Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Citation - WoS: 46Citation - Scopus: 57Barcode Dna Length Polymorphisms Vs Fatty Acid Profiling for Adulteration Detection in Olive Oil(Elsevier Ltd., 2017) Uncu, Ali Tevfik; Uncu, Ayşe Özgür; Frary, Anne; Doğanlar, SamiThe aim of this study was to compare the performance of a DNA-barcode assay with fatty acid profile analysis to authenticate the botanical origin of olive oil. To achieve this aim, we performed a PCR-capillary electrophoresis (PCR-CE) approach on olive oil: seed oil blends using the plastid . trnL (UAA) intron barcode. In parallel to genomic analysis, we subjected the samples to gas chromatography analysis of fatty acid composition. While the PCR-CE assay proved equally efficient as gas chromatography analysis in detecting adulteration with soybean, palm, rapeseed, sunflower, sesame, cottonseed and peanut oils, it was superior to the widely utilized analytical chemistry approach in revealing the adulterant species and detecting small quantities of corn and safflower oils in olive oil. Moreover, the DNA-based test correctly identified all tested olive oil: hazelnut oil blends whereas it was not feasible to detect hazelnut oil adulteration through fatty acid profile analysis. Thus, the present research has shown the feasibility of a PCR-CE barcode assay to detect adulteration in olive oil.Article Citation - WoS: 21Citation - Scopus: 23High-Throughput Single Nucleotide Polymorphism (snp) Identification and Mapping in the Sesame (sesamum Indicum L.) Genome With Genotyping by Sequencing (gbs) Analysis(Springer Verlag, 2016) Uncu, Ayşe Özgür; Frary, Anne; Karlovsky, Petr; Doğanlar, SamiSesame (Sesamum indicum L. syn. Sesamum orientale L.) is considered to be the first oil seed crop known to man. Despite its versatile use as an oil seed and a leafy vegetable, sesame is a neglected crop and has not been a subject of molecular genetic research until the last decade. There is thus limited knowledge regarding genome-specific molecular markers that are indispensible for germplasm enhancement, gene identification, and marker-assisted breeding in sesame. In this study, we employed a genotyping by sequencing (GBS) approach to a sesame recombinant inbred line (RIL) population for high-throughput single nucleotide polymorphism (SNP) identification and genotyping. A total of 15,521 SNPs were identified with 14,786 SNPs (95.26 %) located along sesame genome assembly pseudomolecules. By incorporating sesame-specific simple sequence repeat (SSR) markers developed in our previous work, 230.73 megabases (99 %) of sequence from the genome assembly were saturated with markers. This large number of markers will be available for sesame geneticists as a resource for candidate polymorphisms located along the physical chromosomes of sesame. Defining SNP loci in genome assembly sequences provides the flexibility to utilize any genotyping strategy to survey any sesame population. SNPs selected through a high stringency filtering protocol (770 SNPs) for improved map accuracy were used in conjunction with SSR markers (50 SSRs) in linkage analysis, resulting in 13 linkage groups that encompass a total genetic distance of 914 cM with 432 markers (420 SNPs, 12 SSRs). The genetic linkage map constitutes the basis for future work that will involve quantitative trait locus (QTL) analyses of metabolic and agronomic traits in the segregating RIL 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: 23Citation - Scopus: 33Genomic Simple Sequence Repeat Markers Reveal Patterns of Genetic Relatedness and Diversity in Sesame(Crop Science Society of America, 2015) Uncu, Ayşe Özgür; Gültekin, Visam; Allmer, Jens; Frary, Anne; Doğanlar, SamiSesame (Sesamum indicum L. syn. Sesamum orientale L.) is an orphan crop species with most molecular genetic research work done in the last decade. In this study, we used a pyrosequencing approach for the development of genomic simple-sequence repeat (SSR) markers in sesame. Our approach proved successful in identifying 19,816 nonredundant SSRs, 5727 of which were identified in a contig assembly that covers 19.29% of the sesame genome. Mononucleotide repeats were the most abundant SSR type identified in the sesame genome (48.5% of all SSRs), followed by dinucleotide SSRs (45.0%). Adenine–thymine-rich motifs were predominant, representing 81.7, 51.7, 66.5, and 22.1% of the mononucleotide, dinucleotide, trinucleotide, and tetranucleotide SSRs, respectively. As a result of this work, we introduce 933 experimentally validated sesame specific markers, 849 of which are also applicable in Sesamum mulayanum (syn. Sesamum orientale