Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Genetic Modification of Glycoalkaloid Content in Eggplant by Agrobacterium-Mediated Transformation Technique(Izmir Institute of Technology, 2022) Gültekin, Helin; Frary, AnneEggplant is one of the first plantsthat was cultivated in the Old World. It is economically and agriculturally important for many countries such as Turkey. In addition, eggplant has been used medicinally since ancient times. The medicinal effects of eggplant come from its secondary metabolites. One of the most useful secondary metabolites is steroidal glycoalkaloids (SGA). SGAs have been used in cancer treatment research. The biosynthesis of SGAs in plants is controlled by enzymes and transcription factors. GAME 9 is a transcription factor that has been investigated in tomato and potato and has been shown to be an important element in the production pathway. In this research, a copy of eggplant’s own GAME 9 transcriptional factor was transformed to the eggplant genome with Agrobacterium-mediated transformation. To this end, the GAME 9 gene was amplified from the eggplant genome and inserted into the pSoup/pGreen0029 vector system. This vector system was inserted into Agrobacterium. Eggplant seedling explants were incubated with transgenic Agrobacterium. The transformation of regenerated plants was confirmed with PCR and efficiency was found to be 1.3%. RNA expression levels were checked by RT-QPCR for 12 confirmed transgenic plants. On the metabolite level, the leaves of transgenic plants were assayed for SGA content using Dragendorff’s reagent method. The transgenic plants’ mRNA and metabolite levels showed plant to plant variation due to the random nature of transgene insertion. Of the 12 transgenic eggplant, nine plants had significantly increased production of both mRNA (at least 2-fold difference) and metabolite levels. In addition, two plants did not show any difference in mRNA level but their SGA amount was significantly increased. The remaining plant had a 0.16-fold decrease in mRNA level but a significantly greater level of SGA than control plants. In the future, these transgenic plants can help illuminate the SGA production pathway of eggplant and be used for the production of economically and medicinally valuable SGAs.Master Thesis Induction of Hairy Root Culture in Eggplant With Rhizobium Rhizogenes(Izmir Institute of Technology, 2021) Öztürk, Tuba; Doğanlar, SamiIn this study, It has been used two agropine strains (ATCC 15834 and ATCC 43057) of R. rhizogenes to compare hairy root induction in hypocotyl and cotyledon explants of eggplant. Transformation frequency was found to be the highest in hypocotyl explants (49.4%) infected with ATCC 15834. Thirty nine hairy root clones were selected based on their hairy root phenotype. The transgenic status of 15 of these clones was tested by PCR using rol gene primers. Hairy roots infected with ATCC 15834 were grown for 8 weeks in MS liquid medium. At the end of this growth period, the growth ratio of the hairy roots was measured. The root biomass was 6.52 g/DW for hypocotyl and 9.83 g/DW for cotyledon-derived clones. Biochemical analyses of clones were performed. Total phenolic contents were evaluated for hypocotyl and cotyledon-derived clones yielding 8.56 mg/g DW and 8.81 mg/g DW, respectively. The average total flavonoid content was 2.12 mg/g DW in hypocotyl-derived clones, and 1.90 mg/g DW in cotyledon-derived clones. On average, these amounts of both phenolic and flavonoid contents were significantly higher than those obtained for untransformed eggplant roots. Overall the results indicated that eggplant hairy roots are a useful source of secondary metabolites. In the future, the production of metabolites of interest such as steroidal glycoalkaloids or phenolics can be improved using elicitors in eggplant.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 Molecular Genetic Analysis in Sesame (sesamum Indicum L.)(Izmir Institute of Technology, 2010) Seyitalioğlu, Ümmü; Doğanlar, SamiIn this study, 156 Turkish sesame (Sesamum indicum L.) accessions were characterized morphologically and 161 accessions were characterized genotypically. A total of 15 criteria were used for morphological characterization. Simple Sequence Repeats (SSRs, microsatellites) were used to characterize genetic variability among Turkish accessions. A total of 318 new EST based SSRs were developed for genotypic analysis. Also, these microsatellites were screened in Korean-Japan and African sesame accessions (parents) for future map construction studies. According to the morphological analysis, some characters showed variation whereas some characters had no variation among accessions. For example, height of first capsule, capsule number per plant, plant height, number of branches, number seeds/capsule, days to 1st flower and days to %50 flower characters showed variation among accessions. However, stem hair, leaf hairs, axil flower number, number of carpels/capsule and capsule hairs showed variation for only a few accessions. Also, growth habit, branching and capsule splitting characters had no variation. In accordance with genetic characterization, survey results showed only five polymorphic markers among 318 EST based SSR markers. Also, in this study, genetic distance of Turkish sesame accessions was calculated using DICE matrix and UPGMA (Unweighted Pair Group Method) arithmetical averages via 19 EST based SSR fragments. Genetic analysis showed that Turkish sesame accessions have fairly low genetic diversity. As a result, genetic diversity among Turkish sesame accessions were defined and the genetic relationships of Turkish sesame accessions were established.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.Master Thesis Qtl Analysis for Fruit Traits in Solanum Pimpinellifolium Inbred Backcross Lines(Izmir Institute of Technology, 2010) Tamer, Nilüfer; Frary, AnneTomato is one of the most economically and nutritionally important crops. It contains antioxidants such as lycopene, phenolics, vitamins E, C, and .