İlker Büyük

Characterization of stress induced by copper and zinc on cucumber (Cucumis sativus L.) seedlings by means of molecular and population parameters.

Contamination of plants with heavy metals could result in damage in DNA, such as mutations and cross-links with proteins. These altered DNA profiles may become visible in changes such as the appearance of a new band, or loss of an existing band, in the random amplified polymorphic DNA (RAPD) assay. In this study, various concentrations of copper and zinc salts were applied to cucumber seedlings during germination. Results displayed abnormalities in germination and also changes in root elongation, dry weight and total soluble protein level. All treatment concentrations (40, 80, 160, 240, 320, and 640mg/L) used in the study caused a decrease/delay in germination of the cucumbers to different extents. Inhibition or activation of root elongation was considered to be the first effect of metal toxicity in the tested plants. Application of the metal salts and the combined solutions on cucumber (Cucumis sativus L.) seedlings revealed similar consequences for total soluble protein level, dry weight and ultimately in inhibitory rates as well. The data obtained from RAPD band-profiles and genomic template stability (GTS) showed results that were consistent with the population parameters. In this regard, we conclude that molecular marker assays can be applied in combination with population parameters to measure genotoxic effects of heavy metals on plants.

Relationships among lipid peroxidation, SOD enzyme activity, and SOD gene expression profile in Lycopersicum esculentum L. exposed to cold stress

The current study was designed to evaluate lipid peroxidation (via malondialdehyde) levels, the superoxide dismutase (SOD) gene expression profile, and SOD enzyme activity in tomato plants (Lycopersicum esculentum L.) subjected to different time periods of cold stress (control, 2, 4, 6, 8, and 10 days). Results revealed that maximum lipid peroxidation occurred in plants exposed to cold stress for 10 days, and SOD enzyme activity gradually increased with increasing exposure to cold stress. The level of mRNA increased within 4 days of cold treatment. After this period, the level tended to decrease and reached a minimum by the eighth day. A complex gene expression profile was determined, which was not statistically significant until the eighth day. At the 10th day of cold treatment, the mRNA level of SOD increased and changes between the 8th and 10th day were found to be statistically significant at the P < 0.05 level. These results suggest that the SOD gene and enzyme play a key role in resistance to cold stress conditions in tomato plants.

Roles of catalase (CAT) and ascorbate peroxidase (APX) genes in stress response of eggplant (Solanum melongena L.) against Cu +2 and Zn +2 heavy metal stresses

Eggplant (Solanum melongena L.) is a good source of minerals and vitamins and this feature makes its value comparable with tomato which is economically the most important vegetable worldwide. Due to its common usage as food and in medicines, eggplant cultivation has a growing reputation worldwide. But genetic yield potential of an eggplant variety is not always attained, and it is limited by some factors such as heavy metal contaminated soils in today’s world. Today, one of the main objectives of plant stress biology and agricultural biotechnology areas is to find the genes involved in antioxidant stress response and engineering the key genes to improve the plant resistance mechanisms. In this regard, the current study was conducted to gain an idea on the roles of catalase (CAT) and ascorbate peroxidase (APX) genes in defense mechanism of eggplant (S. melongena L., Pala-49 (Turkish cultivar)) treated with different concentrations of Cu+2 and Zn+2. For this aim, the steady-state messenger RNA (mRNA) levels of CAT and APX genes were determined by quantitative real-time PCR (qRT-PCR) in stressed eggplants. The results of the current study showed that different concentrations of Cu+2 and Zn+2 stresses altered the mRNA levels of CAT and APX genes in eggplants compared to the untreated control samples. When the mRNA levels of both genes were compared, it was observed that CAT gene was more active than APX gene in eggplant samples subjected to Cu+2 contamination. The current study highlights the importance of CAT and APX genes in response to Cu+2 and Zn+2 heavy metal stresses in eggplant and gives an important knowledge about this complex interaction.

Genome-wide identification of salinity responsive HSP70s in common bean

The present study is aimed to identify and characterize HSP70 (PvHSP70) genes in two different common bean cultivars under salt stress. For this purpose various in silico methods such as RNAseq data and qRT-PCR analysis were used. A total of 24 candidate PvHSP70 gene were identified. Except for chromosome 4 and 7, these candidate PvHSP70 genes were distributed on the remaining chromosomes. While the lowest number of PvHSP70 genes was determined on chromosomes 1, 3, 5, 7, 9, 10 and 11 (one HSP70 gene), the highest number of PvHSP70s was on chromosomes 6 and 8 (seven HSP70 genes each). Three genes; PvHSP70-5, -9, and -10 were found to have no-introns. In addition, four tandemly and six segmentally duplicated gene couples were detected. A total of 13 PvHSP70 genes were targeted by miRNAs of 44 plant species and the most targeted genes were PvHSP70-5 and -23. The expression profile of PvHSP70 genes based on publicly available RNA-seq data was identified and salt treated leaf tissue was found to have more gene expression levels compared to the root. qRT-PCR analysis showed that the transcript concentrations of upregulated PvHSP70 genes in leaves of Zulbiye (sensitive) were mostly higher than those of Yakutiye (resistant). The present study revealed that PvHSP70 genes might play an important role in salt stress response for common bean cultivars and variability between cultivars also suggests that these genes could be used as functional markers for salt tolerance in common bean.

