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    Determination of Some Biochemical Properties and DNA Barcoding of 'Şam' and 'Gündüzbey' Peaches
    (Springer, 2025) Koc, Besime; Murathan, Zehra Tugba; Sevindik, Emre
    The peach, with its juicy flesh and sweet aroma, is not only a beloved summer fruit but also a symbol of longevity and prosperity in many cultures. In this study, some biochemical properties of '& Scedil;am' and 'G & uuml;nd & uuml;zbey' peaches were revealed and can be genetically distinguished from other Prunus species with the chloroplast DNA barcoding (cpDNA) method. Total phenolic contents were determined as 139.9 mg/100 g in the 'G & uuml;nd & uuml;zbey' genotype and 41.4 mg/100 g in the '& Scedil;am' genotype, while total flavonoid contents were determined as 9.5 mg/100 g and 2.4 mg/100 g, respectively. Chlorophyll a contents were determined as 1.13 mu g/g in the 'G & uuml;nd & uuml;zbey' genotype and 1.82 mu g/g in the '& Scedil;am' genotype; chlorophyll b value was determined as 0.86 mu g/g in the 'G & uuml;nd & uuml;zbey' genotype, 1.14 mu g/g in the '& Scedil;am' genotype and total carotenoid values were determined as 0.10 mu g/g, 0.44 mu g/g, respectively. The 'G & uuml;nd & uuml;zbey' genotype had 72.5% 2,2 '-Azino-bis-3-ethylbenzthiazoline-6-sulfonic acid (ABTS +) radical scavenging activity, 72.2% 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity and 281.4 mu mol Fe II/g ferric reducing antioxidant power (FRAP); '& Scedil;am' genotype had 64.2% ABTS radical scavenging activity, 55.2% DPPH radical scavenging activity and 169.3 mu mol Fe II/g FRAP. 'G & uuml;nd & uuml;zbey' and '& Scedil;am' peach genotypes were found in a group with Prunus mira, P. kansuensis, P. dulcis, P. bucharica, P. argentea, P. grayana, P. virginiana, and P. serotina species in the phylogenetic trees obtained using chloroplast (cpDNA) rbcL sequences.
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    DNA Barcoding and Sequence Analysis of the cpDNA rbcL Region in Some Pyrus communis L. (Rosaceae) Genotypes from Ardahan/Turkiye
    (Springer, 2023) Sevindik, Emre; Murathan, Zehra Tugba
    In this study, we performed barcode and sequence analysis using the cpDNA rbcL region of seven Pyrus communis genotypes grown in Ardahan/Turkiye. The rbcL region of chloroplast DNA was amplified using primers rbcLaF and rbcLaR. The neighbor joining tree was created to determine the relationships between Pyrus communis genotypes. Amplified cpDNA rbcL sequences ranged between 546 and 551 nucleotides. The average nucleotide ratio was determined as 30.0% thymine, 20.1% cytosine, 26.8% adenine and 23.1% guanine. The neighbour joining phylogenetic tree was composed of two clades. The divergence values differed between 0.000 and 0.002. In addition, the sequences of Alchemilla, Cotoneaster, Fragaria, Malus, Prunus, Rosa, Sorbus and Rubus belonging to the Rosaceae family were obtained from the National Center for Biotechnology Information, and a neighbor joining tree was constructed. The phylogenetic relationship between the sequence data of these species and Pyrus communis genotypes was revealed. In the rbcL results, Pyrus communis genotypes were not resolved in themselves and were polytomic. In addition, Malus, Cotoneaster, Sorbus and Prunus species appeared in the same clade.
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    Evaluating DNA barcoding using cpDNA matK and rbcL for species identification and phylogenetic analysis of Prunus armeniaca L. (Rosaceae) genotypes
    (Springer, 2024) Sevindik, Emre; Korkom, Yunus; Murathan, Zehra Tugba
    In this study, DNA barcoding and phylogenetic analysis of five Prunus armeniaca L. genotypes (Cataloglu, Hacihaliloglu, Hasanbey, Hudayi, and Kabaasi) grown in Malatya/Turkiye were conducted using chloroplast DNA (cpDNA) matK and rbcL regions. The cpDNA matK region was amplified using matK472F and matK1248R primers, while the rbcL region was amplified with rbcLaF and rbcLaR primers. The matK and rbcL sequences were utilized to assess nucleotide ratios, genetic distance, and nucleotide diversity (p). The neighbor- joining (NJ) tree including other Prunus species from NCBI was created. In addition, physiochemical and 3-D analysis of matK and rbcL proteins were performed. As a result, p = 0.000549 for matK sequence and p = 0.002657 for rbcL sequence were determined. NJ (neighbor joining) phylogenetic trees formed with both matK and rbcL sequences were found to be compatible with each other. The matK and rbcL gene regions were found to be suitable for phylogenetic analysis.