-carotene at high levels. These traits are of interest to consumers and plant breeders for their health-related contributions. The main aim of plant breeding is to improve agronomically relevant traits by combining characters from different parental lines or their relatives. Genetic markers reveal these characters and other genetic differences between organisms. In this study both health-related and agronomically important traits were phenotypically identified by using 120 BC2F7, BC2F8, and BC2F9 IBLs. Also the lines were genotypically identified using the BC2F10 IBL population. A total of 66 COSII and 11 COS markers were positioned on the IBL map. A total of 103 QTLs were identified. Of these QTLs, 25 loci were identified for antioxidant traits: total water soluble antioxidant capacity, vitamin C content, lycopene and phenolic content. In addition, 78 QTLs were identified for agronomic traits: fruit weight, fruit shape, fruit firmness, stem scar size, external and internal color, locule number, fruit wall size, and soluble solid content. For most of the antioxidant QTLs, alleles from the S. pimpinellifolium parent were favorable. This result indicates that S. pimpinellifolium can be used as a source of high nutritional traits in order to improve elite tomato lines.Master Thesis Molecular Mapping of N Gene Conferring Resistance To Root-Knot Nematodes in Pepper(Izmir Institute of Technology, 2013) Arslan, Mehmet Enes; Doğanlar, Sami; Doğanlar, SamiPepper (C. annuum) is one of the most important agricultural crops worldwide and Turkey ranks third among all countries in pepper production. Pepper species have economical and also pharmaceutical importance so, it is vital to develop different methods to increase pepper yields. The root-knot nematode (Meloidogyne species) is one of the most important biotic factors that affect pepper growth and development in Turkey. The dominantly inherited N gene which was mapped on chromosome P9, 7 cM from Me1 and 2 cM from Me3, confers resistance to pepper species against Meloidogyne species. The aim of this work was to develop a marker tightly linked to the N gene which can be used in marker-assisted selection. A total of 132 SSR Hpms primers, 230 EST-SSR markers and 45 chromosome 9 specific primers were used to a construct linkage map and find an N linked marker. Hpms SSR markers gave 19% polymorphism by capillary electrophoresis, EST-SSR markers showed 5.2% polymorphism by agarose gel electrophoresis while the chromosome 9 specific markers, yielded 20% polymorphism by fragment analyzer. When all 407 analyzed markers are considered, only 11.3% polymorphism was observed and these results were expected because we used an intraspecific population. The, polymorphic markers were mapped in a "Carolina Wonder" X "AZN-1" F2 population and analyzed with JoinMap software. Three markers were linked with the N gene. These markers are ScarPM6a (3.6 cM), ScarPM6b (10.2 cM) and ScarN (22.6 cM) which are located with same segregation group with the N gene. These markers will allow development of a marker tightly linked to the N gene which can be used in marker-assisted selection to increase the efficiency and effectiveness of pepper breeding for nematode resistance.Master Thesis Genetic Diversity of Turkish Spinach Cultivars(Izmir Institute of Technology, 2011) Avşar, Bihter; Doğanlar, SamiIn this study, 95 Turkish spinach (Spinacia oleracea L.) accessions were used for genetic diversity analysis by using the SRAP (Sequence Related Amplified Polymorphism) marker system and also 81 of the spinach accessions were used for morphological data analysis using data from the Centre for Genetic Resources, Wageningen University, The Netherlands. In the study, a total of 25 SRAP marker combinations were used and 19 of these were suitable for genetic analysis because they gave amplification and they were polymorphic. For the 19 SRAP markers, 123 bands were amplified and 67 were polymorphic. These polymorphic bands were used to construct a dendogram for spinach cultivars and to determine the genetic distance. Dendrogram analysis was done UPGMA method which was calculated using DICE matrix. Genetic similarity ranged between 0.30 and 0.95. Group B had most related accessions, 0.77 similar, and Group A, C and D had more distinct accessions, 0.60 similarity. For the morphological data PCA(Principal Component Analysis) was performed and no any apparent group was seen so high diversity was indicated by the 2D plot. All these results showed that the SRAP marker system was a suitable marker to determine genetic diversity, that Turkish spinach germplasm is diverse and that accessions should be preserved. Another importance of this results is that it is the first and only study that has been done with Turkish spinach germplasm.Master Thesis Determination of Genetic Diversity in Watermelon (citrullus Lanatus (thunb.) Matsum & Nakai) Germplasms(Izmir Institute of Technology, 2009) Ulutürk, Zehra İpek; Frary, AnneWith 1.4 million tons of production, Turkey ranks second behind China in worldwide production of watermelon. Watermelon is grown at different times throughout the country with highest consumption during the summer and fall. Watermelon is an economically and socio-economically important crop throughout the country and especially in coastal regions where much of the cultivation occurs. In this research, 90 watermelon accessions collected from different regions of the world by the USDA were molecularly characterized using 40 SRAP marker combinations based on the UPGMA (Unweighted Pair Group Method) and Neighbor Joining methods. According to this molecular analysis, genetic diversity between all watermelon accessions was very low. However, SRAP markers showed high polymorphism (97%) so these markers were determined to be suitable for studies of genetic diversity in crops like watermelon.