Browsing by Author "Kocak, Metin"

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Analysis of Genetic Diverity Among Different Melon Accessions Using Peroxidase Gene Markers
(Parlar Scientific Publications (p S P), 2020) Kocak, Metin; Turan, Sibel; Erdinc, Ceknas; Yildiz, Mehtap
Plant peroxidases encoded by a broad multi gene family have important roles in many physiological events such as salt tolerance, auxin metabolism, seeding, protection against pathogens and oxidative stress. In this study the genetic diversity and population structure of 45 different melon (Cucumis melo L.) genotypes from a variety of regions in Turkey and different countries were investigated using peroxidase gene polymorphism markers. 12 polymorphic primers were used to obtain 97 scorable bands for the 45 melon genotypes. Of these bands, only 62.9% were determined to be polymorphic. The number of bands per primer ranged from 6 to 11 and the average number of bands was 8.08. The lowest and the highest polymorphism information contents (PIC) were 0.49 (Pox 12 FaRa) and 0.99 (Pox 13), respectively. The mean PIC value was 0.75. The lowest genetic similarity was found between CU-365 (conomon) and CU-247 (0.143), on the other hand, the highest genetic similarity was observed between CU-360 (cantalopensis) and CU-389 (cantalopensis) (0.875). Using the STRUCTURE computer program, all melon accessions were determined to separate into two subpopulations. These results support the usability of the PDX gene marker system in genetic diversity studies. Also, the data obtained are considered to be a guide for other studies to be performed on melons in the future.
Application of Ipbs-Retrotransposons Markers for the Assessment of Genetic Diversity and Population Structure Among Sugar Beet (Beta Vulgaris) Germplasm From Different Regions of the World
(Springer, 2025) Sadik, Gokhan; Yildiz, Mehtap; Taskin, Bilgin; Kocak, Metin; Cavagnaro, Pablo Federico; Baloch, Faheem Shehzad
Sugar beet is an important agricultural crop product that has been produced and consumed worldwide since the eighteenth century and can adapt to various climatic and soil conditions. The two fundamental building blocks of any crop improvement program are germplasm resources, which contain genetic diversity and phenotypic expression of desired traits. In this study, a total of 58 sugar beet genotypes including 12 from Turkey, 4 from India, 12 from the United States of America, 16 from Iran, 12 from England and Beta vulgaris L. subsp. maritima L. Arcang. as wild species were characterized using 15 inter-primer binding site (iPBS) markers that produced intense and polymorphic bands in the germplasm library. Using these 15 iPBS markers, 102 polymorphic bands were produced and the average number of polymorphic bands was determined as 6.8. Polymorphism information content (PIC) values ranged between 0.58 and 0.83, and the average PIC value was found to be 0.70. It was determined that the most genetically different genotypes were PI 590697-US11 and PI 171508-TR8, with a distance of 0.73. Clustering algorithms Unweighted Pair Group Method Algorithm (UPGMA) and Principal Coordinate Algorithm (PCoA) confirmed that genotypes are an important factor in clustering, and STRUCTURE analysis divided sugar beet gene resources into six populations. Also, the analysis of molecular variance (AMOVA) showed that there was 8% variance among populations and 92% variance within populations. This is the first study to investigate the genetic diversity and population structure of sugar beet germplasm using the iPBS-retrotransposon marker system. The results of this research emphasized that iPBS markers are very successful and effective in examining the genetic diversity of sugar beet germplasm. The results obtained in this study provide a theoretical basis for future selection and breeding of superior sugar beet germplasm sources.
