Doğanlar, Sami
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Doğanlar, S.
Doganlar, S
Doganlar, S.
Doğanlar, S
Doganlar, Sami
Doganlar, S
Doganlar, S.
Doğanlar, S
Doganlar, Sami
Job Title
Email Address
samidoganlar@iyte.edu.tr
Main Affiliation
04.03. Department of Molecular Biology and Genetics
Status
Current Staff
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ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Sustainable Development Goals
1NO POVERTY
0
Research Products
2ZERO HUNGER
33
Research Products
3GOOD HEALTH AND WELL-BEING
5
Research Products
4QUALITY EDUCATION
2
Research Products
5GENDER EQUALITY
0
Research Products
6CLEAN WATER AND SANITATION
2
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7AFFORDABLE AND CLEAN ENERGY
8
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8DECENT WORK AND ECONOMIC GROWTH
2
Research Products
9INDUSTRY, INNOVATION AND INFRASTRUCTURE
24
Research Products
10REDUCED INEQUALITIES
0
Research Products
11SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
12RESPONSIBLE CONSUMPTION AND PRODUCTION
4
Research Products
13CLIMATE ACTION
10
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14LIFE BELOW WATER
4
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15LIFE ON LAND
5
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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17PARTNERSHIPS FOR THE GOALS
0
Research Products
Documents
79
Citations
2564
h-index
27
Documents
42
Citations
1453
Scholarly Output
105
Articles
72
Views / Downloads
156711/63212
Supervised MSc Theses
24
Supervised PhD Theses
6
WoS Citation Count
1878
Scopus Citation Count
2253
Patents
0
Projects
24
WoS Citations per Publication
17.89
Scopus Citations per Publication
21.46
Open Access Source
90
Supervised Theses
30
| Journal | Count |
|---|---|
| Euphytica | 7 |
| Molecular Breeding | 6 |
| Molecular Genetics and Genomics | 4 |
| Turkish Journal of Agriculture and Forestry | 3 |
| ANADOLU Ege Tarımsal Araştırma Enstitüsü Dergisi | 2 |
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Scopus Quartile Distribution
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105 results
Scholarly Output Search Results
Now showing 1 - 10 of 105
Article Citation - WoS: 40Citation - Scopus: 46Genome-Wide Snp Discovery and Qtl Mapping for Fruit Quality Traits in Inbred Backcross Lines (ibls) of Solanum Pimpinellifolium Using Genotyping by Sequencing(BioMed Central Ltd., 2017) Çelik, İbrahim; Gürbüz, Nergiz; Uncu, Ali Tevfik; Frary, Anne; Doğanlar, SamiBackground: Solanum pimpinellifolium has high breeding potential for fruit quality traits and has been used as a donor in tomato breeding programs. Unlocking the genetic potential of S. pimpinellifolium requires high-throughput polymorphism identification protocols for QTL mapping and introgression of favourable alleles into cultivated tomato by both positive and background selection. Results: In this study we identified SNP loci using a genotyping by sequencing (GBS) approach in an IBL mapping population derived from the cross between a high yielding fresh market tomato and S. pimpinellifolium (LA1589) as the recurrent and donor parents, respectively. A total of 120,983,088 reads were generated by the Illumina HiSeq next-generation sequencing platform. From these reads 448,539 sequence tags were generated. A majority of the sequence tags (84.4%) were uniquely aligned to the tomato genome. A total of 3.125 unique SNP loci were identified as a result of tag alignment to the genome assembly and were used in QTL analysis of 11 fruit quality traits. As a result, 37 QTLs were identified. S. pimpinellifolium contributed favourable alleles for 16 QTLs (43.2%), thus confirming the high breeding potential of this wild species. Conclusions: The present work introduced a set of SNPs at sufficiently high density for QTL mapping in populations derived from S. pimpinellifolium (LA1589). Moreover, this study demonstrated the high efficiency of the GBS approach for SNP identification, genotyping and QTL mapping in an interspecific tomato population.Article Citation - WoS: 16Citation - Scopus: 17Authentication of Botanical Origin in Herbal Teas by Plastid Noncoding Dna Length Polymorphisms(American Chemical Society, 2015) Uncu, Ali Tevfik; Uncu, Ayşe Özgür; Frary, Anne; Doğanlar, SamiThe aim of this study was to develop a DNA barcode assay to authenticate the botanical origin of herbal teas. To reach this aim, we tested the efficiency of a PCR-capillary electrophoresis (PCR-CE) approach on commercial herbal tea samples using two noncoding plastid barcodes, the trnL intron and the intergenic spacer between trnL and trnF. Barcode DNA length polymorphisms proved successful in authenticating the species origin of herbal teas. We verified the validity of our approach by sequencing species-specific barcode amplicons from herbal tea samples. Moreover, we