Application of molecular markers to detect DNA damage caused by environmental pollutants in lichen species.

Pseudevernia furfuracea L. (Zopf), Peltigera praetextata (Flörke ex Sommerf.) Zopf, Lobaria pulmonaria (L.) Hoffm., and Usnea longissima Ach. lichen species were used as bioindicators to assess the genotoxicity of air pollutants. In the present study, we examined significant environmetal pollutants and investigate how changes may lead to damage in DNA structure using RAPD markers. In the study area (Erzurum, Turkey), poor-quality lignite, which generates a large amount of sulfur dioxide, nitrogen oxides, and particle matter, is used for domestic heating, and vehicles also contribute to air pollution. Control lichen samples were collected far from large urban and industrial settlements and transplanted to four polluted sites for 4, 8, or 12 months. The total soluble protein content of the examined four lichen species did not significantly change with exposure time (P < 0.05). The four lichen samples exposed to the pollutants for 8 months had the highest ratio of DNA changes. The ratio of band differences in P. praetextata was higher than that in the other three lichen species, possibly because it has broad leaves that accumulated more pollutants. The average incidences of polymorphism were 64.14, 54.58, 65.76, and 43.06% for P. furfuracea, P. praetextata, L. pulmonaria, and U. longissima, respectively. The genomic template stability (GTS) significantly decreased following exposure to pollutants. GTS ratios revealed that the highest value (98.36%) belonged to U. longissima samples from Site 1 (10 m) after 4 months of exposure, and the lowest values belonged to P. praetextata (73.58%) from Site 3 (100 m) after 8 months of exposure. Based on our findings, we recommend the use of P. praetextata as an indicator of genotoxicity.

Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers

We conducted SSR analyses of 59 accessions, including 29 traditional plum (Prunus domestica), 24 sweet cherry (Prunus avium), and 1 sour cherry (Prunus cerasus) selected from East Anatolian gene sources and 3 plum and 2 cherry reference accessions for molecular characterization and investigation of genetic relationships. Eight SSR loci [1 developed from the apricot (UDAp-404), 4 from the peach (UDP96-010, UDP96-001, UDP96-019, Pchgms1) and 3 from the cherry (UCD-CH13, UCD-CH17, UCD-CH31) genome] for plum accessions and 9 SSR loci [5 developed from the cherry (PS12A02, UCD-CH13, UCD-CH17, UCD-CH31, UCD-CH21), 3 from the peach (Pchgms1, UDP96-001, UDP96-005) and 1 from the plum (CPSCT010) genome] for cherry accessions were used for genetic identification. A total of 66 and 65 alleles were obtained in the genetic analyses of 31 plum and 28 cherry accessions, respectively. The number of alleles revealed by SSR analysis ranged from 4 to 14 alleles per locus, with a mean value of 8.25 in plum accessions, and from 5 to 10 alleles per locus with a mean value of 7.2 in cherry accessions. Only one case of synonym was identified among the cherry accessions, while no case of synonym was observed among the plum accessions. Genomic SSR markers used in discrimination of plum and cherry accessions showed high cross-species transferability in the Prunus genus. Because of their appreciable polymorphism and cross species transferability, the SSR markers that we evaluated in this study will be useful for studies involving fingerprinting of cherry and plum cultivars.

Transcriptome – Scale characterization of salt responsive bean TCP transcription factors

TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) proteins are important regulators of growth and developmental processes including branching, floral organ morphogenesis and leaf growth as well as stress response. This study identified 27 TCP genes of Phaseolus vulgaris (common bean), which were divided into three clusters based on phylogenetic relationship. In addition, this study showed that some of TCP genes such as Pvul-TCP-4 and Pvul-TCP-15 located on chromosomes 3 and 7, Pvul-TCP-7 and Pvul-TCP-20 located on chromosome 7 and 9, were segmentally duplicated. On the other hand, a total of 20 Pvul-TCP genes have predicted to be targeted by microRNAs (miRNA). Most of the miRNA-target genes were Pvul-TCP-1, -11, -13 and -27, which were targeted by 13, 17, 22 and 13 plant miRNAs, respectively. miR319 was one of the highly represented regulatory miRNAs to target TCP transcripts. Promoter region analysis of TCP genes resulted that the GT-1 motif, which was related to salt stress, was found in 14 different Pvul-TCP genes. Expression profiling of 10 Pvul-TCP genes based on RNA-sequencing data further confirmed with quantitative real-time RT-PCR measurements identified that Pvul-TCP genes under salt stress are expressed in a cultivar- and tissue-specific manner.

