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- ArticleAçık Erişim2021Determination of genetic divergence in some bread wheat varieties by IRAP and ISSR analyses
Olgun, Murat; Ayter, Nazife Gozde; Agar, Guleray; Basçıftçı, Zekıye Budak; Yildirim, Nalan; Sunar, Serap
In this study, it was aimed to detect the differences of genotypes through the measurement of genetic distancein bread wheat (Triticum aestivum L.) genotypes. The genetic diversity of 12 bread wheat genotypes (Bozkır,Harmankaya 99, Altay 2000, Yıldırım, Bezostaja 1, Ahmetağa, Müfitbey, Aldane, Es 26, Alperbey, Atay 85 adEraybey) was examined through ISSR and IRAP techniques. As fast molecular techniques, ISSR and IRAP methodscan be effectively included in breeding programs both for genetic exploration and evaluation and for the protection ofelite breeding and production materials. 12 genotypes were classified into two main clusters in the dendrogramproduced by using the ISSR and IRAP markers. While Cluster I included Bozkır, Harmankaya 99, Altay 2000 andYıldırım, cluster II included Bezostaja 1, Ahmetağa, Müfitbey, Aldane, Es 26, Alperbey, Atay 85 and Eraybey.Furthermore, the results obtained in this study indicated that ISSR and IRAP methods were effective for the definitionof bread wheat genotypes.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2020EFFECTS of CARBENDAZIM on DNA DAMAGE and RETROTRANSPOSON POLYMORPHISM in Zea mays
Yildirim, Nalan; Sunar, Serap; Agar, Guleray
Carbendazim (CBZ, methyl 2-benzimidazolecarbamate) is used widely in agriculture against fungal diseases. We aimed to determine the effects of CBZ (0, 0.1, 0.2 and 0.4 mM) on long terminal repeat (LTR) retrotransposon polymorphism and genomic template stability (GTS), DNA damage using ınter-simple sequence repeats (ISSR) and inter-retrotransposon amplified polymorphisms (IRAP) marker techniques. Our results showed that all doses of CBZ compose retrotransposition polymorphism. In additional, our result showed that all CBZ treatment decrease genomic template stability (GTS) and DNA damage increased. These results suggest that carbendazim, widely used in agriculture, can influence unfavorable growth and development of both target and non-target organisms and impend risk to organisms even in trace levels.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2019Analysis of genomic stability and DNA damage in plants exposed to cement dust pollution using the RAPD analysis
Ertürk, Filiz Aygün; Agar, Guleray; Sunar, Serap
One of the most important environmental pollutants is cement dust. In this study, RAPD technology was used todefine the potential genotoxic impact of cement dust on plants. For this purpose, the DNA comparison of 12 plant species(Convolvulus sepium, Astragalus christianus, Taraxacum androssovii Medicago varia, Alyssum murale, Artemisiaspisigera, Falcaria vulgaris, Anchusa strigose, Glaucium leiocarpum, Salvia syriaca, Cryciata taurica Tragopogonalbinervis)collected from the areas of 10000 m (Control area) or 0-100 m away from Askale cement factory in Erzurum;was performed. 16 primers were used, and 390 bands were obtained. Important differences were observed in plant RAPDprofiles collected from 0-100 m areas when compared to their respective controls (10000 m away from the factory). Somebands in control plants got lost, and new band formations were observed. The Genomic template stability (GTS) valuedecreased significantly in plants collected from 0-100 m area as compared to the controls (%56.20). Soil samples from 0-100 m and control area were collected and examined for their heavy metal contents. According to the analysis results,Nickel, Cadmium, Zinc, Lead and Copper concentrations were found to be dramatically high in the soil collected from 0-100 m as compared to the control area. These results indicate that the high heavy metal content in the soil causes thechanges in RAPD profiles and GTS in plants. The data also indicated that RAPD and GTS assays are basic, effective andreproducible means of the genotoxicity control of environmental pollution.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2019Nitric oxide alleviates the effects of copper-induced DNA methylation, genomic instability, LTR retrotransposon polymorphism and enzyme activity in lettuce
Yagci, Semra; Yildirim, Ertan; Yildirim, Nalan; Shams, Mostafakamal; Agar, Guleray
