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Title: GENE EXPRESSION PROFILES DURING COLD ACCLIMATION IN BLUEBERRY UNDER FIELD AND COLD ROOM CONDITIONS USING CDNA MICROARRAYS

Author
item DHANARAJ, ANIL - IOWA STATE UNIVERSITY
item ALFHAROUF, NADIM - USDA/ARS/SGIL
item Beard, Hunter
item CHOUIKHA, IMED - GEORGE MASON UNIVERSITY
item Matthews, Benjamin - Ben
item WEI, HUI - IOWA STATE UNIVERSITY
item ARORA, RAJEEV - IOWA STATE UNIVERSITY
item Rowland, Lisa

Submitted to: Planta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/11/2006
Publication Date: 2/1/2007
Citation: Dhanaraj, A.L., Alfharouf, N.W., Beard, H.S., Chouikha, I.B., Matthews, B.F., Wei, H., Arora, R., Rowland, L.J. 2006. Gene expression profiles during cold acclimation in blueberry under field and cold room conditions using cdna microarrays. Planta. DOI10.1007/s00425-006-0382-1. 225:735-751.

Interpretive Summary: Blueberry is an important small fruit crop in the U.S. that is rich in health-promoting nutrients. Damages from winter freezes and spring frosts, however, result in significant losses in fruit yield to blueberry growers particularly in the mid-Atlantic, northern, and midwestern U.S. By studying the genetics of cold hardiness, scientists hope to develop more cold hardy blueberry cultivars. Genetic evidence from numerous plants indicates that cold hardiness is determined by several genes, not just a single gene. Within the last few years, methods have been developed to study thousands of genes at a time in response to environmental conditions such as cold treatment. Here, we report using such a method to examine expression of over 2500 blueberry genes in response to cold treatments. Treatments included natural field conditions in winter and artificial conditions of placing greenhouse plants in a cold room. The expression of numerous blueberry genes was found to change during exposure to cold. More genes were found to go up under artificial conditions than under field conditions. Thus, caution should be exercised in evaluating changes in gene expression from controlled cold exposure vs. “real world” conditions. Many genes were identified that respond to cold in both artificial and natural conditions, including genes not previously associated with resistance to cold. These genes are now available for scientists to test their involvement in cold tolerance directly.

Technical Abstract: Environmental stresses, including low temperature extremes, reduce crop yields and impact the profitability and competitiveness of U.S. producers. The U.S. is the world’s leading blueberry (Vaccinium section Cyanococcus) producer. The blueberry industry, however, needs cultivars with enhanced cold hardiness. Our laboratory has been working toward increasing our understanding of the genetic control of cold hardiness in blueberry to ultimately use this information to develop more cold hardy cultivars. Here, we report using cDNA microarrays to monitor changes in gene expression at multiple times during cold acclimation under field (~0, 400, 800, and 1200 chill units) and cold room (~0, 500, and 1000 chill units) conditions. Microarrays contained over 2500 cDNA inserts, approximately half of which had been picked and single-pass sequenced from each of two cDNA libraries that were constructed from cold acclimated floral buds (collected in mid-winter) and non-acclimated floral buds (collected in fall) of the fairly cold hardy cv. Bluecrop (Vaccinium corymbosum L.). Two biological samples were examined at each time point. Microarray data were analyzed statistically using t-tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). A large percentage of gene transcripts was found to be cold responsive and, interestingly, more transcripts were found to be upregulated under cold room conditions than under field conditions. Many of the genes induced only under cold room conditions could be divided into three major types: 1) genes associated with stress tolerance; 2) those that encode glycolytic and TCA cycle enzymes; and 3) those associated with protein synthesis machinery. A few of the genes induced only under field conditions appear to be related to light stress. Possible explanations for these differences are discussed in physiological context. We show that, although many similarities exist in how plants.