Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology

Jiao Wu; Yali Zhang; Huiqin Zhang; Hong Huang; Folta, Kevin M.; Jiang Lu
January 2010
BMC Plant Biology;2010, Vol. 10, p234
Academic Journal
Background: Downy mildew (DM), caused by pathogen Plasmopara viticola (PV) is the single most damaging disease of grapes (Vitis L.) worldwide. However, the mechanisms of the disease development in grapes are poorly understood. A method for estimating gene expression levels using Solexa sequencing of Type I restrictionendonuclease- generated cDNA fragments was used for deep sequencing the transcriptomes resulting from PV infected leaves of Vitis amurensis Rupr. cv. Zuoshan-1. Our goal is to identify genes that are involved in resistance to grape DM disease. Results: Approximately 8.5 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from PV pathogen-infected leaves, and about 7.5 M were sequenced from the cDNA library constructed from the control leaves. When annotated, a total of 15,249 putative genes were identified from the Solexa sequencing tags for the infection (INF) library and 14,549 for the control (CON) library. Comparative analysis between these two cDNA libraries showed about 0.9% of the unique tags increased by at least five-fold, and about 0.6% of the unique tags decreased more than five-fold in infected leaves, while 98.5% of the unique tags showed less than five-fold difference between the two samples. The expression levels of 12 differentially expressed genes were confirmed by Real-time RT-PCR and the trends observed agreed well with the Solexa expression profiles, although the degree of change was lower in amplitude. After pathway enrichment analysis, a set of significantly enriched pathways were identified for the differentially expressed genes (DEGs), which associated with ribosome structure, photosynthesis, amino acid and sugar metabolism. Conclusions: This study presented a series of candidate genes and pathways that may contribute to DM resistance in grapes, and illustrated that the Solexa-based tag-sequencing approach was a powerful tool for gene expression comparison between control and treated samples.


Related Articles

  • Reference Gene Selection and Validation for the Early Responses to Downy Mildew Infection in Susceptible and Resistant Vitis vinifera Cultivars. Monteiro, Filipa; Sebastiana, Mónica; Pais, Maria Salomé; Figueiredo, Andreia // PLoS ONE;Sep2013, Vol. 8 Issue 9, p1 

    The pivotal role of cultivated grapevine (Vitis vinifera L.) in many countries economy is compromised by its high susceptibility to Plasmopara viticola, the causal agent of downy mildew disease. Recent research has identified a set of genes related to resistance which may be used to track downy...

  • Subcellular localization and functional analyses of a PR10 protein gene from Vitis pseudoreticulata in response to Plasmopara viticola infection. He, Mingyang; Xu, Yan; Cao, Jiangling; Zhu, Ziguo; Jiao, Yuntong; Wang, Yuejin; Guan, Xin; Yang, Yazhou; Xu, Weirong; Fu, Zhenfang // Protoplasma;Feb2013, Vol. 250 Issue 1, p129 

    Downy mildew, caused by the oomycete Plasmopara viticola, is a serious fungal disease in the cultivated European grapevines (Vitis vinifera L.). The class 10 of pathogenesis-related (PR) genes in grapevine leaves was reported to be accumulated at mRNA level in response to P. viticola infection....

  • Identification of suitable reference genes for real-time RT-PCR normalization in the grapevine-downy mildew pathosystem. Selim, M.; Legay, S.; Berkelmann-Löhnertz, B.; Langen, G.; Kogel, K.-H.; Evers, D. // Plant Cell Reports;Jan2012, Vol. 31 Issue 1, p205 

    Due to its reproducibility and sensitivity, real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become the method of choice for quantifying gene expression. However, the accuracy of RT-qPCR is prone to bias if proper precautions are not taken, e.g. starting with...

  • Genetic dissection of sex determinism, inflorescence morphology and downy mildew resistance in grapevine. Marguerit, Elisa; Boury, Christophe; Manicki, Aurélie; Donnart, Martine; Butterlin, Gisèle; Némorin, Alice; Wiedemann-Merdinoglu, Sabine; Merdinoglu, Didier; Ollat, Nathalie; Decroocq, Stéphane // Theoretical & Applied Genetics;May2009, Vol. 118 Issue 7, p1261 

    A genetic linkage map of grapevine was constructed using a pseudo-testcross strategy based upon 138 individuals derived from a cross of Vitis vinifera Cabernet Sauvignon × Vitis riparia Gloire de Montpellier. A total of 212 DNA markers including 199 single sequence repeats (SSRs), 11 single...

  • Expression patterns of prion protein gene in differential genotypes sheep: quantification using molecular beacon real-time RT-PCR. Chuan Wang; Run Wu; Fa-Di Li; Lei Liu; Xiao-Li Zhang; Chun-Lin Zhao; Xiao-Long Diao; Hong-Wei Guan // Virus Genes;Jun2011, Vol. 42 Issue 3, p457 

    Determination of the transcription level of cellular prion protein (PrP) is essential for understanding its role in organisms and revealing mechanism of susceptibility and resistance to scrapie. However, the expression of prion protein (PrP) mRNA in sheep has not been quantified in great detail...

  • Gene Expression Profiling in Ecotoxicology. Terry W. Snell; Sara E. Brogdon; Michael B. Morgan // Ecotoxicology;Dec2003, Vol. 12 Issue 6, p475 

    Gene expression profiling is a powerful new end point for ecotoxicology and a means for bringing the genomics revolution to this field. We review the usefulness of gene expression profiling as an end point in ecotoxicology and describe methods for applying this approach to non-model organisms....

  • Herbicide Resistance of Tobacco Chloroplasts Expressing the bar Gene. Tae-Jin Kang; Jo-Eun Seo; Nguyen-Hoang Loc; Moon-Sik Yang // Molecules & Cells (Springer Science & Business Media B.V.);2003, Vol. 16 Issue 1, p60 

    The chloroplast transformation system has the potential advantages of maternal inheritance and high-level expression of heterologous genes. We studied the expression of the bar gene in tobacco chloroplasts to test these ideas. The bar gene conferring tolerance to the herbicide phosphinothricin...

  • MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments. Bustin, Stephen A.; Beaulieu, Jean-François; Huggett, Jim; Jaggi, Rolf; Kibenge, Frederick S. B.; Olsvik, Pål A.; Penning, Louis C.; Toegel, Stefan // BMC Molecular Biology;2010, Vol. 11, p74 

    The conclusions of thousands of peer-reviewed publications rely on data obtained using fluorescence-based quantitative real-time PCR technology. However, the inadequate reporting of experimental detail, combined with the frequent use of flawed protocols is leading to the publication of papers...

  • Efficacy of SSH PCR in isolating differentially expressed genes. Wan Ji; Wright, Matthew B.; Li Cai; Flament, Angel; Lindpaintner, Klaus // BMC Genomics;2002, Vol. 3, p12 

    Background: Suppression Subtractive Hybridization PCR (SSH PCR) is a sophisticated cDNA subtraction method to enrich and isolate differentially expressed genes. Despite its popularity, the method has not been thoroughly studied for its practical efficacy and potential limitations. Results: To...


Read the Article


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

Try another library?
Sign out of this library

Other Topics