Browsing by Author "Demirel, Serap"

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Assessment of Genetic Diversity and Population Structure in Local Alfalfa Genotypes Using Ipbs Molecular Markers
(Springer, 2023) Eren, Baris; Keskin, Bilal; Demirel, Fatih; Demirel, Serap; Turkoglu, Aras; Yilmaz, Abdurrahim; Haliloglu, Kamil
iPBS retrotransposon markers, in other words, inter-primer binding site markers based on retrotransposon, have been helpful for the determination of genetic diversity in several plants. The study was evaluated using 10 iPBS molecular markers on the level of genetic diversity and genetic structure of alfalfa genotypes. A total of 280 alleles in 50 alfalfa genotypes (48 local genotypes and 2 commercial varieties) were obtained by 267 polymorphic markers with an average of 28 per locus, ranging from 9 to 41 alleles. The rate of polymorphism of the markers ranged from 86.36 to 100% with an average of 93.71%. The average number of polymorphic bands per marker was detected as 26.7. The mean PIC value and Dice's similarity index were calculated as 0.14 and 0.50 respectively. The results of UPGMA analysis, principal coordinate analysis (PCoA), and STRUCTURE demonstrated that the 50 alfalfa genotypes could be classified into 4 subpopulations, namely the Q1, Q2, Q3, and Q4. The Nei's genetic distances ranged from 0.0121 to 0.0359. iPBS markers and alfalfa genotypes used in this study may be used in studies of alfalfa breeding and germplasm conservation.
Bazı Pamuk Çeşitlerinde İpbs Analiziyle Genetik Varyasyonun Ortaya Çıkarılması
(2021) Demırel, Fatıh; Yıldırım, Bünyamın; Kumlay, Ahmet Metin; Eren, Barış; Demirel, Serap
Bu çalışmada, 10 adet pamuk (Gossypium hirsutum L.) çeşidinin moleküler karakterizasyonu yapılmıştır. DNA temelli 6 adet iPBS markörleri kullanılmış olup, toplamda 36 adet polimorfik bant görülmüş ve ortalama polimorfizm oranı %77.65 olarak saptanmıştır. Markörlerin ortalama polimorfizm değeri (PIC) de 0.27, ortalama gen çeşitliliği (H) değerleri 0.34, ortalama Dice benzerlik katsayı değeri 0.37, korelasyon katsayı değeri (r) de 0.9026 olarak hesaplanmıştır. Genotipler arasındaki genetik ilişki, NTSYS-pc yazılımı kullanılarak belirlenmiş ve 0.0456 ile 0.8387 arasında değiştiği saptanmıştır. İlk üç eigen değerleri toplamı, toplam varyasyonun %71.93’ünü açıklamıştır. Genotiplerin moleküler varyasyon gösterdiği belirlenmiş olup, genetik çeşitlilik sonuçlarının gelecekteki pamuk ıslah çalışmalarının planlanmasında kullanılabileceği sonucuna varılmıştır.
Cloning, Bacterial Expression, Purification and the Antiviral Effect on Zucchini Yellow Mosaic Virus (zymv) of Tritin Protein Gene Which Is Inactivating Ribosome in Wheat (triticum Aestivum L.)
(2022) Demirel, Serap; Usta, Mustafa
Bitki virüsleri ekonomik olarak önemli kayıplara neden olan ve etkin mücadele yöntemleri çoğunlukla olmayan patojenlerdir. Bu tez çalışması kapsamında, buğday bitkisinden rekombinant tritin proteinin elde edilmesi ve proteinin sakız kabağı (Cucurbita pepo L.) bitkisinde Zucchini yellow mosaic virus (ZYMV)'üne karşı antiviral aktivitesi ortaya konmaya çalışılmıştır. Ekmeklik buğday çeşidi Kutluk-94'ten izole edilen total ribonükleik asit (RNA) komplementer DNA sentezinde (cDNA) kullanılmıştır. Gen spesifik primerlerle tritin geni RT-PZR ile çoğaltılarak izole edilmiştir. Tritin geni pGEM-T Easy ve pETDuet-1 vektörüne klonlanmıştır. E. coli BL21 (DE3) hücrelerinde tritin proteinin ekpresyonu sağlandıktan sonra, tritin proteini izole edilmiş ve saflaştırılmıştır. SDS-PAGE ile doğrulananan proteinin konsantrasyonu 12.56 mg/ml olarak belirlenmiştir. Sadece ZYMV uygulanan bitkilerde hastalık şiddeti %92.74 iken, 2 mg/ml tritin uygulanan bitkilerde hastalık şiddeti %46.66 olarak hesaplanmıştır. Hastalık şiddetinde azalışa neden olan tritin proteini, aynı zamanda ZYMV-CP geninin ekpresyon seviyesinde de azalışa neden olmuştur. Tritin uygulanan bitkilerde pathogenesis related gene 1 (PR1) geninin ifadesinin arttığı real time PZR ile ortaya konmuştur. Tritinin ZYMV virüsüne karşı antiviral etkisine ilaveten, morfolojik veriler farklı konsantrasyonlardaki tritin proteinin sakız kabağı bitkilerine fitotoksik etki ettiğini göstermiştir.
