title: High-throughput transcriptome analysis of barley (Hordeum vulgare) exposed to excessive boron.
abstract: Boron (B) is an essential micronutrient for optimum plant growth. However, above certain threshold B is toxic and causes yield loss in agricultural lands. While a number of studies were conducted to understand B tolerance mechanism, a transcriptome-wide approach for B tolerant barley is performed here for the first time. A high-throughput RNA-Seq (cDNA) sequencing technology (Illumina) was used with barley (Hordeum vulgare), yielding 208 million clean reads. In total, 256,874 unigenes were generated and assigned to known peptide databases: Gene Ontology (GO) (99,043), Swiss-Prot (38,266), Clusters of Orthologous Groups (COG) (26,250), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) (36,860), as determined by BLASTx search. According to the digital gene expression (DGE) analyses, 16% and 17% of the transcripts were found to be differentially regulated in root and leaf tissues, respectively. Most of them were involved in cell wall, stress response, membrane, protein kinase and transporter mechanisms. Some of the genes detected as highly expressed in root tissue are phospholipases, predicted divalent heavy-metal cation transporters, formin-like proteins and calmodulin/Ca(2+)-binding proteins. In addition, chitin-binding lectin precursor, ubiquitin carboxyl-terminal hydrolase, and serine/threonine-protein kinase AFC2 genes were indicated to be highly regulated in leaf tissue upon excess B treatment. Some pathways, such as the Ca(2+)-calmodulin system, are activated in response to B toxicity. The differential regulation of 10 transcripts was confirmed by qRT-PCR, revealing the tissue-specific responses against B toxicity and their putative function in B-tolerance mechanisms.
authors.affiliation: Department of Biology, Faculty of Science and Arts, Fatih University, Istanbul, Turkey; Vocational High School of Health Services, Fatih University, Istanbul, Turkey.
authors.forename: Guzin
authors.initials: G
authors.lastname: Tombuloglu
authors.affiliation: Department of Biology, Faculty of Science and Arts, Fatih University, Istanbul, Turkey.
authors.forename: Huseyin
authors.initials: H
authors.lastname: Tombuloglu
authors.affiliation: Department of Biology, Suleyman Demirel University, Isparta, Turkey.
authors.forename: M Serdal
authors.initials: MS
authors.lastname: Sakcali
authors.affiliation: Department of Biology, Faculty of Science, Cankiri Karatekin University, Cankiri, Turkey. Electronic address: turgayunver@gmail.com.
authors.forename: Turgay
authors.initials: T
authors.lastname: Unver
mesh_terms: D001483:Base Sequence; D001895:Boron / Q000633:toxicity*; D002147:Calmodulin / Q000096:biosynthesis; D027682:Cation Transport Proteins / Q000096:biosynthesis; D018744:DNA, Plant / Q000235:genetics; D030562:Databases, Protein; D004789:Enzyme Activation / Q000187:drug effects; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D017343:Genes, Plant / Q000235:genetics; D005969:Glutamate Dehydrogenase / Q000096:biosynthesis; D059014:High-Throughput Nucleotide Sequencing; D001467:Hordeum / Q000187:drug effects* / Q000235:genetics*; D010740:Phospholipases / Q000096:biosynthesis; D018515:Plant Leaves / Q000187:drug effects / Q000235:genetics; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics; D017346:Protein Serine-Threonine Kinases / Q000096:biosynthesis; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics; D044767:Ubiquitin-Protein Ligases / Q000096:biosynthesis
chemical_list: D002147:Calmodulin; D027682:Cation Transport Proteins; D018744:DNA, Plant; D005969:Glutamate Dehydrogenase; D044767:Ubiquitin-Protein Ligases; D017346:Protein Serine-Threonine Kinases; D010740:Phospholipases; D001895:Boron
keywords: Barley; Boron toxicity; Ca(2+)–calmodulin system; Gene expression; RNA-sequencing; Transcriptome