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    Evaluation of Antioxidant, Antibiofilm, and Mutagenic Properties of Different Grape Fruits
    (Pleiades Publishing Inc, 2025) Murathan, Zehra Tugba; Erbil, Nurcan; Arslan, Mehmet; Sevindik, Emre
    Grape is a plant belonging to the Vitis genus of the Vitaceae family and has thousands of different varieties grown in many regions of the world. In this study, total phenolic content, total flavonoid content, antioxidant activity, antibiofilm activity and mutagenic activity values of pericarp samples of Banaz & imath; karas & imath;, K & ouml;hn & uuml;, Kurey & scedil;, P & uuml;t & uuml;rge K & imath;rm & imath;z & imath;s & imath;, Hatun parma & gbreve;& imath;, Gelin parma & gbreve;& imath;, Bo & gbreve;azkere, Mikeri, Maz & imath;k & imath;ran, A & scedil;& imath;k beyaz & imath;, Asmal & imath;k, Ternebi, & Scedil;am, & Ouml;k & uuml;zg & ouml;z & uuml;, & Idot;zmir and & Ccedil;ekirdeksiz grape varieties grown in Malatya/T & uuml;rkiye were studied. The highest total phenolic content, DPPH and ABTS radical scavenging activity and FRAP values were determined in the Maz & imath;k & imath;ran variety (163.6 mg/g, 52.8%, 48.2% and 264.2 mu mol/g), the highest total flavonoid content was determined in the Gelin parma & gbreve;& imath; variety (26.4 mg/100 g). It was observed that fruit extracts of all varieties had different levels of antibiofilm activity against Listeria monocytogenes ATCC 19115 at different content amounts. However, it was determined that fruit extracts of Hatun parma & gbreve;& imath;, Banaz & imath; karas & imath;, Maz & imath;k & imath;ran, Mikeri and & Idot;zmir varieties showed over 90% antibiofilm activity. 50 and 100 mu L/plate doses of fruit extracts tested in P & uuml;t & uuml;rge K & imath;rm & imath;z & imath;s & imath; samples showed mutagenic properties in TA98 and TA100 strains compared to the control.
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    Genetic Diversity and Biological Characteristics of Grape Variety (Vitis vinifera) Leaves
    (Springer, 2025) Murathan, Zehra Tugba; Sevindik, Emre; Arslan, Mehmet; Erbil, Nurcan
    Grapes are an agricultural product that is consumed frequently around the world both as a fruit and in other forms and is known to have health-supporting properties. Grape leaves are also consumed as food, fresh or pickled, in different parts of the world. In this study, leaf samples of 16 different grape varieties widely grown in Malatya/T & uuml;rkiye were analyzed: 'Banaz & imath; Karas & imath;', 'K & ouml;hn & uuml;', 'Kurey & scedil;', 'P & uuml;t & uuml;rge K & imath;rm & imath;z & imath;s & imath;', 'Hatun Parma & gbreve;& imath;', 'Gelin Parma & gbreve;& imath;', 'Bo & gbreve;azkere', 'Mikeri', 'Maz & imath;k & imath;ran', 'A & scedil;& imath;k beyaz & imath;', 'Asmal & imath;k', 'Ternebi', '& Scedil;am', '& Ouml;k & uuml;zg & ouml;z & uuml;', '& Idot;zmir', and '& Ccedil;ekirdeksiz'. Bioactive compounds, antioxidant capacities, antibiofilm activities, and mutagenic properties of leaf samples were determined. The genetic relationship between the varieties was determined using ISSR markers. According to the results, the 'Bo & gbreve;azkere' variety was found to have the highest levels of bioactive compound and antioxidant activity. The leaf extracts of '& Scedil;am', 'Banaz & imath; Karas & imath;', 'K & ouml;hn & uuml;', and 'P & uuml;t & uuml;rge K & imath;rm & imath;z & imath;s & imath;' varieties exhibited over 90% antibiofilm activity against Listeria monocytogenes ATCC 19115. In TA100 strains, leaf extracts of '& Ccedil;ekirdeksiz' (100 mu L/plate), 'K & ouml;hn & uuml;' (25 mu L/plate), 'Hatun Parma & gbreve;& imath;' (25 mu L/plate), 'Asmal & imath;k' (25 mu L/plate), 'Bo & gbreve;azkere' (100 mu L/plate), '& Ouml;k & uuml;zg & ouml;z & uuml;' (50 mu L/plate), '& Idot;zmir' (25 mu L/Plate), and 'A & scedil;& imath;k Beyaz & imath;' (50 mu L/plate) showed mutagenic properties compared to the solvent control methanol. '& Idot;zmir' and 'Bo & gbreve;azkere' genotypes were determined to be the closest genotypes to each other, while 'Bo & gbreve;azkere' and 'Asmal & imath;k' genotypes were determined to be the farthest apart. A total of 136 bands and a polymorphism rate of 97.05% were obtained in the ISSR-PCR analyses. In conclusion, the data obtained from this study reveal important biological properties of grape leaves that may have an effect on human health, and they provide insight into the levels of genetic relatedness of the varieties used in the study.