Coat Protein of Alfalfa Mosaic Alfamovirus (Amv) From Türkiye: Genetic Inference and in Silico Docking Analysis for Potential Antiphytoviral Purposes
(Univ Agr Sci & veterinary Med Cluj-napoca, 2024) Demirel, Serap; Guller, Abdullah; Usta, Mustafa; Kurt, Zeynelabidin; Korkmaz, Gulustan
In 2021, a study was conducted in the Denizli region of Turkiye to investigate the phylogenetic relationship and presence of alfalfa mosaic alfamovirus (AMV) infecting pepper plants exhibiting viral disease symptoms. A total of 57 samples were collected, of which twenty-four tested positive for AMV with reverse transcriptase polymerase chain reaction (RT-PCR) assays. Samples from pepper plants displaying virus symptoms gave positive bands on the agarose gel, while healthy plants yielded negative results. One of the positive samples was randomly selected, cloned and sequenced. This sequence of the Denizli AMV isolate (753 bp) was recorded in the GenBank database with accession number OQ845956. The nucleotide sequence showed a high nucleotide consensus of 97%-99% compared with the nucleotide sequences of the same variants from different origins in GenBank. According to the phylogenetic tree generated through the Neighbour Joining (NJ) method, this AMV isolate belongs to the same group as Iranian isolates from various of hosts. Furthermore, in silico docking analysis of the coat protein (CP) of the AMV isolate and promising 12 essential oil compounds was performed to enable potential antiviral drug development. Docking study showed that eucalyptol, eugenol and carvacrol can make important contributions to the advancement of drug -based strategies for the managing of plant viruses by interacting with the virus coat protein of high binding energies, -5.3, -5.2 and -5.0 kcal mol-1, respectively. Although the presence of AMV in Denizli province has been reported previously, this study reports the phylogenetic relationships and docking analysis of the new AMV isolate in pepper crops.
Comprehensive Survey of Common Potato Viruses in Eastern Anatolia Region of Turkey: New Isolates and Phylogenetic Insights
(Springer, 2025) Korkmaz, Gueluestan; Usta, Mustafa; Guller, Abdullah; Demirel, Serap
Potatoes (Solanumtuberosum L.) are a vital crop in Turkey, contributing significantly to the country's economy. However, they are susceptible to various viral infections, causing substantial yield losses if left unmanaged. This study aimed to conduct a comprehensive survey of economically significant viruses affecting potatoes in the Eastern Anatolia Region, Turkey, including the identification of new isolates and the inference of their phylogenetic relationships. A total of 1130 fresh leaf samples, including asymptomatic and symptomatic plant samples, were tested using the multiplex RT-PCR (m-RT-PCR) method to determine the prevalence of five viral pathogens. The test results revealed the presence of four viral pathogens, with an overall infection incidence of 37.08%. PVY was found in 35% of the samples, PVS in 8.5%, PVX in 1.8%, and PLRV in 1%. However, PVA was not detected. In addition, 74 of the 98 samples tested were positive for PVY + PVS, 13 for PVY + PVX, 2 for PVY + PLRV, 8 for PVY + PVS + PVX, and 1 for PVY + PVS + PLRV. From each sample that tested positive, two isolates were selected, and the complete coat protein (CP) gene regions of these isolates were cloned and sequenced. The sequences of the new potato virus isolates were deposited in the GenBank. Nucleic acid sequence comparisons revealed a consensus of over 99% among all available isolates and those from other regions of the world. However, this similarity is not specific to any particular host or region. In support of the similarities in nucleic acid, phylogenetic analyses also provided information on the evolutionary relatedness of these isolates from various origins and hosts. This finding suggests that the genetic makeup of these isolates is highly conserved across different populations and environments. This study, conducted in the Eastern Anatolia Region of Turkey, is the first comprehensive report on the presence and molecular phylogeny of four viral pathogens of economic importance in potato crops.