Copper is an essential element for plant growth, but higher concentration can damage proteins, DNA and lipids. Nitric oxide (NO) is a highly reactive and lipophilic molecule and is functional during plant defense responses. Hence, this study aims to evaluate the role of the exogenous NO treatment (0 µM, 200 µM and 300 µM of sodium nitroprusside) on the DNA damage levels, DNA methylation, retrotransposon polymorphism and enzyme activity in lettuce seedlings grown under the non-stress and copper stressed conditions (200 and 400 µM of CuSO4·7H2O). The inter-retrotransposon amplified polymorphism (IRAP) and couple restriction enzyme digestion-random amplification (CRED-RA) were applied to define the genomic template stability (GTS) levels, DNA methylation, and retrotransposon polymorphism. Copper stress (400 µM) decreased the POD activity as compared to control, whereas combined application of NO (300 µM) and copper increased it as compared to the plants treated with 400 µM copper and without NO. The results of this study highlighted that copper stress increased genomic template instability, DNA methylation and long terminal repeat retrotransposon polymorphism. However, simultaneous treatment of NO and copper caused a decrease in retrotransposon polymorphism and DNA methylation, and an increase in GTS and enzyme activity accompanied it. The results implied that in the presence of excess copper the exogenous NO treatment mitigate the adverse effects of copper stress on the GTS, DNA methylation and retrotransposon polymorphism in lettuce seedlings by increasing antioxidant enzyme activity.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2017Determination of genetic diversity among silene species using RAPD and ISSR techniques
Sengul, Meryem; Yildirim, Nalan; Karadayi, Gokce Nardemir; Agar, Guleray
In this study, Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) analysis were used to examine phenotypic and genetic relationships among 10 Silene species (S. vulgaris var. vulgaris, S. multifida, S. alba L. subsp. eriocalycina, S. alba L. subsp. divaricata, S. bu-pleuroides L. subsp. solanocalyx, S. compacta, S. ampullata, S. stenobotrys, S. dichotoma subsp. dichotoma, S. spergulifolia) growing wild in the eastern Anatolia region of Turkey. Sixteen RAPD primers and eight ISSR primers were used to examine polymorphism. According to the RAPD results, 120 amplicons in the size range of 250-4000 bp were produced from 16 primers in 10 Silene species. On the other hand, ISSR primers were produced total 70 amplicons in the size range of 300-2000 bp. The UPGMA cluster was constructed using a combination of data from RAPD and ISSR markers. Genetically, two major clusters were determined among the species of Si-lene. The greatest similarity was observed between the species S. vulgaris and S. multifida (0.098), and the greatest dissimilarity was observed between the species S. vulgaris and S. stenobotrys (0.931). High genetic variations among Silene species growing wildly in eastern Anatolia region of Turkey may imply the differences in their origins. The results in the present study suggested that both RAPD and ISSR analysis are useful for differentiation of Silene species.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2017Protective role of humic acids against picloram-induced genomic instability and DNA methylation in Phaseolus vulgaris
Taspinar, Mahmut Sinan; Aydin, Murat; Sigmaz, Burcu; Yildirim, Nalan; Agar, Guleray
Picloram (4-amino-3,5,6-trichloropicolinic acid) is a liquid auxinic herbicide used to control broad-leaved weeds. Picloram is representing a possible hazard to ecosystems and human health. Therefore, in this study, DNA methylation changes and DNA damage levels in Phaseolus vulgaris exposed to picloram, as well as whether humic acid (HA) has preventive effects on these changes were investigated. Random amplified polymorphic DNA (RAPD) techniques were used for identification of DNA damage and coupled restriction enzyme digestion-random amplification (CRED-RA) techniques were used to detect the changed pattern of DNA methylation. According to the obtained results, picloram (5, 10, 20, and 40 mg/l) caused DNA damage profile changes (RAPDs) increasing, DNA hypomethylation and genomic template stability (GTS) decreasing. On the other hand, different concentrations of applied HA (2, 4, 6, 8, and 10%) reduced hazardous effects of picloram. The results of the experiment have explicitly indicated that HAs could be an alternative for reducing genetic damage in plants. In addition to the alleviate effects of humic acid on genetic damage, its epigenetic effect is hypomethylation.