Assessment of Genetic Diversity Among 131 Safflower (Carthamus Tinctorius L.) Accessions Using Peroxidase Gene Polymorphism (Pogp) Markers
(Springer, 2022) Yildiz, Mehtap; Altaf, Muhammad Tanveer; Baloch, Faheem Shehzad; Kocak, Metin; Sadik, Gokhan; Kuzgun, Cansu; Tuncturk, Murat
Background Safflower (Carthamus tinctorius L.) is an old oilseed crop with a 1.4 GB genome size and its flowers are used for food coloring, dyes and pharmaceutical industries. It was domesticated from its putative wild ancestor Carthamus palestinus about forty-five hundred years ago in the fertile crescent region.The current study was aimed to determine the genetic diversity, population structure and to check the applicability of iPBS-retrotransposons markers. Methods and results Eleven POGP primers yielded 70 bands of which 61 were highly polymorphic with 87.14% polymorphism. A great level of genetic variation was examined with higher values of overall gene diversity (0.27), genetic distance (0.53), number of effective alleles (1.46), Shannon's information index (0.41) and polymorphism information contents (0.71). Analysis of molecular variance revealed high genetic variation with 79% within the population. The STRUCTURE, PCoA and Neighbor-joining analysis separated the safflower germplasm into 2 major populations and 1 un-classified population. The accessions which were from Asian countries i.e., China, Afghanistan, Turkey, Iran and Pakistan were genetically similar and clustered together in both populations A and B. The maximum genetic distance was measured 0.88 between Pakistan 26 x Pakistan 24. Conclusion Findings of this research such as maximum diversity indices, higher PIC values showed the effectiveness and utility of POGP markers for the evaluation of genetic relationships among safflower accessions. The results of this study also showed that POGP markers are less effective compared to ISSRs, iPBS-retrotransposons and DArTSeq markers. AMOVA showed high genetic variation (79%) within a population and maximum genetic distance was found between the accessions Pakistan 26- Pakistan 24 and may be suggested as candidate parents for future breeding activities of safflower. The accessions from the fertile crescent region were clustered together and proved the origin of safflower domestication. This study highlights genetic variation among safflower germplasm and could be helpfull for parental selection and planning for future breeding programs.
Characterization of a Diverse Okra (Abelmoschus Esculentus L. Moench) Germplasm Collection Based on Fruit Quality Traits
(Mdpi, 2025) Yildiz, Mehtap; Sirke, Sibel Turan; Kocak, Metin; Mancak, Ibrahim; Ozkaya, Aslihan Agar; Abak, Kazim; Cavagnaro, Pablo Federico
Okra is an important dietary component of many Asian countries, providing high levels of dietary fiber, phytonutrients (e.g., antioxidant vitamins and pigments), and essential minerals. Evaluation of okra germplasm collections can improve the curation of genebanks and help identify superior materials for breeding. In this study, 66 okra accessions from diverse geographical origins were characterized based on fruit quality traits, including fruit fresh (FFW) and dry weights (FDW), dry matter (DM), diameter, length, and diameter of the fruit peduncle; concentration of vitamin C, chlorophyll a and b, and total chlorophyll; and color-chroma values. Significant (p < 0.05) and substantial variation was found among the accessions for all traits. Mean FFW and FDW varied nearly three-fold, with ranges of 3.76-9.99 g and 0.43-1.34 g, respectively, with a range in DM content of 10.5-19.4%. Vitamin C and total chlorophyll content varied 6.4- and 8.3-fold, with ranges of 12.8-82.8 and 1.07-8.91 mg/100 g fw, respectively, with substantial variation also observed in chlorophyll composition. Significant positive correlations were found between vitamin C and total and subtypes of chlorophyll levels (r = 0.29-0.32), whereas the strongest correlations were between FFW and FDW (r = 0.88) and between total chlorophyll and chlorophyll subtypes a and b (r = 0.90-0.95). Additionally, a dendrogram constructed based on these phenotypic data grouped the accessions in general agreement with their geographical origins and fruit traits. Overall, our results revealed broad phenotypic diversity in the evaluated germplasm, which is exploitable in okra breeding programs aimed at increasing fruit quality and nutraceutical value.
Determination of the Effective Radiation Dose for Mutation Breeding in Purple Carrot (Daucus Carota L.) and Possible Variations Formed
(Springer, 2022) Yarar, Gulistan; Kocak, Metin; Denli, Nihal; Cavagnaro, Pablo F.; Yildiz, Mehtap
Background Plant breeding allows altering the genetic structure of plants to meet human needs. The use of radiation technology for inducing mutations and -thereby- new phenotypic variants has become increasingly common as a tool for developing new crops. The aim of this study was to determine the effective gamma irradiation dose for inducing mutations in purple carrot. Methods and results Increasing gamma radiation doses [0, 50, 100, 200, 300, 400, 500, and 600 Gy] were applied to purple carrot seeds. The irradiated seeds were sown in pots and the emergence and survival rates of the seedlings were analyzed. Considering plant emergence (%) as a response variable, the LD50 dose was 387.5 Gy. Analysis of root length, root width (shoulder diameter) and plant height in control (0 Gy) and irradiated plants (50-600 Gy) revealed an inverse association between these morphological traits and radiation dose. SRAP and ISSR markers were used to identify DNA polymorphisms in irradiated and control plants. The range of amplicons per primer set revealed by ISSR and SRAP markers was 4-10 and 2-13, respectively. In the ISSR analysis of the irradiated carrots (for the 8 doses used), we obtained range values for the average Nei's gene diversity, Shannon's information index, and polymorphism information content (PIC) of 0.13-0.25, 0.20-0.35, and 1.39-1.67, respectively, whereas in the SRAP analysis, the range values for these parameters were 0.15-0.25, 0.23-0.37, and 0.43-0.58, respectively. Cluster analysis revealed three main groups; (a) non-irradiated (control) plants, (b) plants from the 600 Gy dose, and (c) a third group with two subgroups: one with individuals from the lowest irradiation doses (50-200 Gy) and a second group with individuals from the highest irradiation doses (300-500 Gy). Conclusions This is the first report on determining effective mutagen doses and genetic characterization of induced mutagenesis via gamma irradiation in purple carrot. ISSR and SRAP markers were successful in detecting variations among different levels of mutagen doses.