var. malabaricum Nar.), the wild progenitor of cultivated sesame. Using a subset of the newly identified SSR markers, we analyzed molecular genetic diversity and population structure of a collection of world accessions. Results of the two analyses almost overlapped and suggested correlation between genetic similarity and geographical proximity. Indeed, a pattern of gene flow among sesame diversity centers was apparent, with levels of variability in some regions similar to that seen in the domestication origin of the crop. Taken together with the high rate of genomic marker transferability detected between S. indicum and S. mulayanum, our results represent additional molecular genetic evidence for designating the two taxa as cultivated and wild forms of the same species.Article Citation - WoS: 9Citation - Scopus: 10A Primer To Molecular Phylogenetic Analysis in Plants(Taylor and Francis Ltd., 2015) Uncu, Ayşe Özgür; Uncu, Ali Tevfik; Çelik, İbrahim; Doğanlar, Sami; Frary, AnneReconstructing a tree of life by inferring evolutionary history is an important focus of evolutionary biology. Phylogenetic reconstructions also provide useful information for a range of scientific disciplines such as botany, zoology, phylogeography, archaeology and biological anthropology. Until the development of protein and DNA sequencing techniques in the 1960s and 1970s, phylogenetic reconstructions were based on fossil records and comparative morphological/physiological analyses. Since then, progress in molecular phylogenetics has compensated for some of the shortcomings of phenotype-based comparisons. Comparisons at the molecular level increase the accuracy of phylogenetic inference because there is no environmental influence on DNA/peptide sequences and evaluation of sequence similarity is not subjective. While the number of morphological/physiological characters that are sufficiently conserved for phylogenetic inference is limited, molecular data provide a large number of datapoints and enable comparisons from diverse taxa. Over the last 20 years, developments in molecular phylogenetics have greatly contributed to our understanding of plant evolutionary relationships. Regions in the plant nuclear and organellar genomes that are optimal for phylogenetic inference have been determined and recent advances in DNA sequencing techniques have enabled comparisons at the whole genome level. Sequences from the nuclear and organellar genomes of thousands of plant species are readily available in public databases, enabling researchers without access to molecular biology tools to investigate phylogenetic relationships by sequence comparisons using the appropriate nucleotide substitution models and tree building algorithms. In the present review, the statistical models and algorithms used to reconstruct phylogenetic trees are introduced and advances in the exploration and utilization of plant genomes for molecular phylogenetic analyses are discussed.Article Citation - WoS: 7Citation - Scopus: 10Biotechnology for Enhanced Nutritional Quality in Plants(Taylor and Francis Ltd., 2013) Uncu, Ayşe Özgür; Doğanlar, Sami; Frary, AnneWith almost 870 million people estimated to suffer from chronic hunger worldwide, undernourishment represents a major problem that severely affects people in developing countries. In addition to undernourishment, micronutrient deficiency alone can be a cause of serious illness and death. Large portions of the world population rely on a single, starch-rich crop as their primary energy source and these staple crops are generally not rich sources of micronutrients. As a result, physical and mental health problems related to micronutrient deficiencies are estimated to affect around two billion people worldwide. The situation is expected to get worse in parallel with the expanding world population. Improving the nutritional quality of staple crops seems to be an effective and straightforward solution to the problem. Conventional breeding has long been employed for this purpose but success has been limited to the existing diversity in the gene pool. However, biotechnology enables addition or improvement of any nutrient, even those that are scarce or totally absent in a crop species. In addition, biotechnology introduces speed to the biofortification process compared to conventional breeding. Genetic engineering was successfully employed to improve a wide variety of nutritional traits over the last decade. In the present review, progress toward engineering various types of major and minor constituents for the improvement of plant nutritional quality is discussed. © 2013 Copyright Taylor and Francis Group, LLC.