Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
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Article Determination of Resistance Levels To Clavibacter Michiganensis Subsp. Michiganensis in Some Solanum Species(Ege Tarımsal Araştırma Enstitüsü, 2022) Frary, Anne; Şanver, Utku; Akköse Baytar, Asena; Özaktan, Hatice; Doğanlar, SamiClavibacter michiganensis subsp. michiganensis (Cmm), is a devastating bacterial disease agent causing bacterial wilt and canker in tomatoes. There is no definitive solution to prevent yield losses by Cmm in tomatoes. Moreover, there is currently no commercially successful Cmm resistant tomato cultivar on the market. Therefore, we aimed to determine the tolerance level of some tomato accessions to Cmm in the present study. For this purpose, we screened seven tomato accessions representing four species (Solanum arcanum, S. habrochaites, S. pennellii, and S. peruvianum) from Peru, Ecuador, and Mexico against the highly virulent isolates Cmm-244 and Cmm-9. A root immersion method was used to identify new sources of resistance to this important disease. Two accessions, S. habrochaites LA1777, and S. arcanum LA2157 were found to be moderate and highly tolerant, respectively, and could serve as tolerance resources for tomato breeding in Türkiye. These materials can also be investigated more extensively to determine their intrinsic Cmm tolerance mechanism.Article Citation - WoS: 8Citation - Scopus: 8Association Analysis of Germination Level Cold Stress Tolerance and Candidate Gene Identification in Upland Cotton (gossypium Hirsutum L.)(Springer, 2022) Akköse Baytar, Asena; Peynircioğlu, Ceng; Sezener, Volkan; Frary, Anne; Doğanlar, SamiCotton originated from ancestors in the Gossypium genus that grew in semi-desert habitats. As a result, it is adversely affected by low temperatures especially during germination and the first weeks of growth. Despite this, there are relatively few molecular studies on cold stress in cotton. This limitation may present a future breeding handicap, as recent years have witnessed increased low temperature damage to cotton production. Cold tolerance is a sustainable approach to obtain good production in case of extreme cold. In the present study, 110 Upland cotton (Gossypium hirsutum) genotypes were evaluated for cold tolerance at the germination stage. We identified vigorous genotypes with cold-related parameters that outperformed the panel’s average performance (x¯ = 76.9% CG, 83.9% CSI, 167.5 CWVI). Molecular genetic diversity analysis with 101 simple sequence repeat (SSR) markers yielding 416 loci was used to select tolerant genotypes that could be important materials for breeding this trait. A total of 16 marker-cold tolerance trait associations (p < 0.005) were identified with 10 of them having major effects (PVE > 10%). Based on the positions of these markers, candidate genes for cold tolerance in the G. hirsutum genome were identified. Three of these markers (BNL0569, CIR081 and CIR202) are important candidates for use in marker-assisted breeding for cold tolerance because they mapped to genes previously associated with cold tolerance in other plant species such as Arabidopsis thaliana, rice and tomato.Article Citation - WoS: 4Citation - Scopus: 4Development of Liposomal Formulations of the Eggplant Glycoalkaloids Solasonine and Solamargine(Elsevier, 2022) Tatlıdil, Engin; Gürbüz, Nergiz; Doğanlar, Sami; Frary, AnneThe eggplant glycoalkaloids solasonine and solamargine are efficient biomacromolecules against skin diseases but are water-insoluble which results in inefficient treatment due to inadequate transdermal delivery. To address this problem, several liposomal formulations were prepared and evaluated for parameters including lecithin type, hydration temperature, and pH. The optimal formula with high physical and chemical stability included the lecithin Phospholipon 80H hydrated with 10 mM NaCl (pH 5.5). Solasonine - solamargine loaded liposomes were tested for their physical and chemical stability and drug leakage over a three-month period. Furthermore, the drug release profile of the loaded liposomes was evaluated with different release media. The glycoalkaloids and their liposomal formulations were assessed for their biological activity in culture using HaCaT and SCC-25 cell lines. This work resulted in a biologically effective liposomal formulation that was stable (size <220 nm, PDI [removed]80%) for at least three months.Article Citation - WoS: 3Citation - Scopus: 3Molecular Mapping of Qtls for Fiber Quality Traits in Gossypium Hirsutum Multi-Parent Recombinant Inbred Lines(Springer, 2021) Akköse Baytar, Asena; Peynircioğlu, Ceng; Sezener, Volkan; Frary, Anne; Doğanlar, SamiCotton is a valuable fiber crop which supplies raw material to more than 50 industries and is produced in more than 70 countries worldwide. The superiority of cotton fiber over other crops is primarily dependent on its quality. However, further improvements in fiber length and strength are required for modern processing technology and for cotton to maintain its position in the global market. Association mapping enables identification of QTLs controlling fiber quality-related traits which can be useful in cotton breeding. In the present study, we performed genetic diversity, linkage