Diyarbakır İlinde Yetiştirilen Hıyar Bitkilerinde Hıyar Mozayik Virüsü’nün Genetik Çeşitliliği
(2024) Güller, Abdullah; Demirel, Serap; Usta, Mustafa; Korkmaz, Gülüstan
Hıyar bitkisi (Cucumis sativus L.) dünya çapında üretilen önemli bir kültür bitkisidir. Yaygın viral hastalıklarından biri olan Hıyar mozayik virüsü (Cucumber mosaic virus, CMV) hıyar bitkisinde verim ile birlilkte kaliteyi düşürerek ekonomik kayıplara neden olmaktadır. Diyarbakır ilinde 2021 yılı Eylül ayında yapılan gözlemlerde, yapraklarda mozaik, düzensiz sarımsı lekeler ve deformite gibi virüs benzeri simptomlar gösteren hıyar bitkileri gözlenmiştir. Simptom gösteren ve göstermeyen örnekler toplanarak CMV spesifik primerler kullanılarak ters transkriptaz polimeraz zincir reaksiyonu (RT-PZR)’na tabi tutulmuş ve üretilen DNA bantları agaroz jelde görüntülenmiştir. CMV infeksiyonu 15 örnekten yedisinde belirlenmiştir. Rastgele seçilen bir örneğin bakteriyel klonlanması ve dizilenmesi sonucunda, CMV kısmi kılıf proteni geninin 593 bp uzunluğunda olduğu belirlenmiş ve NCBI veri tabanına MW962979.1 erişim numarası ile kaydedilmiştir. CMV’nin farklı izolatlarıyla gerçekleştirilen filogenetik ağaca göre, Diyarbakır CMV izolatı Subgrup IA grubunu oluşturan Avustralya, İsrail, İspanya, Macaristan, Japonya ve Kore’ye ait CMV izolatları ile kümelenmiştir. Diyarbakır bölgesinde yetiştirilen hıyar bitkilerinde CMV’nin varlığı ve grup/subgrup teşhisi ilk defa bu çalışma ile doğrulanmıştır.
Dna Methylation Change and Antioxidant Enzyme Activity of Drought Stress and Putrescine Treatment in Ancient Wheat (Triticum Monococcum L.)
(Springer Heidelberg, 2024) Demirel, Serap; Eroglu, Ayten; Eren, Baris; Demirel, Fatih
Drought stress reduces crop productivity and harms cereals on morphological, physiological, biochemical, and molecular levels. Yet, exogenous application of certain active compounds like putrescine may mitigate these drought-related consequences. In this study, five distinct drought treatments (0, - 2, - 4, - 6, and - 8 bar) and four distinct priming treatments with putrescine (0, 0.01, 0.1, and 1 mM) were used. According to the findings of the enzyme activity, the activities of enzymes like superoxide dismutase (SOD) and catalase (CAT) all reduced when the plants were subjected to drought stress; however, it was determined that the putrescine treatment at - 2 bar PEG6000 resulted in an increase in the activity of CAT. iPBS (inter-primer binding site) markers were employed to detect cytosine methylation in treated wheat plants (Triticum monococcum L). The results confirmed that DNA methylation alterations were triggered by drought stress. The study revealed a positive correlation between drought intensity and cytosine methylation levels, while it was found that the application of putrescine resulted in a decrease in methylation levels and conferred a protective effect against drought-induced stress. Moreover, results of in silico docking that showed putrescine can bind to DNA methyltransferase2, that is, the decrease in DNA methylation may be related to this. Drought-stressed wheat is less methylated after being treated with putrescine, according to in silico docking and CRED-iPBS data. Testing the protective effects of polyamines on plants is an area that needs further attention.
Effect of Rhizobacteria Application on Nutrient Content, Bioactive Compounds, Antioxidant Activity, Color Properties and Fruit Characteristics of Strawberry Cultivars
(Mdpi, 2024) Elikara, Alper Umut; Popescu, Gheorghe Cristian; Demirel, Serap; Sumbul, Ahmet; Yaman, Mehmet; Demirel, Fatih; Gunes, Adem
The aim of this study was to determine the effects of single and combined applications of plant-growth-promoting rhizobacteria (PGPR) bacteria on plant nutrition, biochemical content and fruit characteristics in Albion and Monterey strawberry cultivars. Bacillus subtilis OSU-142, Bacillus megaterium M3 and Paenibacillus polymyx were the PGPR used in the experiment. For each bacterial treatment, 10 mL of a 108 CFU mL-1 suspension was applied to the soil where Albion and Monterey cultivars were grown. PGPR bacteria were applied as single treatments and a mixture of equal amounts of these three bacterial species was applied as a mixed treatment. This study was carried out with a total of four different bacterial treatments and one control group. The highest fruit weight was obtained in the Monterey cultivar with 12.67 g in the Mix treatment and in the Albion cultivar with 11.79 g in the Bacillus megaterium M3 treatment. Regarding biochemical properties, Paenibacillus polymyxa was effective in influencing nutrient element content in fruits, while Bacillus subtilis OSU-142, Paenibacillus polymyxa and Bacillus megaterium M3 applications were more effective in leaf nutrient element content. It has been observed that the Mix treatment resulting from the combined use of bacteria, rather than their separate use, has a greater impact on fruit weight. Consequently, it has been understood that PGPR bacteria are potentially effective in improving the agronomic, pomological, and biochemical characteristics of strawberry cultivars and can be used in studies and breeding programs aimed at increasing strawberry yield and quality.