Varied expression pattern of the small heat shock protein gene encoding HSP17.7 against UVA, UVB, Cu 2+ and Zn 2+ stresses in sunflower

Büyük İ., Aras S., Cansaran-Duman D. (2016): Varied expression pattern of the small heat shock protein gene encoding HSP17.7 against UVA, UVB, Cu2+ and Zn2+ stresses in sunflower. Plant Protect. Sci., 52: 99–106. Today, one of the main objectives of agricultural biotechnology area is to find the responsible genes involved in stress response and engineering these genes to improve the plant response mechanisms. Therefore the current study was conducted to gain an insight on the role of HSP17.7 gene, which is a member of sHsps family, in defence mechanism of sunflower (Helianthus annuus L. cv. Confeta –Turkish cultivar) treated with different doses of UVA and UVB (4, 8, 12 and 20 kJ/m2) and concentrations of copper (Cu2+) and zinc (Zn2+) (80, 160, 320, 640, and 1280 μM) heavy metals. Based on our data, it was observed that different doses of UVA and UVB irradiation resulted in increased levels of HSP17.7 mRNA in sunflower plants. The highest levels of these increases (8 and 12 kJ/m2 of UVA) were seen under UVA stress. In contrast to UV stress, only the Cu2+concentration of 1280 μM led to higher expression levels of HSP17.7 gene compared to the control. Besides this, the 1280 μM concentration of Zn2+ treatment was the peak point of increased HSP17.7 mRNA levels for all stress conditions with nearly 8 times more than in the control sample. Negative correlations were found between malondialdehyde (MDA) levels and expression levels of HSP17.7 gene in sunflower plants subjected to current abiotic stress conditions. This correlation might indicate that an effective defence mechanism was in action and it might be concluded that the HSP17.7 gene can be used for identification of cultivars tolerant to UV and high doses of Cu2+ and Zn2+ for molecular breeding studies in the near future. These findings provide evidence of the HSP17.7 gene contribution to abiotic stress response in sunflower and will be helpful for the next studies about stress tolerance improvement in sunflower plants.

Determination of the DNA changes in the artichoke seedlings (Cynara scolymus L.) subjected to lead and copper stresses

This study aims at determining the effects of lead (Pb) and copper (Cu) on the hyperaccumulator artichoke. The effect of Pb and Cu toxicity with different levels of concentrations (20, 40, 80, 160, 240, 320, 640 and 1280 ppm) caused a decrease in the root length and total soluble protein of the artichoke. As a result of treatment with the Pb and Cu solutions, the changes occurred in RAPD profiles of seedlings and revealed variations like increment and/or loss of bands compared to the control plants. These changes showed a decrease in genomic template stability (GTS, changes in RAPD profile) caused by genotoxicity. RAPD data and GTS values seemed consistent with the results of the root length measurements and total soluble protein analysis. In addition, it was seen that the genomic template stability was significantly affected by direct proportion of primary root length, root dry weight and root total soluble protein content in artichoke subjected to Pb and Cu stresses. As a result, it can be concluded that RAPD analysis based on the used primers in the current study can be applied in combination with physiological and biochemical parameters to measure genotoxic effects of lead and copper on artichoke plants.

Presence of Dianthus roseoluteus Velen. (Caryophyllaceae) in Turkey and a New Species: Dianthus macroflorus Hamzaoğlu

Abstract The presence of Dianthus roseoluteus Velen. species in Turkey is based on specimens collected from Antalya province. After the publication of Flora of Turkey, many specimens have been collected from Thrace (Kırklareli and Edirne provinces) that belong to this species. A comparison of the specimens collected from Antalya and Thrace revealed that they were morphologically different. The literature survey verified that the specimens collected from Thrace were Dianthus roseoluteus. The species collected from Antalya province is a new species, Dianthus macroflorus Hamzaoglu, and its description, pictures, distribution, habitat, and threatened categories are given. Its general morphology and seed micromorphology are compared with the related species, Dianthus roseoluteus. In addition to phylogenetic relationships between some closely related Dianthus species that belong to section Dentati in Turkey, Dianthus macroflorus and 13 additional Dianthus species sequences obtained from GenBank were examined with DNA sequence data from the nuclear ribosomal ITS region. These analyses were supported with morphological data.