displayed the utility of PCR-CE assays coupled with sequencing to identify the origin of undeclared plant material in herbal tea samples. The PCR-CE assays proposed in this work can be applied as routine tests for the verification of botanical origin in herbal teas and can be extended to authenticate all types of herbal foodstuffs.Article Citation - WoS: 17Citation - Scopus: 20Molecular Genetic Diversity of the Turkish National Hazelnut Collection and Selection of a Core Set(Springer Verlag, 2017) Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Kayalak Balık, Selda; Kızılcı, Gökhan; Duyar, Ömür; Doğanlar, Sami; Frary, AnneEuropean hazelnut (Corylus avellana L.) is an economically and nutritionally important nut crop with wild and cultivated populations found throughout Europe and in parts of Asia. This study examined the molecular genetic diversity and population structure of 402 genotypes including 143 wild individuals, 239 landraces, and 20 cultivars from the Turkish national hazelnut collection using simple sequence repeat (SSR) markers. A total of 30 SSR markers yielded 407 polymorphic fragments. Diversity analysis of the Turkish hazelnut genotypes indicated that they fell into three subpopulations according to ad hoc statistics and neighbor-joining algorithm. Although all cultivars clustered together, they overlapped with the wild accessions and landraces. Thus, the dendrogram, principal coordinate, and population structure analyses suggest that they share the same gene pool. A total of 78 accessions were selected as a core set to encompass the molecular genetic and morphological diversity present in the national collection. This core set should have priority in preservation efforts and in trait characterization.Master Thesis The Use of Crispr Cas9 Technology To Reduce Polyphenol Oxidase (PPO) Enzyme Activity in Eggplant(01. Izmir Institute of Technology, 2024) Doğanlar, Sami; Dalgıç, Fatma Hacımalak; Doğanlar, SamiPatlıcan (Solanum melongena), Solanaceae ailesinin önemli bir üyesidir ve ekonomik potansiyeli ve zengin besin değeriyle öne çıkmaktadır. Patlıcan, dünyada en fazla üretimi yapılan sebzelerden biridir. Ayrıca, patlıcanın benzersiz genetik yapısı ve zorlu çevre koşullarına uyum sağlayabilme potansiyeli, ürün dayanıklılığı, verim ve besin içeriğini yükseltmeyi amaçlayan çalışmalar için önemli bir hedef haline getirmektedir. Genom düzenleme teknolojilerindeki son gelişmeler, özellikle CRISPR/Cas9 teknolojisi, patlıcanda spesifik genlerin düzenlemesi için umut vadetmektedir. Patlıcanın hasat edildikten sonra işlenmesinde önemli bir sorun olan enzimatik kararma, fenolik bileşiklerin oksidasyon reaksiyonundan kaynaklanmaktadır. Polifenol oksidazlar, kısaca PPO'lar bu reaksiyonu katalize etmektedir. Patlıcanda enzimatik esmerleşme yalnızca görünümde olumsuz etkilere neden olmamakla birlikte, raf ömrünü ve tüketici talebini de negatif şekilde etkilemektedir. Çalışmada, bir Türk patlıcan çeşidi olan Aydın Siyahı çeşidinin enzimatik esmerleşme sorununa hızlı ve kalıcı bir çözüm sağlamak amacıyla CRISPR/Cas9 teknolojisi kullanılmıştır. PPO genlerinde mutasyonlar oluşturularak, ilgili genlerin ifadesinde azalma ve esmerleşmenin azalması hedeflenmektedir. Geleneksel yöntemlerle esmerleşme probleminin çözümü zaman alıcı olacaktır ve ayrıca tüketicilerin tercih ettiği özelliklerin kaybolmasına neden olabilir. Sonuç olarak, bu çalışma ile Türk tipi patlıcanda birden fazla PPO genini hedefleyebilen CRISPR/Cas9 protokolü başarıyla optimize edilmiş ve uygulanmıştır. Bir Türk patlıcan çeşidi olan Kemer tipi Aydın Siyahı için, maksimum üç rehber RNA içerecek şekilde hazırlanan vektörler ve doku kültürü rejenerasyon protokolleri bu çalışmanın önemli başarılarıdır.Article Citation - WoS: 1Citation - Scopus: 1Association Mapping and Candidate Gene Identification for Yield Traits in European Hazelnut (<i>corylus Avellana</I> L.)(John Wiley & Sons Ltd, 2024) Baytar, Asena Akkoese; Yanar, Ertugrul Gazi; Frary, Anne; Doganlar, SamiEuropean hazelnut (Corylus avellana L.) is an important nut crop due to its nutritional benefits, culinary uses, and economic value. T & uuml;rkiye is the leading producer of hazelnut, followed by Italy and the United States. Quantitative trait locus studies offer promising opportunities for breeders and geneticists to identify genomic regions controlling desirable traits in hazelnut. A genome-wide association analysis was conducted with 5,567 single nucleotide polymorphisms on a Turkish core set of 86 hazelnut accessions, revealing 189 quantitative trait nucleotides (QTNs) associated with 22 of 31 traits (p < 2.9E-07). These QTNs were associated with plant and leaf, phenological, reproductive, nut, and kernel traits. Based on the close physical distance of QTNs associated with the same trait, we identified 23 quantitative trait loci. Furthermore, we identified 23 loci of