TITLE

Identification of tissue-specific, abiotic stressresponsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets

AUTHOR(S)
Tillett, Richard L.; Ergül, Ali; Albion, Rebecca L.; Schlauch, Karen A.; Cramer, Grant R.; Cushman, John C.
PUB. DATE
January 2011
SOURCE
BMC Plant Biology;2011, Vol. 11 Issue 1, p86
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Abiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, Vitis vinifera L. Large-scale expressed sequence tags (ESTs) were generated, curated, and analyzed to identify major genetic determinants responsible for stressadaptive responses. Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited to date. To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses. Results: A total of 62,236 expressed sequence tags (ESTs) were generated from leaf, berry, and root tissues from vines subjected to abiotic stresses and compared with 32,286 ESTs sequenced from 20 public cDNA libraries. Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences, with 2302 singletons and 10,976 mapped to V. vinifera gene models. Of these, 739 transcripts were found to have significant differential expression in stressed leaves and berries including 250 genes not described previously as being abiotic stress responsive. In a second analysis of 16,452 ESTs from a normalized root cDNA library derived from roots exposed to multiple, shortterm, abiotic stresses, 135 genes with root-enriched expression patterns were identified on the basis of their relative EST abundance in roots relative to other tissues. Conclusions: The large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of abiotic stress conditions revealed distinct, tissue-specific expression patterns, previously unrecognized stress-induced genes, and many novel genes with root-enriched mRNA expression for improving our understanding of root biology and manipulation of rootstock traits in wine grape. mRNA abundance estimates based on EST library-enriched expression patterns showed only modest correlations between microarray and quantitative, real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods highlighting the need for deep-sequencing expression profiling methods.
ACCESSION #
62641700

 

Related Articles

  • Mustard plant passes the salt. Dove, Alan // Nature Biotechnology;Oct99, Vol. 17 Issue 10, p942 

    Reports on a research conducted by botanists at the University of Toronto in Toronto, Canada that reveals effect of over expression of an ion transport protein in Arabidopsis. Link between soil salinity levels and gene expression; Effect of increased soil salinity on plant production.

  • RNA surveillance by nuclear scanning? Wilkinson, Miles F.; Shyu, Ann-Bin // Nature Cell Biology;Jun2002, Vol. 4 Issue 6, pE144 

    Provides information on nonsense-mediated decay (NMD) pathway, one of the many quality-control mechanisms that ensure the high fidelity of gene expression. Destruction of aberrant mRNA that contain premature termination codons generated as a result of programmed gene mutations; Proposed...

  • The effect of mild cold exposure on UCP3 mRNA expression and UCP3 protein content in humans. Schrauwen, P.; Westerterp-Plantenga, M.S.; Kornips, E.; Schaart, G.; Lichtenbelt, W.D. van Marken // International Journal of Obesity & Related Metabolic Disorders;Apr2002, Vol. 26 Issue 4, p450 

    Examines the effect of mild cold exposure on the messenger RNA (mRNA) and protein expression of UCP3 in humans. Increase of energy expenditure; Down-regulation of UCP protein content with prolonged cold exposure; Effect of cold adaptation on mRNA and protein content.

  • Taking a census of mRNA populations with microbeads. Tyagi, Sanjay // Nature Biotechnology;Jun2000, Vol. 18 Issue 6, p597 

    Discusses the need to define cellular responses and cell types by profiling messenger RNA populations. Techniques to analyze expression of large sets of genes in parallel; Mechanism of global analysis of gene expression; Methods to minimize the sequencing effect.

  • The Relationship Between Third-Colon Position Nucleotide Content, Codon Bias, mRNA Secondary.... Carlini, David B.; Ying Chen; Stephan, Wolfgang // Genetics;Oct2001, Vol. 159 Issue 2, p623 

    Examines the correlation between colon bias, messenger RNA secondary structure, third-codon position nucleotide distribution and gene expression. Reduction of codon bias; Effect of secondary structure on gene expression; Regulation of the level of gene expression.

  • Expression analysis using low amounts of mRNA and GeneChips. Pilarsky, Christian; Schmitt, Armin; Hille, Simone; Rosenthal, André // Nature Genetics;Nov99 Supplement, Vol. 23, p68 

    Presents an abstract for the article on gene expression analysis using amounts of messenger RNA and a GeneChip containing known tumor-associated genes.

  • Messenger RNA exchange between scions and rootstocks in grafted grapevines. Yingzhen Yang; Linyong Mao; Jittayasothorn, Yingyos; Youngmin Kang; Chen Jiao; Zhangjun Fei; Gan-Yuan Zhong // BMC Plant Biology;10/19/2015, Vol. 15, p1 

    Background: Grafting has been widely practiced for centuries in the propagation and production of many vegetable and fruit species. However, the underlying molecular and genetic mechanisms for how the graft partners interact with each other to produce a successful graft remain largely unknown....

  • Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening.  // BMC Plant Biology;2011, Vol. 11 Issue 1, p149 

    The article presents a study which examines fruit ripening in Trincadeira grapes taking into account the transcriptional and metabolic profilings complemented with biochemical data. The study compared mRNA expression profiles of four time points spanning developmental stages from pea size green...

  • Cytokine mRNA expression in normal skin of various age populations before and after engraftment onto nude mice. Gilhar, Amos; Ullmann, Yehuda; Shalagino, Raya; Weisinger, Gary // Acta Dermato-Venereologica;4/20/98, Vol. 78 Issue 1, p36 

    Whether the impact of skin biological age on cytokine expression is a result of this tissue's proliferation potential or not is an important issue in dermatology. We investigated these questions by monitoring cytokine marker mRNA expression from human skin samples from healthy groups of...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics