Frary, Anne
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Frary, A.
Frary, A
Frary, A
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annefrary@iyte.edu.tr
Main Affiliation
04.03. Department of Molecular Biology and Genetics
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Current Staff
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Sustainable Development Goals
1NO POVERTY
0
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2ZERO HUNGER
29
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3GOOD HEALTH AND WELL-BEING
9
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4QUALITY EDUCATION
3
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5GENDER EQUALITY
0
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6CLEAN WATER AND SANITATION
10
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7AFFORDABLE AND CLEAN ENERGY
10
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8DECENT WORK AND ECONOMIC GROWTH
3
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
24
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10REDUCED INEQUALITIES
0
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11SUSTAINABLE CITIES AND COMMUNITIES
1
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
10
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13CLIMATE ACTION
13
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14LIFE BELOW WATER
7
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15LIFE ON LAND
6
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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17PARTNERSHIPS FOR THE GOALS
1
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Documents
90
Citations
5944
h-index
31
Documents
91
Citations
5445
Scholarly Output
111
Articles
81
Views / Downloads
172715/64436
Supervised MSc Theses
21
Supervised PhD Theses
4
WoS Citation Count
2205
Scopus Citation Count
2645
Patents
0
Projects
22
WoS Citations per Publication
19.86
Scopus Citations per Publication
23.83
Open Access Source
97
Supervised Theses
25
| Journal | Count |
|---|---|
| Euphytica | 7 |
| Molecular Breeding | 6 |
| Molecular Genetics and Genomics | 4 |
| Turkish Journal of Agriculture and Forestry | 3 |
| Theoretical and Applied Genetics | 3 |
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111 results
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Now showing 1 - 10 of 111
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 Determination of Genetic Diversity and Antioxidant Content of the National Melon (cucumis Melo) Collection(Izmir Institute of Technology, 2008) Şığva, Hasan Özgür; Frary, Anne; Frary, AnneIn this study, characterization with 19 morphological criteria and two types of PCRbased molecular marker systems, Simple Sequence Repeats (SSRs, microsatellites) and Amplified Fragment Length Polymorphisims (AFLPs), were used to characterize genetic variability among 238 national melon (Cucumis melo L.) accessions and 12 different members of the Cucurbitaceae family.According to morphological analysis, all accessions were vigourous. The accessions showed a great variety of fruit shape, 53 (38.4%) accessions were globular (round), 51 (37.0%) were eliptical, 15 (10.9%) were ovate, 7 (5.1%) oblate, 2 (1.4%) elongate and one accession was flattened. Another agronomically important criterion was predominant fruit skin colour. A total of 55 (39.9%) accessions had light yellow predominant skin colour, 34 (24.6%) were pale green, 29 (21.0%) were orange, 9 (6.5%) were cream, 6 (4.4%) were green, 4 (2.9%) were blackish-green and 1 (0.7%) was dark green.In accordance with genetic characterization, a total of 345 polymorphic AFLP fragments (products of 10 AFLP primer combinations) and 93 SSR fragments (products of 12 SSR markers) were detected and used to calculate genetic distance using DICE matrix and UPGMA (Unweighted Pair Group Method) arithmetical averages. The average polymorphic AFLP fragments per combination was 34.5 and SSR fragments per marker was 7.75. The phylogenetic tree showed that groups were clearly separated by both marker systems. This study allowed the identification of the relationship between national melon accessions based on genetic similarity or differences.Forty three melon accessions were also analyzed for total water soluble antioxidant and total phenolic compound activities.Doctoral Thesis Molecular genetic analyses in Origanum (Lamiaceae) taxa in Türkiye(01. Izmir Institute of Technology, 2022) Taşcıoğlu, Tülin; Frary, Anne; Frary, AnneMedicinal and aromatic plants (MAPs) belonging to the genus, Origanum L. (Lamiaceae), are called “oregano”. They are economically important and beneficial for trade, medicine, food, cosmetics, and ornamental purposes with their bioactive compound diversity and richness. Although Türkiye is the gene center for generation, speciation, and diversification of oregano throughout the world, their uncontrolled consumption and other factors threaten their status. According to Ietswaart (1980), there are ten morphological sections in the genus. Of these, 25 taxa (including 13 endemics) and 13 hybrids from eight sections grow naturally in Türkiye. The cross-pollinating and gynodioecious nature of oreganos makes their taxonomic classification difficult. In this dissertation, molecular markers (EST-SSRs and SRAPs) were used to assess the complex evolutionary relationships in a herbarium and the Turkish national AARI Gene Bank collection. Cross hybridization due to high gene flow was found to be the main source of genetic diversity within both collections. In both collections, the highest gene flow was observed between two sections, ANA and BRE, with diecious flowers which supports their frequent hybridization when compared to gynodioecious oreganos in nature. The Aegean and Mediterranean regions had the highest gene flow among all regions, while five province pairs