Location: Grape Genetics ResearchTitle: Genome wide transcriptional profile analysis of Vitis amurensis in response to cold stress) Author
Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/5/2013
Publication Date: 3/13/2013
Citation: Xin, H., Zhu, W., Wang, L., Xiang, Y., Fang, L., Li, J., Sun, X., Wang, N., Londo, J.P., Li, S. 2013. Genome wide transcriptional profile analysis of Vitis amurensis in response to cold stress. PLoS One. 8(3):e58740.doi:10.1371/journal.pone.0058740. Interpretive Summary: Grape is one of the most important fruit crops worldwide and is cultivated on all of the continents except Antarctica. However, temperatures, specifically low temperatures, limit the geographical locations and productivity of grapes. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. The use of V. amurensis as breeding stock with V. vinifera cultivars offers the potential for increasing freezing tolerance of cultivated grape. However, the molecular and genetic mechanisms that contribute to V. amurensis ability to survive low temperatures are unknown. In this study, deep sequencing of the transcriptome of cold stressed grapevine tissue was used to identify unique genes that are expressed in the cold hardy grapevine species. Comparative analysis between the two grapevine species indicate several candidate genes that function only in the cold hardy V. amurensis. Future studies can now investigate these candidate genes to determine how V. amurensis can survive low temperatures with the goal of transferring those genes and traits to cultivated grapevine.
Technical Abstract: Grape is one of the most important fruit crops worldwide and is cultivated on all of the continents except Antarctica. However, low temperatures can limit the geographical locations and productivity of grapes. Vitis amurensis is a wild grapevine species with remarkable cold-tolerance, exceeding that of Vitis vinifera, the dominant cultivated species of grapevine. The molecular mechanisms that contribute to enhanced freezing tolerance of V. amurensis remain unknown. Here we use deep sequencing data from Type I restriction endonuclease-generated cDNA fragments to evaluate the whole genome wide modification of the transcriptome of V. amurensis under cold treatment. V. vinifera cv. Muscat of Hamburg was used as control to help investigate the distinctive features of V. amurensis in responding to low temperature stress. Alignment of tags to the V. vinifera cv. Pinot noir (PN40024) annotated genome identified over 15,000 transcripts in each library in V. amurensis and more than 16,000 in Muscat of Hamburg. Common DEGs suggest that some genes provide fundamental roles during cold stress in grapes. The two varieties of grapevine also had significant differences in the most robust DEGs (>20 fold), indicating that V. amurensis may trigger species specific pathways in response to cold stress. Functional categories of DEGs indicated that up-regulated transcripts related to metabolism, transport, signal transduction and transcription were more abundant in V. amurensis than in Muscat of Hamburg. Several highly expressed transcripts that were found uniquely accumulated in V. amurensis and represent candidate genes for improved cold hardiness and are discussed in detail.