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

BMC Plant Biology

Research Article

Ali Ergül¹  John C Cushman²  Rebecca L Albion²  Richard L Tillett²  Karen A Schlauch²  Grant R Cramer² 

[1] Biotechnology Institute, Ankara University, Merkez Laboratuvari, Rektorluk Binasi Arkasi, 06100, Ankara, Turkey;Department of Biochemistry and Molecular Biology, MS330, University of Nevada, 89557-0330, Reno, NV, USA;

关键词: cDNA Library;    Massively Parallel Signature Sequencing;    Wine Grape;    Berry Development;    Pterostilbene;   

DOI  :  10.1186/1471-2229-11-86

 received in 2011-02-14, accepted in 2011-05-18,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundAbiotic 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 stress-adaptive 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.ResultsA 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, short-term, 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Tillett et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.