had the highest gene flow among all provinces. In conclusion, molecular markers were shown to be a useful tool for examinations of genetic diversity and evolution in oregano.Master Thesis Bacterial Cellulose Production With Gluconoacetobacter Xylinus From Hazelnut Waste(01. Izmir Institute of Technology, 2024) Gazioğlu, Metehan; Frary, Anne; Büyükkileci, Ali OğuzBakteriyel selüloz (BC), biyomedikal, kozmetik ve elektronik gibi birçok endüstriyel alanda önemli potansiyele sahip doğal bir biyopolimerdir. BC'nin özellikleri arasında yüksek yüzey alanı, sıvı ve gaz geçirgenliği, biyobozunabilirlik ve modifiye edilebilirlik bulunur. Bu çalışmada bakteriyel selüloz üretimi gluconacetobacter xylinus tarafından gerçekleştirilmiştir. BC üretimini optimize etmek için çeşitli çevresel koşullar ve besiyerleri test edilmiştir. Bu çalışmada, fındık kabuklarının asit ve baz kimyasal ön işlemleri ile elde edilen şekerlerin kullanımına odaklanılmıştır. Fındık kabuğunun kimyasal içeriği belirlenmiş ve lignin, selüloz ve hemiselüloz oranları sırasıyla %42,09, %21,84 ve %22,99 olarak bulunmuştur. Bu içerikler, farklı ön işlem yöntemlerinin etkinliğini değer- lendirmek için kullanılmıştır. Fındık kabukları, farklı kimyasallar ile ön işlem- den geçirilmiş ve şeker salınımı açısından değerlendirilmiştir. Alkali ön işlemler, şeker salınımı açısından daha etkili bulunmuştur. Özellikle, %1'lik potasyum hidroksit ve %3'lük sodyum hidroksit ile ön işlem gören numuneler sırasıyla 37,8 ve 39 g/L en yüksek şeker konsantrasyonuna sahip olmuştur. Optimiza-syon çalışmaları kapsamında inokülasyon oranı, pH değeri, gün ve etanol varlığı gibi parametreler incelenmiştir. %10 inokülasyon oranı, 10 gün ve pH 6 ile en yüksek BC verimi elde edilmiştir. Kıyaslanan kültürlere bakıldığında %1 potasyum hidroksit ile ön işlem görmüş sonrasında da besiyeri içerisinde %1'lik etanol bulunan besiyerinde 2369 mg/L' de en çok bakteriyel selüloz üretildiği belirlenmiştir. Farklı kültürlerden alınan bakteriyel selülozlarda etanol ilavesinin su tutma kapasitesini azalttığ görülmüştür. FT-IR sonuçları bütün örneklerin saf olarak elde edildiğini ve yapısal bütünlüğün korunduğu göstermiştir. Bu tez, BC üretimini optimize etmek için gerekli olan koşulları belirlemekte ve fındık kabuklarının sürdürülebilir bir şeker kaynağı olarak kullanılabileceğini göstermektedir.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.Master Thesis Characterization of World Spinach Genetic Collection by Using Molecular Markers(Izmir Institute of Technology, 2015) Göktay, Mehmet; Frary, AnneSpinach (Spinacia oleracea L.) belongs to the Amaranthaceae family and is a popular and nutritious vegetable. It is believed that this green leafy plant originated from Persia which is now modern Iran and neighboring countries. In this study we screened 176 spinach world collection germplasm accessions with 15 known SSR markers. The markers produced 58 bands with 57 identified as polymorphic. PIC values of the markers ranged between 0.01 and 0.44. Average PIC value was 0.28. Based on allele analysis with Darwin5 and STRUCTURE tools, 176 individual were clustered into three groups. The first cluster mostly consisted of accessions from Europe and USA and contained 69 samples. The second cluster mostly consisted of lines from Asia and neighboring countries and contained 89 samples. The third cluster did not represent any characteristic according to geographic region, thus it was called an intermixed cluster which contained 18 samples. The maximum genetic dissimilarity of spinach accessions was 0.551 and minimum was 0.019. Average genetic dissimilarity was 0.217. Moreover we sequenced S. oleracea L. cv. Universal nuclear genome via IIIumina MiSeq technology and genome assembly was performed to develop new spinach–specific SSR markers. As a result, 3853 SSRs were identified in the assembled genome and we successfully designed 3275 primer pairs for these identified SSR motifs. These newly developed SSR markers will be helpful to scientists who are interested in spinach genome diversity and breeding.Master Thesis Determination of Genetic Diversity in National Olive Collection (olea Europaea L.) Using Ssr and Srap Markers and Development of Snp Marker for Traceability of Memecik Olive Cultivar(Izmir Institute of Technology, 2010) Işık, Neslihan; Frary, AnneIn this study genetic diversity of the Turkish olive collection was successfully characterized by using 13 SSR and 12 SRAP markers. For SSR marker analysis, we also added 3 European accessions to the national cultivars and binominal microsatellite data were detected by Qiaxcel software and clustered by NTSYS program. The UPGMA dendrogram showed good fit with the distance matrix (r . 0.85). While the outgroups were clustered with 0.27 similarity to national accessions, Turkish accessions clustered with 0.55 minimum similarity. Using SRAP markers we found 0.66 minimum similarity among Turkish accessions with a good fit between the distance data and UPGMA dendrogram (r . 0.83). The SSR and SRAP distance matrices were compared and they were found to correlated at r .0.23. To support the tree, ordination tests (PCA) for each marker system were performed and similar clustering was seen as in the trees. The other aim of this research was to develop SNP markers for traceability of Memecik accessions. We sequenced the anthocyanidin synthase gene of 11 exported olive accessions and aligned using Biolign program. There was no unique SNP that could be used to separate Memecik from the other accessions so we used a combination of SNPs. By using two probes at the same time, Memecik accession was distinguished from the other 10 exported accessions. In addition to find the SNP marker to trace Memecik accession, we developed the SNP marker to trace Trabzon Yağlık accessions.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.