Abstract
Grape is one of the most important fruit crops worldwide. The suitable geographical locations and productivity of grapes are largely limited by temperature. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. However, the molecular mechanisms that contribute to the enhanced freezing tolerance of V. amurensis remain unknown. Here we used deep sequencing data from restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of transcriptome of V. amurensis under cold treatment. Vitis vinifera cv. Muscat of Hamburg was used as control to help investigate the distinctive features of V. amruensis in responding to cold stress. Approximately 9 million tags were sequenced from non-cold treatment (NCT) and cold treatment (CT) cDNA libraries in each species of grapevine sampled from shoot apices. Alignment of tags into V. vinifera cv. Pinot noir (PN40024) annotated genome identified over 15,000 transcripts in each library in V. amruensis and more than 16,000 in Muscat of Hamburg. Comparative analysis between NCT and CT libraries indicate that V. amurensis has fewer differential expressed genes (DEGs, 1314 transcripts) than Muscat of Hamburg (2307 transcripts) when exposed to cold stress. Common DEGs (408 transcripts) suggest that some genes provide fundamental roles during cold stress in grapes. The most robust DEGs (more than 20-fold change) also demonstrated significant differences between two kinds of grapevine, indicating that cold stress may trigger species specific pathways in V. amurensis. Functional categories of DEGs indicated that the proportion of up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in V. amurensis. Several highly expressed transcripts that were found uniquely accumulated in V. amurensis are discussed in detail. This subset of unique candidate transcripts may contribute to the excellent cold-hardiness of V. amurensis.
Highlights
Temperature is one of the primary environmental factors that influences and limits the growth and development of plant species
In order to activate plant cold stress responses and trigger changes in gene regulation, a total of 8 hours of cold treatment was used, with four hours gradient cooling from 24 uC to 4uC and another four hours held at 4uC
A total of four digital expression libraries were constructed from non-cold treatment (NCT) and cold treatment (CT) shoot apex of both V. amurensis and V. vinifera cv
Summary
Temperature is one of the primary environmental factors that influences and limits the growth and development of plant species. While much is unknown about the actual perception of cold, recent studies indicate that plant cell membranes may play a major role in sensing decreasing temperatures. This perception results in transient increases in cytosolic Ca2+ levels, triggering a cascading biochemical and molecular reactions [3,5,7]. In the CBF-dependent pathway, the CBF protein recognizes the CRT/DRE cis-element in the promoter regions of COR (cold response) genes, which in turn activate transcription of these downstream genes and leads to chilling and freezing tolerance to plants. In a CBF-independent pathway, the transcription factors HOS10 (a R2R3 myeloblastosis type) play pivotal roles in the regulation of cold-responsive genes and freezing tolerance [20]. Great progress has been made in recent years in understanding cold signal transduction in plant, the differences in genes or expression patterns in sensitive and tolerant species under cold stress still needs further investigation
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