RDL Kalıcı Kaydıİncele - Conference ObjectYalnız künye2016Cytotoxic and proliferative effects of Fe3O4@UA and usnic acid on MCF-7 cell line
Anar, Mustafa; Diyarbakir, Busra; Dincer, Busra; Karaoglu, Ebubekir; Agar, Guleray; Halici, Zekai
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2016Genetic diversity and relationships detected by ISSR and RAPD analysis among Aethionema species growing in Eastern Anatolia (Turkey)
Sunar, Serap; Yildirim, Nalan; Sengul, Meryem; Agar, Guleray
In this study, Random amplified polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) analysis were used to examine the genetic relationships among eight Aethionema species (Aethionema caespitosum, A. arabicum, A. cordatum, A. fimnraitum, A. armenum, A. speciosum supsp. speciosum, A. memraneceum, A. grandiflorum var. grandiflorum) growing in the wild in Eastern Anatolia, Turkey. Fourteen RAPD primers and 7 ISSR primers were used. The UPGMA cluster was constructed using a combination of data from RAPD and ISSR markers. The Aethionema species were classified into two major groups. The similarity matrix values of between 0.182 (A. cordatum, A. speciosum supsp. speciosum) and 0.927 (A. grandiflorum var. grandiflorum, A. cordatum). High genetic variations among Aethionema species growing in the wild in Eastern Anatolia, Turkey may reveal differences in their origin. The present study suggests that both RAPD and ISSR analysis are useful for the differentiation of the Aethionema species.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2016Antioxidant and antigenotoxic potencies of Sempervivum armenum on human lymphocytes in vitro
Sunar, Serap; Anar, Mustafa; Sengul, Meryem; Agar, Guleray
In this research, the genotoxic and antigenotoxic effects of methanol extract of Sempervivum armenum (MSA) were studied using micronucleus (MN) test and sister chromatid exchange (SCE) test systems in cultured human peripheral blood cells. According to the SCE and MN tests results, MSA reduced the genotoxic effects of aflatoxin B1. In order to explain the reason for the antigenotoxic effects of MSA, antioxidants levels were determined. Cotreatments of 5, 10, 20 mg/mL concentrations of MSA with aflatoxin B1 decreased the frequencies of SCE, MN and the malondialdehyde level and increased the amount of superoxide dismutase, glutathione and glutathione peroxidase which were decreased by aflatoxin. The results of this experiment showed that MSA has strong antioxidative and antigenotoxic effects and this antigenotoxic activities of MSA can be due to the antioxidant activities.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2016Determination of genotoxic effects of fipronil in Vicia faba using random amplified polymorphic DNA analysis
Yildirim, Nalan; Agar, Guleray
This study was undertaken to appreciate genotoxic potential of fipronil herbicides in the roots of Vicia faba seedlings. Fipronil was clearly dose dependent on root growth inhibitors, total soluble protein, and random amplified polymorphic DNA (RAPD) assays. Increase in concentration of fipronil resulted in decreased amount of root length and increased level of protein. For the RAPD analyses, 15 RAPD primers were found to produce unique polymorphic band patterns and were subsequently used to produce a total of 110 bands of 45-1250 bp. Each primer generated 4-11 RAPD bands across 15 primers. The changes occurring in RAPD profiles following fipronil treatment included variation becoming evident as disappearance and/or appearance of DNA bands compared with the normal seedlings. These results indicated that genomic template stability was significantly affected at the above fipronil concentration. This study further confirmed that the RAPD assays are useful in determining potential genotoxicity of fipronil.