PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Review Citation - WoS: 10Citation - Scopus: 12Genetic and Biotechnological Approaches To Improve Fruit Bioactive Content: a Focus on Eggplant and Tomato Anthocyanins(Mdpi, 2024) Cammareri, Maria; Frary, Amy; Frary, Anne; Grandillo, SilvanaAnthocyanins are a large group of water-soluble flavonoid pigments. These specialized metabolites are ubiquitous in the plant kingdom and play an essential role not only in plant reproduction and dispersal but also in responses to biotic and abiotic stresses. Anthocyanins are recognized as important health-promoting and chronic-disease-preventing components in the human diet. Therefore, interest in developing food crops with improved levels and compositions of these important nutraceuticals is growing. This review focuses on work conducted to elucidate the genetic control of the anthocyanin pathway and modulate anthocyanin content in eggplant (Solanum melongena L.) and tomato (Solanum lycopersicum L.), two solanaceous fruit vegetables of worldwide relevance. While anthocyanin levels in eggplant fruit have always been an important quality trait, anthocyanin-based, purple-fruited tomato cultivars are currently a novelty. As detailed in this review, this difference in the anthocyanin content of the cultivated germplasm has largely influenced genetic studies as well as breeding and transgenic approaches to improve the anthocyanin content/profile of these two important solanaceous crops. The information provided should be of help to researchers and breeders in devising strategies to address the increasing consumer demand for nutraceutical foods.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.Article Citation - WoS: 8Citation - Scopus: 10Interaction With Fungi Promotes the Accumulation of Specific Defense Molecules in Orchid Tubers and May Increase the Value of Tubers for Biotechnological and Medicinal Applications: the Case Study of Interaction Between Dactylorhiza Sp. and Tulasnella Calospora(Frontiers Media S.A., 2022) Hampejsová, Romana; Berka, Miroslav; Berková, Veronika; Jersáková, Jana; Domkářová, Jaroslava; von Rundstedt, Friederike; Frary, Anne; Saiz-Fernández, Iñigo; Brzobohatý, Břetislav; Černý, MartinTerrestrial orchids can form tubers, organs modified to store energy reserves. Tubers are an attractive source of nutrients, and salep, a flour made from dried orchid tubers, is the source of traditional beverages. Tubers also contain valuable secondary metabolites and are used in traditional medicine. The extensive harvest of wild orchids is endangering their populations in nature; however, orchids can be cultivated and tubers mass-produced. This work illustrates the importance of plant-fungus interaction in shaping the content of orchid tubers in vitro. Orchid plants of Dactylorhiza sp. grown in asymbiotic culture were inoculated with a fungal isolate from Tulasnella calospora group and, after 3 months of co-cultivation, tubers were analyzed. The fungus adopted the saprotrophic mode of life, but no visible differences in the morphology and biomass of the tubers were detected compared to the mock-treated plants. To elucidate the mechanisms protecting the tubers against fungal infestation, proteome, metabolome, and lipidome of tubers were analyzed. In total, 1,526, 174, and 108 proteins, metabolites, and lipids were quantified, respectively, providing a detailed snapshot of the molecular process underlying plant-microbe interaction. The observed changes at the molecular level showed that the tubers of inoculated plants accumulated significantly higher amounts of antifungal compounds, including phenolics, alkaloid Calystegine B2, and dihydrophenanthrenes. The promoted antimicrobial effects were validated by observing transient inhibition of Phytophthora cactorum growth. The integration of omics data highlighted the promotion of flavonoid biosynthesis, the increase in the formation of lipid droplets and associated production of oxylipins, and the accumulation of auxin in response to T. calospora. Taken together, these results provide the first insights into the molecular mechanisms of defense priming in orchid tubers and highlight the possible use of fungal interactors in biotechnology for the production of orchid secondary metabolites.Article Citation - WoS: 3Citation - Scopus: 3Chromatographic Analysis for Targeted Metabolomics of Antioxidant and Flavor-Related Metabolites in Tomato(Bio-Protocol, 2021) Gürbüz Çolak, Nergiz; Tek, Neslihan; Frary, Anne; Doğanlar, SamiTargeted metabolomics is a useful approach to evaluate crop breeding studies. Antioxidant and flavor-related traits are of increasing interest and are considered quality