Microarray Analysis of Late Response to Boron Toxicity in Barley (Hordeum vulgare L.) Leaves

Date

2009-01-01

Author

Oz, Mehnnet Tufan
Yilmaz, Remziye
Eyidogan, Fuesun
de Graaff, Leo
Yucel, Meral
Öktem, Hüseyin Avni

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

99
views

0
downloads

DNA microarrays, being high-density and high-throughput, allow quantitative analyses of thousands of genes and their expression patterns in parallel. In this study, Barley1 GereChip was used to investigate transcriptome changes associated with boron (B) toxicity in a sensitive barley cultivar (Hordeum vulgare L. cv. Hamidye). Eight-day-old aseptically grown seedlings were subjected to 5 or 10 mM boric acid (B(OH)(3)) treatments for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues. Among the 22,840 transcripts - each represented with a probe set on the GeneChip - 19,424 probe sets showed intensity values greater than 20(th) percentile in at least one of the hybridizations. Compared to control (10 mu M B(OH)(3)), 5 mM B(OH)(3) treatment resulted in differential expression of 168 genes at least by twofold. Moreover, 10 mM B(OH)(3) treatment resulted in at least twofold induction or reduction in expression of 312 transcripts. Among these genes, 37 and 61 exhibited significantly (P < 0.05) altered levels of expression under 5 and 10 mM B(OH)(3) treatments, respectively. Differentially expressed genes were characterized using expression-based clustering and HarvEST:Barley. Investigations of expression profiles revealed that B toxicity results in global changes in the barley transcriptome and networks of signaling or molecular responses. A noticeable feature of response to 8 was that it is highly interconnected with responses to various environmental stresses. Additionally, induction of jasmonic acid related genes was found to be an important late response to B toxicity. Determination of responsive genes will shed light on successive studies aiming to elucidate molecular mechanism of B toxicity or tolerance. To the best of our knowledge, this is the first report on global expression analysis of barley seedlings under B toxicity.

Subject Keywords

Barley, Barley1 GeneChip, Boron toxicity, Gene expression, Microarray, Transcriptome analysis

URI

https://hdl.handle.net/11511/55966

Journal

TURKISH JOURNAL OF AGRICULTURE AND FORESTRY

Collections

Department of Biology, Article

Suggestions

OpenMETU
Core

Comparing Clustering Techniques for Real Microarray Data Purutçuoğlu Gazi, Vilda (2012-08-29) The clustering of genes detected as significant or differentially expressed provides useful information to biologists about functions and functional relationship of genes. There are variant types of clustering methods that can be applied in genomic data. These are mainly divided into the two groups, namely, hierarchical and partitional methods. In this paper, as the novelty, we perform a detailed clustering analysis for the recently collected boron microarray dataset to investigate biologically more interes...
Mathematical Modeling and Approximation of Gene Expression Patterns Yılmaz, Fatih; Öktem, Hüseyin Avni (2004-09-03) This study concerns modeling, approximation and inference of gene regulatory dynamics on the basis of gene expression patterns. The dynamical behavior of gene expressions is represented by a system of ordinary differential equations. We introduce a gene-interaction matrix with some nonlinear entries, in particular, quadratic polynomials of the expression levels to keep the system solvable. The model parameters are determined by using optimization. Then, we provide the time-discrete approximation of our time...
Determination of the effect of polyadenylation SLR values on microarray data classification Aslan, Ümit; Can, Tolga; Department of Computer Engineering (2014) Microarray data classification is generally used to predict unknown sample outcomes by the help of models created using the preprocessed and categorized microarray data that includes gene expression values. Preparation of microarray experiments, design of Affymetrix chips and availability of previous microarray experiments give the opportunity to extract a new kind of data; differential expressions of proximal and distal probes (Short to Long Ratio -SLR- values), which is used to predict the alternative pol...
A Comparative Study of Statistical and Artificial Intelligence based Classification Algorithms on Central Nervous System Cancer Microarray Gene Expression Data Arslan, Mustafa Turan; Kalınlı, Adem (2016-09-03) A variety of methods are used in order to classify cancer gene expression profiles based on microarray data. Especially, statistical methods such as Support Vector Machines (SVM), Decision Trees (DT) and Bayes are widely preferred to classify on microarray cancer data. However, the statistical methods can often be inadequate to solve problems which are based on particularly large-scale data such as DNA microarray data. Therefore, artificial intelligence-based methods have been used to classify on microarray...
Investigation of structural properties of methylated human promoter regions in terms of DNA helical rise Yaldız, Burcu; Aydın Son, Yeşim; Department of Bioinformatics (2014) The infamous double helix structure of DNA was assumed to be a rigid, uniformly observed structure throughout the genomic DNA. However, the differences in physical structure of DNA in terms of local helical parameters such as twist, tilt, roll, rise and angles between adjacent base pairs in B-DNA molecule have been shown in many studies. This observed flexibility satisfies the known physical and chemical properties of DNA while providing a better model to explain how DNA fulfills its biological functions. W...

Citation Formats

M. T. Oz, R. Yilmaz, F. Eyidogan, L. de Graaff, M. Yucel, and H. A. Öktem, “Microarray Analysis of Late Response to Boron Toxicity in Barley (Hordeum vulgare L.) Leaves,” TURKISH JOURNAL OF AGRICULTURE AND FORESTRY, pp. 191–202, 2009, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/55966.