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2016Relationships Among some Pears Genotypes (Pyrus Communis L.) Based on ISSR and RAPD Analysis; [Bestimmung der genetischen Verwandtschaft bei Birnen mit Hilfe der ISSR und RAPD Methoden]
Kalkışım, Ozgun; Okcu, Melih; Okcu, Zuhal; Karabulut, Besim; Yildirim, Nalan; Agar, Guleray
Thirty one pears genotypes from east blacksea region were evaluated for genetic relationships by using Randomly Amplified Polymorphic DNA (RAPD) and ISSR (Inter-Simple Sequence Repeats) markers from total 70 RAPD and ISSR primer investigated, 22 could amplify clearly and consistently. Cluster analysis of the pears genotypes was performed based on data from polymorphic bands RAPD and ISSR by using Jaccard’s similarity coefficient and the Unweighted pair-group method with arithmetic average (UPGMA) clustering method. The 31 pear genotypes were classified into two major groups. Cluster A was divided into 2 subclusters: Gumushane pears and Trabzon pears. Cluster B consisted of Artvin pears. The similarity matrix values ranged between 0.105 and 0.968.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2015Determination of Genetic Diversity Among Wild Grown Apples From Eastern Black Sea Region in Turkey Using ISSR and RAPDs Markers; [Ermittlung der genetischen Vielfalt bei wildwachsenden Apfelsorten mittels ISSR- und RAPD-Markern in der östlichen Schwarzmeerregion der Türkei]
Okcu, Melih; Kalkışım, Özgün; Okcu, Zühal; Karabulut, Besim; Yildirim, Nalan; Agar, Guleray
In this study, we investigated interspecific variations of apple genotypes using ISSR (Inter-Simple Sequence Repeats) and RAPD (Randomly amplified Polymorphic DNA) technique. Total 19 genotypes of wild grown local varieties were collected from Eastern Black Sea region of Turkey and have been studied for the analysis of ISSR and RAPD profile to examine their relationship. From total 53 RAPD and ISSR primer investigated, 28 could amplify clearly and consistently. All bands obtained from ISSR and RAPDs primer were polymorphic. The dendrogram realized from the RAPD and ISSR markers grouped the 19 genotypes into two major clusters. Cluster I comprised ‘Bey Apple’, ‘Fatty Apple’, ‘Golden Delicious’, ‘Yellow Belly Apple’, ‘Bride Apple’, ‘Green Belly Apple’, ‘Summer Apple’, ‘Yomra Apple’, ‘Tavşanbaşı’, ‘Black Belly Apple’, ‘Chest Apple’, ‘Local Marble’, ‘English Apple’, ‘Willow Apple’, ‘Arabian Girl’, ‘Yellow Hıdır’ and cluster II contained ‘Starking Delicious’, ‘Mahsusa’, ‘Amasya Marble’. Genetic diversity data from this study will be helpful in using and exploiting the wild genetic material for breeding purposes as well as for further research.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2014Protective role of humic acids against dicamba-induced genotoxicity and DNA methylation in Phaseolus vulgaris L.