Exploring the Genetic Variations and Population Structure of Turkish Pepper (Capsicum Annuum L.) Genotypes Based on Peroxidase Gene Markers
(Springer Heidelberg, 2018) Akyavuz, Rifat; Taskin, Bilgin; Kocak, Metin; Yildiz, Mehtap
Capsicum is thought as one of the most diverse and significant genera due to its varied uses in different parts of the world. In this study, we worked with a total of 71 pepper genotypes from different locations of Turkey to investigate the level of their diversity using the peroxidase gene polymorphism (POGP) markers to reveal their population structure. For this purpose, 14 peroxidase primer pairs were used. They produced 139 bands (mean = 9.9 bands/primer), of which similar to 85.6% were polymorphic in the all germplasm collection. Polymorphism information content (PIC) ranged between 0.48 and 0.97 with an average of 0.75. Range and mean values for gene diversity (h) were 0.09-0.22 and 0.17, respectively. Shannon's information index (I) per POGP marker ranged from 0.18 to 0.35 with a mean of 0.29. Using three clustering methods (unweighted pair-group method with arithmetic means, principal coordinate analysis, and STRUCTURE) revealed a clear separation of all the C. annuum accessions from C. frutescens and C. chinense accessions in our study. Clusters did not establish an association between the accessions and their geographical origin. This is the first study exploring the population structure through the genetic diversity of Turkish peppers from different regions of the country based on the peroxidase gene markers.
The First Report About Genetic Diversity Analysis Among Endemic Wild Rhubarb (Rheum Ribes L.) Populations Through Ipbs Markers
(Tubitak Scientific & Technological Research Council Turkey, 2021) Erdinc, Ceknas; Ekincialp, Aytekin; Turan, Sibel; Kocak, Metin; Baloc, Faheem Shahzad; Sensoy, Suat
Approximately 30% of plant species of Turkey, which is among the richest countries in terms of biodiversity, has been endemic. Wild rhubarb (Rheum ribes L.) is a wild vegetable grows especially in the eastern region of Turkey and is an endemic species. In this study, genetic relationships among 80 wild rhubarb genotypes collected from some regions of Lake Van Basin, which are in the distribution area, were tried to be determined by iPBS marker system. At the same time, a commercial variety of R. rhabarbarum, which is a cultivated species, was used as control. PCR studies were conducted with 23 iPBS primers to determine genetic relationships, and a total of 340 scorable bands were obtained. 100% polymorphism rate was obtained from all primers studied. While the average PIC value was found to be 0.90, the highest value was found to be 0.97 from the primer # 2220. It was determined that the genotypes were divided into 3 basic groups in the dendogram created with UPGMA based on Jaccard similarity coefficient.
Genetic Diversity Analysis in the Turkish Pepper Germplasm Using Ipbs Retrotransposon-Based Markers
(Tubitak Scientific & Technological Research Council Turkey, 2020) Yildiz, Mehtap; Kocak, Metin; Nadeem, Muhammad Azhar; Cavagnaro, Pablo; Barboza, Karina; Baloch, Faheem Shehzad; Keles, Davut
Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, including Turkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversity and population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers. A total of 20 iPBS primers were used that generated 172 bands (mean 8.6 bands/primer), of which similar to 92% were polymorphic in the entire germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content of the markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPG MA, STRUCTURE, and principal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a few subclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level, the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between the iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing the genetic diversity and population structure in the Turkish pepper gennplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties.
