Browsing by Author "Kavas, Musa"

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Diverse expression pattern of wheat transcription factors against abiotic stresses in wheat species.
(2014-10-15T00:00:00Z) Baloglu, Mehmet Cengiz; Inal, Behcet; Kavas, Musa; Unver, Turgay
Abiotic stress including drought and salinity affects quality and yield of wheat varieties used for the production of both bread and pasta flour. bZIP, MBF1, WRKY, MYB and NAC transcription factor (TF) genes are the largest transcriptional regulators which are involved in growth, development, physiological processes, and biotic/abiotic stress responses in plants. Identification of expression profiling of these TFs plays a crucial role to understand the response of different wheat species against severe environmental changes. In the current study, expression analysis of TaWLIP19 (wheat version of bZIP), TaMBF1, TaWRKY10, TaMYB33 and TaNAC69 genes was examined under drought and salinity stress conditions in Triticum aestivum cv. (Yuregir-89), Triticum turgidum cv. (Kiziltan-91), and Triticum monococcum (Siyez). After drought stress application, all five selected genes in Kiziltan-91 were induced. However, TaMBF1 and TaWLIP19 were the only downregulated genes in Yuregir-89 and Siyez, respectively. Except TaMYB33 in Siyez, expression level of the remaining genes increased under salt stress condition in all Triticum species. For determination of drought response to selected TF members, publicly available RNA-seq data were also analyzed in this study. TaMBF1, TaWLIP19 and TaNAC69 transcripts were detected through in silico analysis. This comprehensive gene expression analysis provides valuable information for understanding the roles of these TFs under abiotic stresses in modern wheat cultivars and ancient einkorn wheat. In addition, selected TFs might be used for determination of drought or salinity-tolerant and susceptible cultivars for molecular breeding studies.
Effect of drought stress on the antioxidant systems of two sunflower (Healintus annuss) cultivars
(ESCPB, 2006) Kavas, Musa; Kalemtaş, Gülsüm; Akcay, Ufuk C.; Bayrak, Abdullah T.; Özgür, Ebru; Baloğlu, Mehmet Cengiz; Ercan, Oya; Yücel, Meral; Öktem, Hüseyin Avni
Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration.
(2016-02-01T00:00:00Z) Kavas, Musa; Baloğlu, Mehmet Cengiz; Atabay, Elif Seda; Ziplar, Ummugulsum Tanman; Daşgan, Hayriye Yıldız; Ünver, Turgay
Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles in response to stress. Though, most eukaryotes carry the proteins of this family, biological functions of the most bHLH family members are not deeply evaluated in plants. In this study, we conducted a comprehensive genome-wide analysis of bHLH transcription factors in salt tolerant common bean. We identified 155 bHLH protein-encoding genes (PvbHLH) by using in silico comparative genomics tools. Based on the phylogenetic tree, PvbHLH genes were classified into 8 main groups with 21 subfamilies. Exon-intron analysis indicated that proteins belonging to same main groups exhibited a closely related gene structure. While, the PvbHLH gene family has been mainly expanded through segmental duplications, a total of 11 tandem duplication were detected. Genome-wide expression analysis of bHLH genes showed that 63 PvbHLH genes were differentially expressed in at least one tissue. Three of them displayed higher expression values in both leaf and root tissues. The in silico micro-RNA target transcript analyses revealed that totally 100 PvHLH genes targeted by 86 plant miRNAs. The most abundant transcripts, which were targeted by all 18 plant miRNA, were belonging to PvHLH-22 and PvHLH-44 genes. The expression of 16 PvbHLH genes in the root and leaf tissues of salt-stressed common bean was evaluated using qRT-PCR. Among them, two of PvbHLHs, PvbHLH-54, PvbHLH-148, were found to be up-regulated in both tissues in correlation with RNA-seq measurements. The results of this study could help improve understanding of biological functions of common bean bHLH family under salt stress. Additionally, it may provide basic resources for analyzing bHLH protein function for improving economic, agronomic and ecological benefit in common bean and other species.
Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean.
(2015-11-27) Kavas, Musa; Kizildogan, Aslihan; Gökdemir, Gökhan; Baloglu, Mehmet Cengiz
Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the AP2-ERF genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (Phaseolus vulgaris). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of AP2-ERF genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all PvAP2-ERF genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were PvAP2/ERF-20-25-62-78-113-173. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor PvAP2-ERF78, an ortholog of Arabidopsis At2G28550, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.