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Plant Physiology 133:1702-1716 (2003)
© 2003 American Society of Plant Biologists

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BIOINFORMATICS

Photosynthetic Acclimation Is Reflected in Specific Patterns of Gene Expression in Drought-Stressed Loblolly Pine1,[w]

Jonathan I. Watkinson, Allan A. Sioson, Cecilia Vasquez-Robinet, Maulik Shukla, Deept Kumar, Margaret Ellis, Lenwood S. Heath, Naren Ramakrishnan, Boris Chevone, Layne T. Watson, Leonel van Zyl, Ulrika Egertsdotter, Ronald R. Sederoff and Ruth Grene*

Departments of Plant Pathology, Physiology, and Weed Science (J.I.W., C.V.-R., B.C., R.G.) and Computer Science (A.A.S., M.S., D.K., M.E., L.S.H., N.R., L.T.W.), Virginia Tech, Blacksburg, Virginia 24061; Forest Biotechnology Group, Department of Forestry, North Carolina State University, Raleigh, North Carolina 27695 (L.v.Z., R.R.S.); and Institute of Paper Science and Technology, 500 10th Street, N.W., Atlanta, Georgia 30318 (U.E.)

Because the product of a single gene can influence many aspects of plant growth and development, it is necessary to understand how gene products act in concert and upon each other to effect adaptive changes to stressful conditions. We conducted experiments to improve our understanding of the responses of loblolly pine (Pinus taeda) to drought stress. Water was withheld from rooted plantlets of to a measured water potential of -1 MPa for mild stress and -1.5 MPa for severe stress. Net photosynthesis was measured for each level of stress. RNA was isolated from needles and used in hybridizations against a microarray consisting of 2,173 cDNA clones from five pine expressed sequence tag libraries. Gene expression was estimated using a two-stage mixed linear model. Subsequently, data mining via inductive logic programming identified rules (relationships) among gene expression, treatments, and functional categories. Changes in RNA transcript profiles of loblolly pine due to drought stress were correlated with physiological data reflecting photosynthetic acclimation to mild stress or photosynthetic failure during severe stress. Analysis of transcript profiles indicated that there are distinct patterns of expression related to the two levels of stress. Genes encoding heat shock proteins, late embryogenic-abundant proteins, enzymes from the aromatic acid and flavonoid biosynthetic pathways, and from carbon metabolism showed distinctive responses associated with acclimation. Five genes shown to have different transcript levels in response to either mild or severe stress were chosen for further analysis using real-time polymerase chain reaction. The real-time polymerase chain reaction results were in good agreement with those obtained on microarrays.

http://www.plantphysiol.org/cgi/doi/10.1104/pp.103.026914.

1 This work was supported in part by the National Science Foundation (grant nos. EIA-0103660 [Next Generation Software] and IBN-0219332 [Information Technology Research] to L.S.H, N.R., L.T.W., R.G., and B.C.).

[w] The online version of this article contains Web-only data.

* Corresponding author; e-mail grene{at}vt.edu; fax 540-231-5755.

Received May 17, 2003; returned for revision July 7, 2003; accepted August 28, 2003.




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