multiple QTs comprising chromosome locations associated with more than one trait at the same position or in close proximity. A total of 159 candidate genes were identified for 189 QTNs, with 122 of them containing significant conserved protein domains. Some candidate matches to known proteins/domains were highly significant, suggesting that they have similar functions as their matches. This comprehensive study provides valuable insights for the development of breeding strategies and the improvement of hazelnut and enhances the understanding of the genetic architecture of complex traits by proposing candidate genes and potential functions.Doctoral Thesis Development of Single Nucleotide Polymorphism Markes for Fingerprint Analysis of Turkish Olive (olea Europaea L.) Cultivars and Detection of Adulteration in Turkish Olive Oil(Izmir Institute of Technology, 2015) Uncu, Ali Tevfik; Doğanlar, SamiOlive (Olea europaea L.) tree and oil are signature figures of the Mediterranean culture. Because of its high economic value, olive oil is extremely vulnerable to fraud. The aim of this study was to develop molecular tests for authenticating cultivar and botanical origin in olive oils. In order to authenticate the botanical origin and detect adulteration, a plastid DNA region was utilized for standardizing a capillary-electrophoresis barcode assay. The performance of the assay was evaluated on series of olive oil : seed oil admixtures. The assay proved successful in identifying seed oils in olive oil down to a limit of 10%. The molecular assay described in this work enables adulteration detection regardless of compositional similarities between the adulterant and adulterated oil species, thus will complement the shortcomings of analytical chemistry approaches. In order to establish a DNA-based identification key to ascertain the cultivar origin of Turkish monovarietal olive oils, short fragments from five olive genes were sequenced for SNP (Single Nucleotide Polymorphism) identification. CAPS (Cleaved Amplified Polymorphic DNA) assays were designed for SNPs that alter restriction enzyme recognition motifs. When applied on the oils of 17 olive cultivars, a maximum of five CAPS assays were necessary to discriminate the varietal origin of the samples. Admixture detection threshold of the assays was identified as 20% when tested on olive oil admixtures. The SNP-based CAPS assays developed in this work can be used for testing and verification of the authenticity of Turkish monovarietal olive oils, for olive tree certification, and in germplasm characterization and preservation studies.Article Citation - WoS: 23Citation - Scopus: 26Development of Practical Hplc Methods for the Separation and Determination of Eggplant Steroidal Glycoalkaloids and Their Aglycones(Taylor and Francis Ltd., 2008) Eanes, Ritchie C.; Tek, Neslihan; Kırsoy, Öyküm; Frary, Anne; Doğanlar, Sami; Almeida, Adelia E.A practical set of HPLC methods was developed for the separation and determination of the eggplant steroidal glycoalkaloids, solanine, chaconine, solasonine, solamargine, and their aglycones, solasodine and solanidine. A gradient method was initially developed, but proved to be neither robust nor practical. Three separate isocratic methods using acetonitrile and ammonium dihydrogen phosphate were developed and shown to be more repeatable, less subject to fluctuations in mobile phase composition, and less time consuming. The effect of adjusting buffer pH, column temperature, and buffer type (triethylammonium phosphate vs. ammonium dihydrogen phosphate) were evaluated. It was also discovered that, by addition of 10% methanol to the acetonitrile portion of the mobile phase, more control over the separations was possible. The use of methanol as a mobile phase entrainer greatly improved separations in some cases and its effectiveness was also dependent upon column temperature. Assessments of the method recovery, limit of detection, and limit of quantitation were made using extracts from S. melongena and S. linnaeanum.Master Thesis Development and Characterization of Solanum Linnaeanum Hairy Root Lines(01. Izmir Institute of Technology, 2024) Kaya, Aysu; Doğanlar, SamiSolanum lınnaeanum, birçok Afrika ülkesinde geleneksel olarak tedavi edici özellikleri nedeniyle sıkça kullanılır ve Solanum melongena'nın yabani bir akrabasıdır. Fenolik bileşikler ve glikoalkaloitler de dahil olmak üzere bu bitkinin ürettiği birçok ikincil metabolit, antibakteriyel, antifungal ve antiviral özellikler gösterir. Tüylü kök kültürleri ikincil metabolitlerin üretimi ve bitkinin metabolik yolaklarının çalışılması için sıkça kullanılan bir bitki doku kültürü yöntemidir. Bu çalışmada, S. l?nnaeanum ve S. melongena eksplantlarından tüylü kök hatları oluşturmak için Agrobacter?um rh?zogenes'in agropin suşlarından biri olan ATCC 43057 kullanıldı. İstatistiksel olarak