disequilibrium and association mapping analyses in 157 G. hirsutum multi-parent recombinant inbred lines using a total of 102 SSR markers. The population had depressed genetic variability (14%), a result of inbreeding of modern cotton genotypes. Despite this, we identified 11 significant and stable marker-trait associations for seed cotton yield, lint percentage, fiber length and fiber strength (p < 0.005). We also detected QTL co-localizations with positive and negative marker additive effects. Our results indicate that selection against negative alleles may be as important as selection for positive alleles. Analysis of the effects of allelic combinations at different QTLs revealed significant and stable marker clusters that can be selected for or against to provide maximum quality gains in cotton fiber quality.Book Part Citation - WoS: 10Synteny Among Solanaceae Genomes(Springer, 2016) Frary, Amy; Doğanlar, Sami; Frary, AnneThe Solanaceae was among the first plant families to be analyzed via comparative mapping and thus was a pioneer in the realm of synteny studies. Analyses of chromosome content and organization have employed a range of techniques, including linkage mapping of genes and molecular markers, physical mapping via fluorescence in situ hybridization, and sequencing of relatively small genomic segments as well as the complete sequencing of the tomato genome. Early comparisons in the family involved tomato and its close relative potato and have extended outward to include eggplant, pepper, tobacco, and petunia. Not surprisingly, the degree of synteny among these species is a function of the time since their divergence, with inversion, translocation, and transposition being the chief mechanisms of chromosome rearrangement. The results of this work provide important insight into the modes and tempo of plant genome evolution while serving a practical purpose as well: knowledge of genome synteny and colinearity makes it easier to leverage resources from one species to another in this agronomically important family.Article Citation - WoS: 7Citation - Scopus: 10Association Mapping of Agro-Morphological Traits in European Hazelnut (corylus Avellana)(Springer, 2019) Frary, Amy; Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Balık, Selda Kayalak; Kızılcı, Gökhan; Doğanlar, Sami; Frary, AnneMore than half of European hazelnut (Corylus avellana) production occurs in Turkey. Despite this dominance, the yield of Turkish cultivars has remained stagnant over the past 10years with Italian yield nearly double that in Turkey. This difference is due to Turkey's unique cultivation system; hazelnuts are grown in bushy clusters (ocak system), not as single trees. Current hazelnut breeding efforts are shifting toward the development of materials for single plant orchards which are much higher yielding; thus, there is a need to explore germplasm for relevant agro-morphological traits and to determine their genetic control. The objectives of this study were to examine data for 44 such traits in 390 hazelnut accessions: 16 cultivars, 232 landraces and 142 wild individuals from nine provinces in Turkey and to map the loci associated with these characteristics using simple sequence repeat markers. Comparison of cultivars, landraces and wild hazelnut accessions revealed the effects of domestication and selection on the crop and indicated that useful alleles for traits such as cropping and reduced alternate bearing may exist in the wild germplasm. A total of 145 quantitative trait loci (QTL) were detected with the largest proportions identified for involucre (26%) and inflorescence (14%) morphology. Several markers co-localized with more than one trait including markers for male catkin abundance which were shared with plant vigor and height. Similarly, markers for female flower abundance co-localized with suckering and alternate bearing. Such markers and their linked QTL should be studied in more detail as they might help breeders select for plant vigor, decreased suckering and increased flower production: traits which will be extremely useful for Turkey's transition to single plant orchards.Article Citation - WoS: 10Citation - Scopus: 13Analysis of European Hazelnut (corylus Avellana) Reveals Loci for Cultivar Improvement and the Effects of Domestication and Selection on Nut and Kernel Traits(Springer Verlag, 2019) Frary, Amy; Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Kayalak Balık, Selda; Kızılcı, Gökhan; Doğanlar, Sami; Frary, AnneTurkey is a rich source of European hazelnut (Corylus avellana) germplasm with nearly 400 accessions in the national collection. This genetic material encompasses cultivars, landraces and wild genotypes which were characterized for 12 nut and 13 kernel traits over 2years in the 1990s. Analysis of these attributes revealed both the positive and negative impacts that human selection and breeding have had on hazelnut. Thus, while selection has resulted in larger nuts and kernels, cultivars have fewer nuts per cluster and kernels with larger internal cavities. Breeding has also resulted in a propensity for cultivars to have higher proportions of double kernels and empty nuts, two traits which reduce quality and yield. In addition, it is clear that while selection has successfully increased