, S. Chen, M. Bellizzi, V. Pampanwar, H. Kim, R. A. Dean, E. Stahlberg, et al.
Magnaporthe grisea Infection Triggers RNA Variation and Antisense Transcript Expression in Rice
Plant Physiology,
May 1, 2007;
144(1):
524 - 533.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
V Poroyko, W. Spollen, L. Hejlek, A. Hernandez, M. LeNoble, G Davis, H. Nguyen, G. Springer, R. Sharp, and H. Bohnert
Comparing regional transcript profiles from maize primary roots under well-watered and low water potential conditions
J. Exp. Bot.,
January 1, 2007;
58(2):
279 - 289.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Guillaumie, H. San-Clemente, C. Deswarte, Y. Martinez, C. Lapierre, A. Murigneux, Y. Barriere, M. Pichon, and D. Goffner
MAIZEWALL. Database and Developmental Gene Expression Profiling of Cell Wall Biosynthesis and Assembly in Maize
Plant Physiology,
January 1, 2007;
143(1):
339 - 363.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
L. Xiong, R.-G. Wang, G. Mao, and J. M. Koczan
Identification of Drought Tolerance Determinants by Genetic Analysis of Root Response to Drought Stress and Abscisic Acid
Plant Physiology,
November 1, 2006;
142(3):
1065 - 1074.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. M. Brady, T. A. Long, and P. N. Benfey
Unraveling the dynamic transcriptome.
PLANT CELL,
September 1, 2006;
18(9):
2101 - 2111.
[Full Text]
[PDF]
|
|
|
|
|