Evaluation of Genetic Diversity and Population Structure of Peach (Prunus Persica L.) Genotypes Using Inter-Simple Sequence Repeat (Issr) Markers
(Springer, 2024) Demirel, Serap; Pehluvan, Mucahit; Aslantas, Rafet
Peaches are one of the most important food resources widely cultivated all over the world in terms of their high economic value. In the current study, 32 inter-simple sequence repeat (ISSR) markers were used for genetic diversity assessments and population structure of 52 local peach genotypes and 2 commercial peach cultivars from Igdir province of Turkiye. Totally, 213 alleles were scored, of which 154 were polymorphic. The mean of polymorphic band percentage (PPB), Nei's genetic index (H), polymorphism information content (PIC), effective number of alleles (Ne), and Shannon's index value were 70%, 0.24, 0.20, 1.38, and 0.37, respectively. The Jaccard similarity coefficient between local peach genotypes ranged from 0.40 to 0.89, with an average of 0.60. According to the UPGMA dendrogram, Agseftali and Zaferan peach genotypes were classified by admixture pattern into four groups. Results of population structure analysis and PCoA confirmed that 54 genotypes were assigned to four groups. The mean of genetic differentiation among the populations (F-ST) and estimate of gene flow (Nm) were 0.39 and 1.33 for K = 4 subpopulations, respectively, assuming structure analysis. Our result showed that the gene flow value was moderate, explaining the high level of genetic diversity maintained among populations. The present study indicates that ISSR markers are efficient for molecular characterization and analysis of populations of local peach genotypes. Moreover, the ISSR markers identified in the current study can provided a useful information for breeding programs to select individuals to use as parents.
First Report of Natural Infection of Watermelon Mosaic Virus (Wmv) Infecting Bottle Gourd and Snake Melon
(Univ Namik Kemal, 2024) Guller, Abdullah; Usta, Mustafa; Korkmaz, Gulustan; Demirel, Serap
Cucurbitaceous crops, one of the main crops of agriculture, are sensitive to many plant viruses. In August 2019, virus-like symptoms were observed on some cucurbit plants grown in private home gardens in Antalya and Denizli provinces (Turkey). A total of 53 leaf samples were sampled from plants with the most symptoms (melon (Cucumis melo L.), watermelon (Citrullus lanatus L.), bottle gourd (Lagenaria siceraria (Molina) Standl.), and snake melon (Cucumis melo var. flexuosus) and tested by Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) against possible watermelon mosaic potyvirus (WMV) infection. The coat protein gene (CP) specific primer sets amplified a gene product of nearly 820 bp fragment from symptomatic plants. WMV infections were detected in 31 individual cucurbit plants, including 11 melons, 8 watermelons, 7 snake melons and 5 bottle gourds. The presence of viral infection was found only in ornamental squash plants in Antalya province and in all cucurbits sampled in Denizli province. To better comprehend the molecular characteristics of virus isolates, the amplified viral DNA fragments were cloned in a proper prokaryotic plasmid, sequenced by Next Generation Sequencing (NGS) and recorded to GenBank. Bioinformatic analyses using the Basic Local Alignment Search Tool (BLAST) showed that the identified CP gene sequences exhibited significant nucleotide homogeneity, supported by a high nucleotide similarity index with that of other isolates around the world. In addition, Turkish isolates isolated from Antalya and Denizli regions showed approximately 94% nucleotide similarity among themselves. For phylogenetic inference, WMV sequences were subjected to multiple alignments with isolates from different geographic origins of the same viruses. Molecular phylogeny showed that all WMV isolates are closely related to other world WMV isolates at variable rates. WMV is wide host range viruses in cucurbit crops, however, this work is the first scientific report of WMV isolates detected in bottle gourd and snake melon from the South and West Regions of Turkey all over the world.
