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Öğe Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes(Mdpi, 2020) Sultana, Nusrat; Menzel, Gerhard; Heitkam, Tony; Kojima, Kenji K.; Bao, Weidong; Serce, SedatBioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification onVacciniumgenome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid speciesVaccinium myrtillusandVaccinium uliginosum, as well as the tetraploid speciesVaccinium corymbosumandVaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploidV. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity inVaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.Öğe Contribution to the knowledge of genome size evolution in edible blueberries (genus Vaccinium)(Ios Press, 2020) Sultana, Nusrat; Pascual-Diaz, Joan Pere; Gers, Ahsen; Ilga, Kubra; Serce, Sedat; Vitales, Daniel; Garcia, SoniaBACKGROUND: Vaccinium is one of the largest genera (ca. 500 species) of Ericaceae, well known for its edible and ornamental uses. Although there is certain karyological knowledge, information about genome size (GS) is scarce in the genus. OBJECTIVE: The main goal is providing GS data for several Vaccinium species with prevalence in Europe and Western Asia and analysing global GS variation in the genus, considering available data and phylogenetic context. METHODS: New GS assessments were obtained by flow cytometry and chromosome counts were verified. Phylogenetic analyses (using nuclear ITS, and chloroplastic matK and ndhF) were performed by Bayesian inference and reconstruction of ancestral GS by maximum parsimony. RESULTS: We obtained GS data for five Vaccinium species (13 populations). Three species are reported for the first time. Values (2C) ranged between 1.16-1.47 pg at the diploid (2n = 24) and between 3.13-3.16 pg at the tetraploid (2n = 48) levels. The five species here investigated have been placed and analysed in a reconstructed phylogenetic background (including 68 taxa). CONCLUSIONS: GS values of Vaccinium can be considered very small. The preliminary reconstruction of ancestral GS would point to a reduction in Vaccinium, although more data is needed to establish global GS evolutionary trend in the genus.Öğe Determination of Morphological, Pomological and Molecular Variations among Apples in Nigde, Turkey using iPBS Primers(Galenos Publ House, 2022) Gencer, Orkun; Serce, SedatIn addition to morphological and pomological techniques, the molecular analysis produces more information for diversity studies. Recently, the iPBS marker system is one of the techniques and a new marker system for apple studies. In this study, morphological, pomological, and molecular characteristics of local apples were investigated in 48 different samples from 29 different rural areas with varying altitudes between 1125-1726 m in Nigde, Turkey. Fruit size, fruit weight, the color of fruit peel, total soluble solids content, fruit flesh firmness characteristics are important in terms of yield, quality, storage, transportation and attractiveness. According to the pomological results from these traits, CKR2, DMR3, CLL, HCB2, YSL, ULG, ELM1, ICM have been found to superior among genotypes. In order to molecular results, the similarity of the samples varies between 0.61-1.00, under the light of this result, molecular data differentiated all individuals used in the study except one pair. Molecular data displayed that these differences were caused by genotypic differences as well as environmental conditions. This study has contributed further information about the usage of iPBS primers on apple. To protect the plant material used in the study, a collection orchard was established with genotypes. To conclude, the findings are expected to shape future breeding studies.