hazelnut fat content it has not impacted overall flavor, a much more complex trait. The nut and kernel phenotypic data were combined with genotypic data from 406 simple sequence repeat marker alleles for association mapping of the quantitative trait loci (QTL) for the traits. A total of 78 loci were detected in the population with the highest proportions for nut (24%) and kernel (26%) appearance parameters followed by quality (19%), shell thickness (16%) and yield-related (15%) traits. It is hoped that some of the identified QTL will be useful for future breeding of hazelnut for improved nut and kernel yield and quality.Article Citation - WoS: 36Citation - Scopus: 47Mapping of Quantitative Trait Loci for Antioxidant Molecules in Tomato Fruit: Carotenoids, Vitamins C and E, Glutathione and Phenolic Acids(Elsevier, 2020) Gürbüz Çolak, Nergiz; Tek, Neslihan; Ülger, Mehmet; Frary, Anne; Doğanlar, SamiThe nutritional value of a crop lies not only in its protein, lipid, and sugar content but also involves compounds such as the antioxidants lycopene, beta-carotene and vitamin C. In the present study, wild tomato Solanum pimpinellifolium LA 1589 was assessed for its potential to improve antioxidant content. This wild species was found to be a good source of alleles for increasing beta-carotene, lycopene, vitamin C and vitamin E contents in cultivated tomato. Characterization of an LA 1589 interspecific inbred backcross line (IBL) mapping population revealed many individuals with transgressive segregation for the antioxidants confirming the usefulness of this wild species for breeding of these traits. Molecular markers were used to identify QTLs for the metabolites in the IBL population. In total, 64 QTLs were identified for the antioxidants and their locations were compared to the map positions of previously identified QTLs for confirmation. Four (57 %) of the carotenoid QTLs, four (36 %) of the vitamin QTLs, and 11 (25 %) of the phenolic acid QTLs were supported by previous studies. Furthermore, several potential candidate genes were identified for vitamins C and E and phenolic acids loci. These candidate genes might be used as markers in breeding programs to increase tomato's antioxidant content.Article Citation - WoS: 12Citation - Scopus: 14Transcriptomic Analysis of Selenium Accumulation in Puccinellia Distans (jacq.) Parl., a Boron Hyperaccumulator(Elsevier, 2020) Kök, Aysu Başak; Mungan, Mehmet Direnç; Doğanlar, Sami; Frary, AnneSelenium (Se) is present in a wide variety of natural and man-made materials on Earth. Plants are able to tolerate and (hyper)accumulate Se to different extents. In fact, some species can tolerate and accumulate multiple elements. Puccinellia distans (P. distans), weeping alkali grass, is known to hyperaccumulate extreme concentrations of boron and tolerate high levels of salinity, therefore, we investigated the Se accumulation and tolerance capacities of this species. In addition, P. distans' Se tolerance mechanism was studied using a transcriptomic approach. The results of this study indicated that, when grown in a hydroponic system containing 80 or 120 mu M Se, P. distans shoots accumulated from 1500 to 2500-fold more Se than plants grown without the element. Thus, P. distans was discovered to be a novel Se accumulator plant. RNA sequencing results and biochemical analyses helped to shed light on the Se tolerance and accumulation mechanism of P. distans. Here, we suggest that upregulation of Se assimilation and stress response genes may be due to induction of jasmonic acid signaling. In addition, we propose that the cell wall may play an important role in restriction of Se movement to the cytoplasm. Also, we hypothesize that Se accumulates in cells by sequestration of selenate in the vacuole. (C) 2019 Elsevier Ltd. All rights reserved.Article Citation - WoS: 18Citation - Scopus: 21Exploring Wild Alleles From Solanum Pimpinellifolium With the Potential To Improve Tomato Flavor Compounds(Elsevier, 2020) Gürbüz Çolak, Nergiz; Tek, Neslihan; Ülger, Mehmet; Frary, Anne; Doğanlar, SamiMost consumers complain about the flavor of current tomato cultivars and many pay a premium for alternatives such as heirloom varieties. Breeding for fruit flavor is difficult because it is a quantitatively inherited trait influenced by taste, aroma and environmental factors. A lack of genetic diversity in modern tomato cultivars also necessitates exploration of new sources for flavor alleles. Wild tomato S. pimpinellifolium and inbred backcross lines were assessed for individual sugars and organic acids which are two of the main components of tomato flavor. S. pimpinellifolium was found to harbor alleles that could be used to increase glucose and fructose content and adjust acidity by altering malic and citric acid levels. Single nucleotide polymorphism markers were used to detect 14 quantitative trait loci (QTLs) for sugars and 71 for organic acids. Confirmation was provided by comparing map locations with previously identified loci. Thus, seven (50 %) of the sugar QTLs and 22 (31 %) of the organic acids loci were supported by analyses in other tomato populations. Examination of the genomic sequence containing the QTLs allowed identification of potential candidate genes for several flavor components. © 2020 Elsevier B.V.