Fitopatojenlere Karşı Dayanıklılıkta Crıspr/cas Teknolojisi
(2020) Demırel, Fatıh; Demirel, Serap; Usta, Mustafa
Tarım ürünlerinde hem hücre içi hem hücre dışı bitki patojenleri dünya çapında ekonomik olarak önemli kayıplara neden olmaktadır.Genom düzenleme teknolojileri özellikle de CRISPR/cas sistemi, tarım ürünlerinde gerek kalite gerekse verimin iyileştirilmesi amacıylason zamanlarda farklı alanlarda kullanılmıştır. Bakteri, arkea, faj ve yabancı plazmitlere karşı savunma sağlayan CRISPR/cas sistemitarımsal özelliklerin araştırılması ve düzenlenmesi için eşsiz fırsatlar sunan bir araçtır. Bu derlemede hastalıklara neden olanfitopatojenlere karşı mücadelede CRSPR/cas sisteminin kullanım etkinliği irdelenmiştir. Ayrıca CRISPR/cas sistemi aracılığıyla fungus,bakteri ve virüslere karşı konukçu bitkide dayanıklılık ve duyarlılıkta rol oynayan genlerin modifikasyonlarının mevcut durumu ortayakonmuştur. Çalışmalar, CRISPR/cas sisteminin bitkilerde fitopatojenlere karşı dayanıklılık sağlamada etkili olduğunu ortaya koymuştur.Genom düzenleme alanındaki ilerlemeler ve CRISPR/cas ile transgen içermeyen bitkilerin elde edilmesi gelecekte bitki patolojisindeyeni hastalık yönetim ve mücadele stratejilerinin geliştirilmesine olanak sağlayabilecektir. Ayrıca gelecekte CRISPR/cas genomdüzenleme teknolojisi ile birden fazla patojene eş zamanlı olarak dayanıklı bitkilerin geliştirilmesi de mümkün olabilecektir.
Genetic Relationships of Salep Orchid Species and Gene Flow Among Serapias Vomeracea X Anacamptis Morio Hybrids
(Springer, 2023) Palaz, Esra Bulunuz; Demirel, Fatih; Adali, Sumeyye; Demirel, Serap; Yilmaz, Abdurrahim
Orchids are naturally grown in many countries of the Eastern Mediterranean. Salep, produced from orchid tubers via grinding and used as a hot drink, is an essential ingredient of ice cream. Salep orchid species are in danger of extinction due to the absence of cultivation and over-harvesting from nature. In this study, the genetic diversity and population structure between salep orchid species, their hybrids, and commercial species of Phalenopsis sp. were first investigated using inter-Primer Binding Site (iPBS) Retrotransposon markers. A total of 854 bands were scored with a 100% polymorphism rate. Neighbor-joining, model-based structure, and PCoA (Principal Coordinate Analysis) algorithms clustered the 30 salep orchids into three main populations. The analysis of molecular variance revealed variations within and among the populations as 71% and 29%, respectively. Anacamptis morio and Serapias vomeracea had the furthest genetic distances, and F-1 hybrids of S. vomeracea and A. morio had great genetic diversity. The study results will provide helpful information for orchid breeding by eliciting the genetic distances of salep orchids.
Iğdir İli Kabakgil Bitkilerinde Bazı Mozaik Hastalıklarının In Siliko ve Moleküler Analizi
(2024) Güller, Abdullah; Usta, Mustafa; Korkmaz, Gülüstan; Demirel, Serap
Cucumber mosaic cucumovirus (CMV) ve Watermelon mosaic potyvirus (WMV) kabakgilleri infekteleyen ve ekonomik kayıplara neden pozitif tek iplikli RNA genomuna sahip bitki virüslerdir. Her iki virüs kabakgil bitkilerde başta mozaik deseni ve yapraklarda şekil bozukluklarına yol açar. Bu tür belirtiler gösteren 23 kavun ve 28 karpuz bitkisinin yaprakları Iğdır ilinin farklı bölgelerinden örneklendirilmiştir. Simptomlu ve simptomsuz örnekler Reverse Transkripsiyon Polimeraz Zircir Reaksiyonu (RT-PCR) tarafından kılıf protein geni (CP) spesifik primerler kullanılarak testlenmiştir. Polimerizasyon testleri, CMV ve WMV için beklenen boyutta DNA fragmentleri amplifiye etmiştir. Pozitif sonuçlu bazı fragmentler saflaştırılmış, bakteriyel klonlaması gerçekleştirilmiş, nükleotit dizileri ortaya çıkarılmış ve gen bankasına (NCBI) kaydedilmiştir. Dizi analizleri, CMV ve WMV’nin kısmi kılıf protein dizilerine karşılık gelen 593 bp ve 822 bp nükleotit içerdiğini göstermiştir. Her iki virüs için farklı coğrafi bölgelerden sağlanan izolatlar nükleotit sekanslarına dayalı olarak filogenetik ilişkileri ortaya konmuştur. Oluşturulan filogenetik ağaç CMV-Iğdır izolatının Grup I ve alt grup B’de olduğunu ve WMV-Iğdır izolatlarının ise farklı gruplarda yer aldığını doğrulamıştır. Ayrıca virus izolatlarının kılıf proteinleri in silico araçlar ile karakterize edilmiştir. Bu çalışmayla Iğdır ilinde moleküler olarak ilk kez kavunda ve karpuzda CMV ile WMV varlığı saptanmış ve CMV’nin grup/altgrup atamaları gerçekleştirilmiştir.