traits in tomato breeding. The present study presents chromatographic methods to study antioxidants (carotenoids, vitamin C, vitamin E, phenolic compounds, and glutathione) and flavor -related characters (sugars and organic acids) in tomato. Two different extraction methods (for polar and apolar entities) were applied to isolate the targeted compounds. The extraction methods developed in this work were time and cost-effective since no further purification was needed. Carotenoids, vitamin C, glutathione, and phenolic acids were analyzed by HPLC-PDA using a RP C18 column at an appropriate wavelength for each compound. Vitamin E and sugars were analyzed by HPLC with RP C18 and NH2 columns and detected by FLD and RI detectors, respectively. In addition, organic acids were analyzed with GC-FID using a Rtx 5DA column after derivatization with MSTFA. As a result, sensitive analytical methods to quantify important plant metabolites were developed and are described herein. These methods are not only applicable in tomato but are also useful to characterize other species for flavor-related and antioxidant compounds. Thus, these protocols can be used to guide selection in crop breeding.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.Article Citation - WoS: 179Citation - Scopus: 229Health Benefits and Bioactive Compounds of Eggplant(Elsevier, 2018) Gürbüz, Nergiz; Uluışık, Selman; Frary, Anne; Frary, Amy; Doğanlar, SamiEggplant is a vegetable crop that is grown around the world and can provide significant nutritive benefits thanks to its abundance of vitamins, phenolics and antioxidants. In addition, eggplant has potential pharmaceutical uses that are just now becoming recognized. As compared to other crops in the Solanaceae, few studies have investigated eggplant's metabolic profile. Metabolomics and metabolic profiling are important platforms for assessing the chemical composition of plants and breeders are increasingly concerned about the nutritional and health benefits of crops. In this review, the historical background and classification of eggplant are shortly explained; then the beneficial phytochemicals, antioxidant activity and health effects of eggplant are discussed in detail.Article Citation - WoS: 14Citation - Scopus: 16Transcriptomic Analysis of Boron Hyperaccumulation Mechanisms in Puccinellia Distans(Elsevier Ltd., 2018) Öztürk, Saniye Elvan; Göktay, Mehmet; Has, Canan; Babaoğlu, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnnePuccinellia 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 treated for three weeks with normal (0.5 mg L−1) and elevated (500 mg L−1) boron levels in hydroponic solution. Expressed sequence tags (ESTs) derived from shoot tissue were analyzed by RNA sequencing to identify genes up and down-regulated under boron stress. In this way, 3312 differentially expressed transcripts were detected, 67.7% of which were up-regulated and 32.3% of which were down-regulated in boron-treated plants. To partially confirm the RNA sequencing results, 32 randomly selected transcripts were analyzed for their expression levels in boron-treated plants. The results agreed with the expected direction of change (up or down-regulation). A total of 1652 transcripts had homologs in A. thaliana and/or O. sativa and mapped to 1107 different proteins. Functional annotation of these proteins indicated that the boron tolerance and hyperaccumulation mechanisms of P. distans involve 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. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.Article Citation - Scopus: 18Organogenesis From Transformed Tomato Explants(Humana Press, 2005) Frary, Anne; Van Eck, JoyceTomato was one of the first crops for which a genetic transformation system was reported involving regeneration by organogenesis from Agrobacterium-transformed explants. Since the initial reports, various factors have been studied that affect the efficiency of tomato transformation and the technique has been useful for the isolation and identification of many genes involved in plant disease resistance, morphology and development. In this method, cotyledon explants from in vitro-grown seedlings are precultured overnight on a tobacco suspension feeder layer. The explants are then inoculated with Agrobacterium and returned to the feeder layer for a 2-d period of cocultivation. After cocultivation, the explants are transferred to an MS-based selective regeneration medium containing zeatin. Regenerated shoots are then rooted on a separate selective medium. This protocol has been used with several tomato cultivars and routinely yields transformation efficiencies of 10-15%.
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