Yildirim, Nalan; Agar, Guleray; Taspinar, Mahmut Sinan; Turan, Metin; Aydin, Murat; Arslan, Esra
Dicamba is one of herbicides used widely in agriculture today. The wide use of dicamba in agriculture represents a potential danger to the ecosystems and the environment. Thus, the present study is aimed to investigate the DNA damage levels and the DNA methylation changes in Phaseolus vulgaris subjected to whether dicamba and humic acids (HAs) have any protective effect on these changes. Randomly Amplified Polymorphic DNAs (RAPDs) and Coupled Restriction Enzyme Digestion-Random Amplification (CRED-RAs) were used to determinate the DNA damage levels and the changes in the pattern of DNA methylation. The results showed that dicamba (0.2, 0.4 and 0.6 ppm) caused RAPDs profile changes (DNA damage) as increasing, genomic template stability (GTS) as decreasing and DNA hypomethylation. However, these effects of dicamba seen at higher levels decreased after treatment with five different concentrations (2, 4, 6, 8 and10%) of HAs. The results of this experiment have clearly shown that HAs could be used effectively to protect bean seedlings from the destructive effects of dicamba.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2013Determination of the genotoxic effects of Convolvulus arvensis extracts on corn (Zea mays L.) seeds
Sunar, Serap; Yildirim, Nalan; Aksakal, Ozkan; Agar, Guleray
In this research, the methanolic extracts of Convolvulus arvensis were tested for genotoxic and inhibitor activity on the total soluble protein content and the genomic template stability against corn Zea mays L. seed. The methanol extracts of leaf, stem and root of C. arvensis were diluted to 50, 75 and 100 μl concentrations and applied to corn seed. The total soluble protein and genomic template stability results were compared with the control. The results showed that especially 100 μl extracts of diluted leaf, stem and root had a strong inhibitory activity on the genomic template stability. The changes occurred in random amplification of polymorphic DNA (RAPD) profiles of C. arvensis extract treatment included variation in band intensity, loss of bands and appearance of new bands compared with control. Also, the results obtained from this study revealed that the increase in the concentrations of C. arvensis extract increased the total soluble protein content in maize. The results suggested that RAPD analysis and total protein analysis could be applied as a suitable biomarker assay for the detection of genotoxic effects of plant allelochemicals.
RDL Kalıcı Kaydıİncele - ArticleAçık Erişim2011The protective role of zinc and calcium in Vicia faba seedlings subjected to cadmium stress
Taspinar, M. Sinan; Agar, Guleray; Alpsoy, Lokman; Yildirim, Nalan; Bozari, Sedat; Sevsay, Sevgi
The aim of the present study was to evidence the possible antagonistic effect of Zinc (Zn2+) and Calcium (Ca2+) against cadmium (Cd2+)-induced DNA damage by using random amplification of polymorphic DNA (RAPD) and metabolic activities in Vicia faba. The results showed that all doses of Cd2+(10-3M, 10-5M) caused an increase in polymorphism value and a decrease in genomic template stability (GTS %). In addition, when 10-4-10-6M Ca2+, 10-6M Zn2+were added together with 10-3M, 10-4M, 10-5M of Cd2+, polymorphism value decreased besides GTS, total protein and chlorophyll content increased. Results suggested that Zn2+and Ca2+have an antagonistic effect against Cd2+. The order of the antagonisms of Ca2+, Zn2+against Cd2+toxicity was Ca2+> Zn2+. Especially, the degree of antagonistic effect of Zn2+against Cd2+is probably related to its concentration ratio.
RDL Kalıcı Kaydıİncele - ArticleYalnız künye2010Genetic variation within and among three populations of Vicia canescens L. (Fabaceae) as revealed by RAPD and FAMEs analysis
Agar, Guleray; Aksakal, Ozkan; Bozari, Sedat; Sunar, Serap; Erturk, Filiz Aygun; Yildirim, Nalan; Sevsay, Sevgi
The present study employed FAMEs and RAPD to investigate the patterns of biochemical and genetic variation among and within three different populations of Vicia canescens L. Fourteen primers were used for the RAPD and polymorphic bands were obtained with eight primers. Biochemical and genetic distances were calculated and dendrograms were obtained for all studied populations using both RAPD and FAMEs methods. The results of our RAPD analysis suggest that the highest percentage of polymorphic loci (63.7%) was recorded in pine population, which was followed by the campus (60.8%) and colonizing (43.1%) populations. A UPGMA analysis was carried out using Jaccard's index of similarity for 45 individuals in the three populations, which produced a dendrogram. The index revealed that the campus and colonizing populations are the closest ones, while pine and campus populations are the farthest.
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