Elucidating cold acclimation pathway in blueberry by transcriptome profiling

Authors: DIE-RAMON, JOSE - Consejo Superior De Investigaciones Cientificas (CSIC); Rowland, Lisa

Submitted to: Environmental and Experimental Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/28/2013
Publication Date: 1/6/2014
Publication URL: http://handle.nal.usda.gov/10113/61445
Citation: Die-Ramon, J., Rowland, L.J. 2014. Elucidating cold acclimation pathway in blueberry by transcriptome profiling. Environmental and Experimental Botany. 106:87-98.

Interpretive Summary: Blueberry is a major berry crop in the United States and one that has increased in popularity in recent years because of its many health benefits. Freezing temperatures in winter and early spring limit growth and geographical distribution of blueberry plants, however, and can result in reductions in berry yield. A better understanding of genes that protect plants from low temperature are needed to produce blueberry cultivars with enhanced cold hardiness. Woody plants, like blueberry, develop cold hardiness (or cold acclimate) in the fall, in two stages, in preparation for winter. The first stage is triggered by shortening day length and the second stage is brought about by falling temperatures. Here, we have characterized approximately 5000 genes that are expressed in blueberry flower buds during the first two stages of cold acclimation. By studying their expression profiles, we found that certain of the genes involved in lipid (fat) metabolism are expressed preferentially in the first stage of cold acclimation, while genes involved in carbohydrate (sugar and starch) metabolism are expressed primarily in the second stage. This large collection of gene sequences and expression data are a valuable resource for scientists attempting to identify genes that play important roles in the development of cold hardiness in blueberry and related species.

Technical Abstract: A fundamental goal of cold acclimation research is to understand the mechanisms responsible for the increase in freezing tolerance in response to environmental cues. Changes in gene expression underlie some of the biochemical and physiological changes that occur during cold acclimation. Detailed and comprehensive transcriptome annotation can be considered a prerequisite for effective analysis and a fast and cost-effective way to rapidly obtain information in the context of a given physiological condition. By computational predictions and manual curation, we have annotated 454 sequence assemblies from two blueberry cDNA libraries that represent flower buds in the first and second stages of cold acclimation. Gene ontology functional classification terms were retrieved for 4343 (80.0%) sequences. GO annotation files compatible with a commonly used annotation tool have been generated and are publicly available. By mining the dataset further, it was possible to associate presence of certain transcripts related to carbohydrate metabolism and lipid metabolism with different stages of cold acclimation. This was concomitant with differential presence of Zn finger functional domains and C3H-family transcription factors. The expression of a few selected genes was validated by quantitative real-time PCR assay. Results demonstrate that our transcriptome database is a rich resource for mining cold acclimation-responsive genes.