Peroxidase Gene Markers Revealed Genetic Diversity and Population Structure in Okra Germplasm
(Springer, 2022) Yildiz, Mehtap; Furan, Mehmet Alp; Kocak, Metin; Sadik, Gokhan; Kuzgun, Cansu; Al-Khafaji, Mahdi; Bahjat, Noor Maiwan
Okra is a widely grown vegetable crop in various regions of the world and provides significant amounts of vitamins and minerals. Numerous researchers have documented the efficacy of phenotypic and molecular classification of the diverse okra germplasm collections found throughout the world. The genetic variation of Turkish okra germplasm, which included 39 genotypes, was characterized using 14 POGP (peroxidase gene polymorphism) primer pairs in comparison to other world okra genotypes and accessions, which contained 27 genotypes. A total of 84 bands were generated using 14 POGP primer pairs, with 43 (51%) of them being polymorphic between okra accessions. The values of polymorphism information content ranged from 0.03 to 0.99, with an average of 0.48. The range and mean values for gene diversity (h) were 0.03-0.42 and 0.25, respectively. Shannon's information index (I) varied between 0.07 and 0.62 for each POGP marker, with a mean of 0.40. The most divergent genotypes were found to have a GS value of 0.23, with IN-7 and TR20-3 being the genetically most distant. The STRUCTURE, PCoA and Neighbor-joining analysis separated the okra germplasm into three populations. AMOVA revealed 23 and 77% variance across and within populations, respectively. Although the germplasm of okra is generally homogenous, the influence of shared genes is more significant. For the first time, the genetic composition of okra was determined using peroxidase gene markers.
Production of Microspore-Derived Plants by Anther Culture of Cyclamen Coum
(2024) Kocak, Metin; Tütüncü, Mehmet; Khafaji, Mahdi Al; Yildiz, Mehtap
Cyclamen is one of the most important ornamental crops sold worldwide as a potted flower for winter production. Cyclamen species take up a wide swathe of habitats across Türkiye. Ten wild Cyclamen species grow naturally in Türkiye and some of them are endemic. This study aimed to produce haploid plants of C. coum using anther culture. The microspore developmental stage was evaluated by staining anther with acetocarmine (%2), and then the stage was correlated with bud size. It was determined that the buds between 7.64 and 8.23 mm had the appropriate bud size for the late uninuclear stage. Anthers were cultured in B5 medium containing different levels of 1-Naphthaleneacetic acid (NAA) (0.1, 1, 2 mgL-1), 2,4-Dichlorophenoxyacetic acid (2,4-D) (0.1, 1, 2 mgL-1), and kinetin (0, 1 mgL-1), 90 gL-1 sucrose and 3 gL-1 gelrite for haploid embryo production. Anthers were kept at 4°C for 4 days after culture. The explants were incubated at 24°C in a completely dark condition until the embryo was formed, then embryos were transferred to hormone-free media in 16:8 hours (light (75 µmolm-2s-1): dark) photoperiod. The experiment was carried out for two years. In the first year, 12 different media were examined in view of regeneration and the experiments were continued with selected 7 media in the second year. The highest callus regeneration rates were %5.71 and 14.5% and the highest embryo induction rates varied between 8.57% and 4.0% in the first and second year respectively. Embryo/callus formation was observed in 7 of a total of 12 different media tested for haploid plant production, and the best media were kinetin (1 mgL-1) + NAA (1, 2 mgL-1) and kinetin (1 mgL-1) +2,4-D (2 mgL-1). Our findings indicated that cold pre-treated anther explants collected at appropriate flower bud size resulted in embryo production. Additionally, B5 medium supplemented with NAA and kinetin ensured successful embryo regeneration from anther explants in wild C. coum.
Synthetic Seed Production of Flower Bulbs
(Springer Nature Switzerland Ag, 2019) Kocak, Metin; Sevindik, Basar; Izgu, Tolga; Tutuncu, Mehmet; Mendi, Yesim Yalcin
Flower bulbs are perennial or annual plants with underground structures such as bulb, corn, tuber, and rhizomes. These plants have economic value especially in ornamental plant sector as cut flower, potted flower, and outdoor plants. Most of these plants have garish flower, and many of them are monocotyledon. Cyclamen, Tulipa, Lilium, Narcissus, Gladiolus, Hyacinthus, Crocus, Iris, Allium, Alstroemeria, Anemone, Orchis, Rhododendron, Freesia, Hippeastrum, Muscari, Ornithogalum, Ranunculus, and Zantedeschia are the most important geophytes that are commercially used in the world. These plants can be propagated using conventional and tissue culture techniques. Synthetic seed production is one of these techniques. Synthetic seed, namely, artificial seed, is described as artificially encapsulated plant tissues and somatic embryos with alginate hydrogel. Synthetic seed technology has significant effect on the conservation of the plant tissues and sustainability of the plants. Recently, conservation of the plant species studies significantly increased, and artificial seed method was used as the most common process to conserve important species. In this chapter, oldest and newest synthetic seed production researches were discussed and presented chronologically.