anlamlı olmamasına rağmen, transformasyon verimliliği iki tür için de hipokotil eksplantlarında kotiledon eksplantlarına göre daha yüksek olarak bulundu. T-DNA bölgesinin bitki genomuna entegrasyonu PCR ile doğrulandıktan sonra, transforme edilen tüylü kökler sıvı MS besi yerinde büyütüldü ve biyokimyasal analizler yapıldı. Analizler sonucunda, S. melongena tüylü kök hatlarıyla karşılaştırıldığında, S. l?nnaeanum tüylü kök hatlarında total fenolik (5,75 mg/g kuru ağırlık) ve total flavonoid (14,85 mg/g kuru ağırlık) içeriğinin ve total antioksidan kapasitesinin (11,45 mg/g kuru ağırlık) daha yüksek olduğu gözlemlendi. Ayrıca, myb1, HQT ve Game9 genlerinin ekspresyon analizi S. l?nnaeanum tüylü kök kültürlerinde daha fazla mRNA seviyeleri gösterdi. Bu sonuçlar, ikincil metabolit üretimi için S. l?nnaeanum tüylü kök kültürlerinin, elisitörler veya biyoreaktörler kullanılarak daha da geliştirilebilecek potansiyel bir kaynak olabileceğini göstermektedir.Master Thesis Molecular Mapping of Quantitative Trait Loci Conferring Resistance To Verticillium Wilt in Cotton(Izmir Institute of Technology, 2014) Akköse, Asena; Doğanlar, Sami; Doğanlar, SamiCotton with its valuable natural fiber is an economically important field plant. Resistance against stress conditions and diseases are desired traits in cotton production. Verticillium wilt is one of the major factors resulting in huge cotton yield losses. Control of Verticillium disease has not been successful because of low genetic diversity and a complex disease mechanism. Moreover resistance against Verticillium wilt is a quantitative trait that is regulated by more than one gene and under environmental effects. Due to this complex inheritance, conventional breeding methods have not resulted in efficient resistance. Therefore, it is necessary to develop cotton lines resistant to Verticillium wilt using molecular breeding techniques. In this study we aimed to identify the quantitative trait loci which are responsible for Verticillium wilt resistance. For this purpose, we carried out a Verticillium wilt disease test in a natural population composed of 118 individuals. We inoculated the population with Verticillium dahliae in five replicates. After one month, the symptoms were examined and phenotypic variation was detected and scored. We then used 100 SSR markers for genotyping of the population. Population structure was determined with STRUCTURE 2.2.3. According to results, we determined two clusters. There were 44 and 34 individuals in the first and second clusters, respectively. A total of 40 individuals remained intermixed. Association analysis between phenotypic and allelic data was carried out with TASSEL 2.1. In this way we identified 30 SSR markers associated with Verticillium wilt resistance at a significance level of p<0.05. The most significant SSR locus was DPL080-238 (p=0.0014). Moreover, SSRs DPL188-130 and DPL223-251 showed the highest values for dominant and recessive allelic effects, respectively. We hope that our study will be helpful for the development of marker-assisted strategies for breeding of Verticillium wilt resistant cotton cultivars.Article Molecular Genetic Characterization of the Turkish National Green Plum (prunus Cerasifera Ehrh.) Collection(Ege Tarımsal Araştırma Enstitüsü, 2021) Çakır, Gülsüm; Taşcıoğlu, Tülin; Çavdar, Andaç; Doğanlar, Sami; Frary, Amy; Frary, AnnePlum is an important fruit worldwide and has high nutritional value. Prunus cerasifera Ehrh., a type of European plum species, is very popular in Turkey and is usually eaten at the green, unripe stage. In this work for the first time, the genetic diversity and population structure of the 66 accessions housed in the Turkish National P. cerasifera collection were investigated using molecular markers. A total of 47 Sequence-Related Amplified Polymorphism (SRAP) primer pairs were used and found to be highly polymorphic with 98% of the 495 amplified alleles providing polymorphism. Average diversity of the accessions was 0.39 as determined using the dice coefficient and was similar to P. cerasifera germplasm from France, Iran and Belarus but higher than that from China. This difference was expected as Turkey, Iran and Belarus are within the geographical origin of this species which was distributed to Europe during ancient times. The genetic relationships among accessions of the germplasm collection were assessed using unweighted neighbor joining dendrogram and population structure analyses. The dendrogram and population structure results were strongly correlated as both methods clustered the material into two main groups with a much smaller third admixed group. The analysis also indicated that Can and Papaz types, despite their morphological differences are not genetically distinct and provides information about genetic relationships that can be used in future plum breeding.