Molecular and Agro-Morphological Characterization of Ancient Wheat Landraces of Turkey
(Biomed Central Ltd, 2017) Gurcan, Kahraman; Demirel, Fatih; Tekin, Mehmet; Demirel, Serap; Akar, Taner
Background: Turkey is one of the important gene centers for many crop species. In this research, some ancient wheats such as tetraploid and diploid hulled wheats together with hexaploid tir wheats (Triticum aestivum ssp. leucospermum Korn.) landraces mainly adapted to harsh winter conditions of Eastern Anatolian region of Turkey were characterized at agro-morphological and molecular level. Totally 50 hulled wheat population from Kastamonu, Konya and Kayseri provinces and 15 tir wheats from Kars provinces of Turkey were in-situ collected for characterization in 2013. Some quantitative and qualitative traits of each population were determined. Results: Twenty three hulled wheat population collected from Kastamonu province were distinguished into nine emmer and 14 einkorn wheats at morphological level. Additionally, Konya, Kayseri and Kars population were characterized as einkorn, emmer and tir wheat, respectively. Among the evaluated traits, protein ratios of hulled wheats were strikingly higher than registered cultivars. All the populations were also examined by molecular level by using fluorescently labelled 11 polymorphic SSRs primers. The primers exhibited 104 bands, ranging from 6 to 16 with a mean value 9.45 per loci. The clustering analysis separated the germplasm into two clusters which were also divided into two subclusters based on genetic similarity coefficient. Sixty-five population and five checks were analyzed to estimate mean number of alleles (N), expected and observed heterozygoties (He and Ho), polymorphism information content (PIC), Wright fix index (F), genetic deviation from Hardy-Weinberg expectation (Fit-Fis) and genetic variation (Fst) were determined as 9.45, 0.71, 0.07, 0.67, 0.90, 0.39, 0.87 and 0.39, respectively. A clear genetic deviation from Hardy - Weinberg expectation was observed among population in particular. These results showed considerable genetic variation among landraces rather than within population. Conclusions: These molecular information has revealed genetically diverse einkorn, emmer wheat and tir wheat population could be used as parents for further breeding studies in both Turkey and abroad. Furthermore, the molecular analysis has also generally discriminated the germplasm into ploidy level.
Molecular Identification and Population Structure of Emmer and Einkorn Wheat Lines With Different Ploidy Levels Using Ssr Markers
(Springer, 2024) Demirel, Serap; Demirel, Fatih
Ancient species (Triticum monococcum and Triticum dicoccum) of wheat represent a valuable genetic resource for breeding and genetic research. In this study, 81 selected genotypes and 7 commercial cultivars were evaluated with 11 simple sequence repeat (SSR) molecular markers. A total of 93 SSR alleles were detected, giving an average of 8.45 alleles per locus. Consequently, a total of 88 genotypes were assessed for their mean expected heterozygosity (He = 0.486), observed heterozygosity (Ho = 0.121), polymorphism information content (PIC = 0.68), and Shannon's information index (I = 0.918). The clustering analysis separated the genotypes into five subclusters based on the genetic similarity coefficient. Analysis of molecular variance (AMOVA) was performed to evaluate five different clusters. The result of AMOVA was defined as genetic deviation from expectation for clusters (Fis = 0.877, Fit = 0.903, and Fst = 0.211). In Nei's pairwise genetic identity, the highest and lowest were observed between P2-P5 populations (0.39) and P1-P2 populations (0.838). The wide variety of wheat lines can be used as a genetic resource in designing a wheat breeding program to develop new cultivars adapted to different geographic and climatic conditions and can also contribute to breeding programs around the world.
