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

Authors: MEHMET TUFAN ÖZ, REMZİYE YILMAZ, FÜSUN EYİDOĞAN, LEO DE GRAAFF, MERAL YÜCEL, HÜSEYİN AVNİ ÖKTEM

Abstract: 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 GeneChip was used to investigate transcriptome changes associated with boron (B) toxicity in a sensitive barley cultivar (Hordeum vulgare L. cv. Hamidiye). 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 \muM 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 B 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.

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

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