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Title: IDENTIFICATION OF COLD ACCLIMATION RESPONSIVE RHODENDRON GENES FOR LIPID METABOLISM, MEMBRANE TRANSPORT, AND LIGNIN BIOSYNTHESIS: IMPORTANCE OF MODERATELY ABUNDANT ESTS IN GENOMIC STUDIES

Author
item WEI, HUI - IOWA STATE UNIV
item DHANARAJ, ANIK - IOWA STATE UNIV
item ARORA, RAJEEV - IOWA STATE UNIV
item Rowland, Lisa
item FU, YAN - IOWA STATE UNIV
item SUN, LI - IOWA STATE UNIV

Submitted to: Plant Cell and Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2005
Publication Date: 2/1/2006
Citation: Wei, H., Dhanaraj, A., Arora, R., Rowland, L.J., Fu, Y., Sun, L. 2006. Identification of cold acclimation responsive rhodendron genes for lipid metabolism, membrane transport, and lignin biosynthesis: importance of moderately abundant ests in genomic studies. Plant Cell and Environment. 29:558-570.

Interpretive Summary: Cold tolerance is a limiting factor in growing related species of blueberry and rhododendron. We have been using rhododendron, a broad-leaf, woody evergreen species, as a system for studying cold hardiness in related woody plants because there are rhododendron species that are extremely cold hardy, more so than blueberry, and others that are more cold sensitive. Here, we have used a genomic approach to identify genes potentially involved in cold acclimation in rhododendron. We prepared two collections of genes, called libraries, that represent genes that are expressed in leaves in midwinter (when plants are their cold hardiest) and genes that are expressed in the spring (when plants are least cold hardy) and identified those that are expressed at moderately higher levels in the winter than in the spring. In this way, several new genes were identified that may play a role in development of cold hardiness. Scientists will benefit from this work because these genes are now available to test their involvement in cold tolerance directly.

Technical Abstract: We have previously analyzed expressed sequence tags (ESTs) from non-acclimated (NA) and cold acclimated (CA) Rhododendron leaves, and identified highly abundant cDNAs possibly involved in cold acclimation (Wei et al., 2005). A potentially significant, but relatively unexplored, application of these EST datasets is the study of moderately abundant cDNAs, such as those picked only 1 to 3 times from each Rhododendron EST library containing ~430 ESTs. Using statistical tests and northern blots, we established that the probability of differential expression of moderately abundant cDNAs based on the EST data is, indeed, a reasonably accurate predictor of their 'true' up- or down-regulation since 11 out of 13 cDNAs (85%) studied fit this criterion. The analysis also revealed four aspects of cold acclimation in Rhododendron leaf tissues. First, the concomitant up-regulation of long-chain acyl-CoA synthetase, CTP:cholinephosphate cytidylyltransferase, and delta-12 fatty acid desaturase in CA leaf tissues suggests that phospholipid biosynthesis and desaturation are important components of cold hardening in Rhododendron. Second, up-regulation of plastidic NADP-ME in CA tissues suggests malate to be an important source of acetyl-CoA used for fatty acid biosynthesis during cold acclimation. Third, down-regulation of PIP2-1 aquaporin and up-regulation of gated outward rectifying K+ channel (GORK) in CA tissues may be associated with the protection of over-wintering leaves from freeze-induced cellular dehydration. Fourth, up-regulation of coumarate 3-hydroxylase may be associated with cell wall thickening in CA tissues. Physiological implications of these results are discussed revealing potentially novel regulations of cold acclimation in over-wintering woody evergreens. This study highlights the importance of also investigating low / moderately abundant ESTs (in addition to highly abundant ones) in genomic studies, in that, it offers an effective strategy to identify stress-related genes, especially when large-scale cDNA sequencing / microarray studies are not possible.