Natural Diversity of Crataegus Monogyna Jacq. in Northeastern Türkiye Encompassing Morphological, Biochemical, and Molecular Features
(Mdpi, 2025) Erkek, Bora; Yaman, Mehmet; Sumbul, Ahmet; Demirel, Serap; Demirel, Fatih; Coskun, Omer Faruk; Eroglu, Ayten
Hawthorn (Cratageus monogyna Jacq.), one of the important wild fruit species in Turkey, is an important fruit species in many countries due to its use in traditional medicine, landscaping studies, and the food and beverage industry. In this study, morphological characterization revealed significant variation among genotypes, with fruit weight ranging from 0.55 g to 2.87 g, fruit width from 9.74 mm to 18.39 mm, and leaf width from 19.53 mm to 41.19 mm. Genotype-dependent variations were observed in the total phenolic content (151.34 mg-491.88 mg GAE 100 g-1 flesh), the total flavonoid content (16.74-48.13 mg CAE 100 g-1 flesh), the total anthocyanin content (26.34-79.79 mg cyn-3 gluc 100 g-1 flesh), and the antioxidant activity (29.20% to 56.70%). HPLC-based phenolic profiling identified substantial variations in key bioactive compounds, with the highest levels of chlorogenic acid (16.16 mg 100 g-1 fw), caffeic acid (10.21 mg 100 g-1 fw), epicatechin (13.83 mg 100 g-1 fw), rutin (74.05 mg 100 g-1 fw), and protocatechuic acid (2.00 mg 100 g-1 fw). ISSR marker-based molecular analysis revealed a high degree of genetic polymorphism (89.12%), with 55 out of 62 bands classified as polymorphic. The polymorphic information content values ranged from 0.34 to 0.44. The Jaccard similarity coefficient ranged from 0.04 (M9 and M16) to 0.63 (M17 and M3), indicating substantial genetic variability. The tanglegram analysis comparing genetic and morphological-biochemical dendrograms yielded an entanglement score of 0.714, indicating an alignment between molecular and phenotypic data. These findings show that hawthorn genotypes from the Kelkit Valley exhibit extensive genetic and biochemical diversity, which is critical for conservation efforts, breeding programs, and the development of high-value medicinal and functional food products.
Refinement of Surface Sterilization Protocol for in Vitro Olive (Olea Europaea L.) Shoot Proliferation and Optimizing by Machine Learning Techniques
(Korean Soc Horticultural Science, 2025) Palaz, Esra Bulunuz; Demirel, Serap; Popescu, Gheorghe Cristian; Demirel, Fatih; Ugur, Remzi; Yaman, Mehmet; Tunc, Yazgan
The olive tree (Olea europaea L.) is one of the most ancient fruit species grown throughout history. Given the challenges and costs associated with propagating olive cultivars by cuttings and grafting, it is crucial to identify a method for efficient and widespread propagation. Micropropagation is especially advantageous for propagating plants that are conventionally challenging to propagate or for producing virus-free seedlings or plants with specified traits. This work aimed to improve the in vitro shoot proliferation of O. europaea L. 'Sultani' cultivated in T & uuml;rkiye. Machine learning (ML) techniques were used to predict the efficiency of surface sterilization treatments. The explants were subjected to varied concentrations and durations of five disinfectants: hydrogen peroxide (H2O2), silver nitrate (AgNO3), mercuric chloride (HgCl2), sodium hypochlorite (NaOCl), and chlorine dioxide (ClO2). Each disinfectant was assigned three treatment levels (T1, T2, T3), which varied in concentration and exposure duration. The measured variables were contamination rate, survival rate, growth rate, shoot diameter, shoot length, and leaf number. ClO2 and NaOCl were the most efficient disinfection agents for the growth of explants. ClO2 showed particularly excellent results in terms of shoot diameter (0.765 mm), shoot length (43.733 mm), and leaf number (14.578). NaOCl treatment resulted in the greatest growth percentage (70.55%). AgNO3 treatment performed moderately performance in most parameters, but the lowest contamination rate (13.556%) was observed. Ultimately, the selection of chemical and treatment techniques substantially impacted the efficacy of in vitro olive shoot proliferation. The support vector regression, random forest, extreme gradient boosting (XGBoost), elastic net, and Gaussian processes algorithms were used to model and forecast the optimal sterilizing settings. The XGBoost provided the most accurate (R2) for survival rate, growth rate, shoot diameter, shoot length, and leaf number variables; 0.587, 0.959, 0.843, 0.894, and 0.900, respectively. The XGBoost algorithm was used to predict and optimize surface sterilization. The optimal circumstances for survival and development were projected to include explants sterilized with a 30% solution of NaOCl for 20 min. Moreover, it was projected that explants treated with a 15% concentration of ClO2 for 30 min would be possibly ideal in terms of shoot diameter, shoot length, and leaf number values. ML algorithms could further optimize these protocols for better outcomes, reducing the number of treatments needed and improving efficiency.