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    Genetic variation among Brassica rapa subsp. rapa genotypes growing in Malatya/Türkiye
    (Springer, 2024) Kucuk, Rabia; Sevindik, Emre; Cayir, Muhammed Ebrar; Murathan, Zehra Tugba
    In this study, the genetic variation of 18 Brassica rapa subsp. rapa genotypes grown in Malatya was determined using the inter simple sequence repeat - polymerase chain reaciton (ISSR-PCR). Using nine ISSR primers, a total of 73 bands were obtained and the polymorphism rate was 91.78%. The mean polymorphism information content value was determined as 0.3319. The mean gene diversity (H) value was determined as 0.4276. The mean major allele frequency value was determined as 0.6531. Similarity index values were determined to be between 0.0928 and 1.0924. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram consisted of two groups. Principal component analysis analysis and UPGMA dendrogram were compatible. In addition, the groups in the phylogenetic trees were partially compatible with geographical distribution. Our results suggest that ISSR-PCR analysis is a suitable approach for breeding Brassica rapa subsp. rapa genotypes and developing different cultivars.
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    Molecular Genetic Diversity and Phylogenetic Investigation of Pyrus communis L. (Rosaceae) Genotypes Using cpDNA Sequences with RAPD and ISSR Analyses
    (Springer, 2023) Sevindik, Emre; Efe, Fadime; Murathan, Zehra Tugba
    In this study, molecular genetic diversity and phylogenetic investigation of seven Pyrus communis L. genotypes were conducted based on random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) and inter simple sequence repeat PCR (ISSR-PCR) using chloroplast DNA trnL intron and trnL-F sequences. Pyrus communis genotypes were obtained from Ardahan province, Turkiye. A total of 15 RAPD and 18 ISSR primers were used to determine the molecular genetic diversity of the Pyrus communis genotypes. For trnL intron, trnC, trnD, for trnL-F, trnE, and trnF primers were used in PCR for amplification. In all, 57 and 91 bands were obtained by RAPD and ISSR analysis, respectively. Polymorphism rates were 78.94% and 85.71%, respectively. For trnL intron analyses, the average nucleotide composition consisted of 39% thymine, 17.5% cytosine, 28.4% adenine, and 15.1% guanine. In trnL-F assays, the average nucleotide composition consisted of 31.9% thymine, 14.4% cytosine, 37.5% adenine, and 16.1% guanine. The results of the phylogenetic tree constructed with trnL intron and trnL-F sequences of Alchemilla, Rosa, Sorbus, Malus, Prunus, and Cotoneaster species of the Rosaceae family obtained from NCBI were found to be similar. As a result of the study, polymorphisms were obtained at the rates of 78.94% and 85.71% from RAPD and ISSR analyses, respectively. In conclusion, detailed phylogenetic relationships of pear genotypes using chloroplast trnL intron and trnL-F sequences with respect to other species from the same family were revealed.
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    Molecular Genetic Diversity of Prunus armeniaca L. (Rosaceae) Genotypes by RAPD, ISSR-PCR, and Chloroplast DNA (cpDNA) trnL-F Sequences
    (Taylor & Francis, 2020) Sevindik, Emre; Murathan, Zehra Tuğba; Sevindik, Mustafa
    In this study, phylogenetic analysis of some Turkish Prunus armeniaca L. genotypes was conducted based on RAPD-PCR, ISSR-PCR, and chloroplast DNA (trnL-F) sequence analyses. Prunus armeniaca genotypes were obtained from Malatya province, and brought to the laboratory for genomic DNA isolation. Eleven RAPD and fifteen ISSR primers were used to determine molecular characterization of Prunus armeniaca genotypes. For the amplification of the trnL-F region, trne and trnf primers were used in Polymerase Chain Reaction (PCR). A total of 46 and 95 bands were obtained with RAPD and ISSR analysis, respectively. The trnL-F sequences varied from 398 to 403 nucleotides. Average nucleotide composition of trnL-F sequences was 31.0% T, 14.4% C, 37.4% A and 17.2% G. The genetic distance between the five apricot genotypes is 0.00. A maximum likelihood tree was generated to determine genetic relationships among Prunus armeniaca genotypes. Analysis of Prunus armeniaca genotypes based on RAPD, ISSR, and trnL-F sequences revealed that the rate of polymorphism obtained using RAPD and ISSR were higher than those obtained through the trnL-F sequences.