Phd Degree / Doktora

Permanent URI for this collectionhttps://hdl.handle.net/11147/2869

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Author: search.filters.author.Frary, Anne

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  • Doctoral Thesis
    Molecular genetic analyses in Origanum (Lamiaceae) taxa in Türkiye
    (01. Izmir Institute of Technology, 2022) Taşcıoğlu, Tülin; Frary, Anne; Frary, Anne
    Medicinal 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.
  • Doctoral Thesis
    Development of Tomato Plants Over-Expressing Cytokinin Synthesis Gene and Characterization by Proteomic Approach
    (Izmir Institute of Technology, 2020) Şelale, Hatice; Frary, Anne
    Cytokinins (CKs) are plant hormones controlling growth and development including cell division and differentiation, apical dominance and delay of senescence. CKs take part in regulation of the abiotic stress response in plants. In this study, transgenic tomato plants overexpressing the IPT (CK biosynthetic gene) were developed. Homozygous transgenic plants exhibited a phenotype with reduced plant stature and lost apical dominance. Increased shoot biomass and leaf water content with a reduction in fruit yield were observed in all transgenic lines. Proteomics analysis was conducted to understand high CK response in molecular level. Proteins supporting a strong sink phenotype and vasculature development were upregulated in transgenic lines and reflected the phenotypic changes observed in homozygous plants. Proteins related to stress response such as detoxification enzymes and PR proteins were upregulated in a gradual manner in transgenic lines with the strongest up-regulation in T6 homozygous line indicating the metabolic stress induced by high CK levels. The transgenic plants were tested for drought stress and observed to have improved water use efficiency, antioxidant response and delayed senescence compared to nontransgenic plants. Proteomic analyses from leaf total and nuclear enriched extracts were conducted to understand the molecular basis of improved drought tolerance. Proteins related to photosynthesis and oxidative stress response were the most prominent groups of differentially abundant proteins in the transgenic line under drought, which could contribute to tolerance. Eighteen transcription factors were differentially abundant in the nuclear proteome of drought stressed plants. These transcription factors could control the gene expression contributing to tolerance.
  • Doctoral Thesis
    Elucidation of Boron Tolerance Mechanisms in Puccinellia Distans (jacp.) Parl. Using a Transcriptomic Approach
    (Izmir Institute of Technology, 2017) Öztürk, Saniye Elvan; Frary, Anne
    The amount of boron in soil is important for agronomic plants. As an abiotic stress condition, boron toxicity causes significant decreases in crop yields. Puccinellia distans (Jacq.) Parl. (P. distans), common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were analyzed by RNA sequencing to identify genes and miRNAs related to boron tolerance and hyperaccumulation. The results indicated that the hyperaccumulation mechanism of P. distans involves many transcriptomic changes including: alterations in the malate pathway, changes in cell wall components that may allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. MiRNAs are also altered under stress conditions. The presence of miRNAs as stress regulator elements is an example of post-transcriptional regulation of stress related mechanisms. Additionally these small RNAs could affect their target genes by positive or negative regulation. Therefore, changes not only in miRNAs but also in their targets are important to understand their roles in hyperaccumulation. For example, downregulation of miRNA under stress could cause target accumulation. These mechanisms could be key in plant adaptation to new conditions. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.
  • Doctoral Thesis
    Development of Sequence Based Markers for Molecular Genetic Analysis in Sesame (sesamum Indicum L.)
    (Izmir Institute of Technology, 2015) Uncu, Ayşe Özgür; Frary, Anne
    Sesame (Sesamum indicum L.) is an orphan crop with most molecular genetic research work done in the last decade. In this study, pyrosequencing was used for the development of genomic SSR (Simple Sequence Repeat) markers in sesame. The approach proved successful in identifying 19,816 SSRs, 5727 of which were identified in a contig assembly that covers 19.29% of the sesame genome. As a result of this work, 933 experimentally validated sesame specific markers were introduced, 849 of which are applicable in Sesamum mulayanum, the wild progenitor of cultivated sesame. Using a subset of SSR markers, molecular genetic diversity and population structure of a collection of world accessions were analyzed. Results of the analyses revealed a pattern of gene flow among sesame diversity centers. Taken together with the high rate of genomic marker transferability between S. indicum and S. mulayanum, the results provide molecular genetic evidence for designating the two taxa as cultivated and wild forms of the same species.In related work, a Genotyping By Sequencing (GBS) approach was applied on recombinant inbred lines for single nucleotide polymorphism (SNP) identification and mapping in the sesame genome. As a result, 15,521 SNPs were identified and a high-resolution genetic linkage map was constructed using a core set of selected SNPs (781 SNPs) appropriate for use in linkage analysis. The 15,521 putative SNP markers represent a substantial contribution to the existing pool of sesame-specific markers. The genetic linkage map constructed in this work will enable the identification of loci involved in the genetic control of agriculturally important traits in sesame.