Revealing Genetic Diversity and Population Structure in Türkiye's Wheat Germplasm Using Ipbs-Retrotransposon Markers
(Mdpi, 2024) Demirel, Fatih; Yildirim, Bunyamin; Eren, Baris; Demirel, Serap; Tuerkoglu, Aras; Haliloglu, Kamil; Bocianowski, Jan
Investigating the genetic diversity and population structure of wheat germplasm is crucial for understanding the underlying variability essential for breeding programs and germplasm preservation. This research aims to contribute novel insights with respect to the genetic makeup and relationships among these wheat genotypes, shedding light on the diversity present within the Turkish wheat germplasm. In this study, iPBS-retrotransposon markers were employed to analyze 58 wheat genotypes, encompassing 54 landraces and 4 cultivars sourced from Turkiye. These markers serve as genetic indicators that can be used to evaluate genetic variation, build genealogical trees, and comprehend evolutionary connections. The PCR products were visualized on agarose gel, and bands were scored as present/absent. The ten iPBS primers collectively yielded an average of 16.3 alleles, generating a total of 163 polymorphic bands. The number of alleles produced by individual markers ranged from 4 (iPBS-2386) to 29 (iPBS-2219). The genetic parameters were calculated using the popgen and powermarker programs. The genetic relationships and population structures were assessed using the ntsys and structure programs. Polymorphism information content (PIC) per marker varied from 0.13 (iPBS-2390) to 0.29 (iPBS-2386), with an average value of 0.22. Shannon's information index (I) was calculated as 1.48, while the number of effective alleles (Ne) and Nei's genetic diversity (H) were determined to be 0.26 and 0.31, respectively. Genotype numbers 3 (Triticum dicoccum) and 10 (Triticum monococcum) exhibited the maximum genetic distance of 0.1292, signifying the highest genetic disparity. Population structure analysis revealed the segregation of genotypes into three distinct subpopulations. Notably, a substantial portion of genotypes clustered within populations correlated with the wheat species. This population structure result was consistent with the categorization of genotypes based on wheat species. The comprehensive assessment revealed noteworthy insights with respect to allele distribution, polymorphism content, and population differentiation, offering valuable implications for wheat breeding strategies and germplasm conservation efforts. In addition, the iPBS markers and wheat genotypes employed in this study hold significant potential for applications in wheat breeding research and germplasm preservation.
Usage of Machine Learning Algorithms for Establishing an Effective Protocol for the in Vitro Micropropagation Ability of Black Chokeberry (Aronia Melanocarpa (Michx.) Elliott)
(Mdpi, 2023) Demirel, Fatih; Ugur, Remzi; Popescu, Gheorghe Cristian; Demirel, Serap; Popescu, Monica
The primary objective of this research was to ascertain the optimal circumstances for the successful growth of black chokeberry (Aronia melanocarpa (Michx.) Elliott) using tissue culture techniques. Additionally, the study aimed to explore the potential use of machine learning algorithms in this context. The present research investigated a range of in vitro parameters such as total number of roots (TNR), longest root length (LRL), average root length (ARL), number of main roots (NMR), number of siblings (NS), shoot length (SL), shoot diameter (SD), leaf width (LW), and leaf length (LL) for Aronia explants cultivated in different media (Murashige and Skoog (MS) and woody plant medium (WPM)) with different concentrations (0, 0.5, 1, 1.5, and 2 mg L-1) of indole-3-butyric acid (IBA). The study showed that IBA hormone levels may affect WPM properties, affecting the LRL and ARL variables. Aronia explant media treated with 2 mg L-1 IBA had the greatest TNR, NMR, NS, SL, and SD values; 31.67 pieces, 2.37 pieces, 5.25 pieces, 66.60 mm, and 2.59 mm, in that order. However, Aronia explants treated with 1 mg L-1 IBA had the highest LW (9.10 mm) and LL (14.58 mm) values. Finally, Aronia explants containing 0.5 mg L-1 IBA had the greatest LRL (89.10 mm) and ARL (57.57 mm) values. In general, the results observed (TNR, LRL, ARL, NMR, NS, SL, SD, LW, and LL) indicate that Aronia explants exhibit superior growth and development in WPM (25.68 pieces, 68.10 mm, 51.64 mm, 2.17 pieces, 4.33 pieces, 57.95 mm, 2.49 mm, 8.08 mm, and 14.26 mm, respectively) as opposed to MS medium (20.27 pieces, 59.92 mm, 47.25 mm, 1.83 pieces, 3.57 pieces, 49.34 mm, 2.13 mm, 6.99 mm, and 12.21 mm, respectively). In the context of the in vitro culturing of Aronia explants utilizing MS medium and WPM, an analysis of machine learning models revealed that the XGBoost and SVM models perform better than the RF, KNN, and GP models when it comes to making predictions about those variables. In particular, the XGBoost model stood out due to the fact that it had the greatest R-squared value, and showed higher predictive ability in terms of properly forecasting values in comparison to actual outcomes. The findings of a linear regression (LR) analysis were used in order to conduct an efficacy study of the XGBoost model. The LR results especially confirmed the findings for the SD, NS, and NMR variables, whose R-squared values were more than 0.7. This demonstrates the extraordinary accuracy that XGboost has in predicting these particular variables. As a consequence of this, it is anticipated that it will be beneficial to make use of the XGboost model in the dosage optimization and estimation of in vitro parameters in micropropagation studies of the Aronia plant for further scientific investigation.