Öğe 'Eclipse' Thornless Semi-erect Blackberry(Amer Soc Horticultural Science, 2020) Finn, Chad E.; Strik, Bernadine C.; Yorgey, Brian M.; Peterson, Mary E.; Jones, Patrick A.; Buller, Gil; Serce, Sedat[Abstract Not Available]Öğe Effects of Short Day Conditioning, Chilling and GA(3) Treatments to Yield and Fruit Quality in Strawberry Plug Transplants Aiming Early Fruit Production(UNIV AGR SCI & VETERINARY MED CLUJ-NAPOCA, 2013) Ozdemir, Emine; Kaska, Nurettin; Gunduz, Kazim; Serce, SedatIn this study, we tested the effects of short day (SD), chilling (Ch) and gibberalic acid (GA(3)) treatments on the yield and fruit characteristics of 'Camarosa' and 'Sweet Charlie' plug plants under a freeze-protected greenhouse in Mediterranean conditions for two growing seasons in 2006-2007 and 2007-2008. The treatments included control (ambient day length and temperature); SD (8 h days) and ambient temperature, SD + Chilling (Ch) (18/12 degrees C day/night temperatures); SD + Ch (10 degrees C); SD + Ch (2 degrees C); and, GA(3) (10 ppm applied to the plants in November). In each growing season, the plug plants were planted in mid-August using bag culture. Yield, fruit weight, firmness, total soluble solids (SS), titratable acidity (TA), and SS/TA ratio were investigated. Considerable amounts of early yield (March and April) were recovered from 'Sweet Charlie'; 116 and 72 g/plant in the first and second growing seasons, respectively. 'Sweet Charlie' also had consistently higher total yield than 'Camarosa' (457 vs. 400 g/plant in the 2006-2007 season and 446 vs. 406 g/plant in the 2007-2008 season). Treatment did not have a consistent effect on the fruit quality traits measured. The results indicated that although SD conditioning, Ch and GA(3) treatments may have an effect on the total and early yield of strawberries, these effects may be cultivar-dependent and further regulated by environmental factors. Therefore, we propose that low-chilling varieties be utilized for early fruit production that can initiate flower buds in warmer, longer days.Öğe Genetic and phenotypic variation of Turkish Okra (Abelmoschus esculentus L. Moench) accessions and their possible relationship with American, Indian and African germplasms(Springer India, 2016) Yildiz, Mehtap; Ekbic, Ercan; Duzyaman, Eftal; Serce, Sedat; Abak, KazimOkra is an important vegetable crop that provides a significant portion of vitamins and minerals for populations in several countries. Okra has been cultivated in Turkey for centuries, and was likely introduced by the Arabs from Africa in ancient times. In this study, we aimed to clarify the genetic variation within 35 Turkish okra germplasm, by comparing it against 25 different genotypes from India, Africa, and the United States, using 30 morphological characters and 19 sequence-related amplified polymorphism (SRAP) primer combinations. Fruit, leaf, and stem color were the primary characteristics to distinguish the okra accessions. Those features, among 30 individual phenotypic traits, explained 42 % of phenotypic variation in the first three axes of the principal component analysis (PCA) with leaf shape, flower size, cotyledon length, fruit-surface angularity, cotyledon width, and petal color. Phenotypic observation results showed that while 1051 Togo (10.76), Red Wonder (7.99), TR-05-1 (7.2), 1159 Togo (7.17), and Red Balady (7.15) were found to be more divergent accessions, Cajun Queen (5.06), Perkins Spineless (5.09), Jade (5.18), TR-01-1 (5.2), and DLGG (5.32) were the closest okra accessions. According to phenotypic data, Turkish okra accessions were located adjacent to the Indian, American, and African okra accessions in clusters three and four. However, marker data showed that African okra possessed a more distinct form compared to the other okra germplasms. Nineteen SRAP primer combinations produced 92 bands and 29 (31.5 %) of them were found to be polymorphic among okra accessions. 1051 Togo was found to be the most divergent accession in phenotypic observation.Öğe Genome size constancy in Antarctic populations ofColobanthus quitensisandDeschampsia antarctica(Springer, 2020) Pere Pascual-Diaz, Joan; Serce, Sedat; Hradecka, Ivana; Vanek, Martin; Ozdemir, Bahar Sogutmaz; Sultana, Nusrat; Vural, MehtapColobanthus quitensis(Kunth) Bartl. andDeschampsia antarcticaDesv., the only two native flowering plants in the Antarctica, are interesting study cases from the ecological, biogeographic, and evolutionary points of view. Here, we present the first genome size analysis focused in several populations from the Antarctic Peninsula and the surrounding islands for both species, with a broad sampling distributed along a distance of 800 km. We have used flow cytometry to estimate genome size, being the first time that this technique is used forD. antarctica.Average genome sizes forD. antarctica(2C = 10.63 pg) andC. quintesis(2C = 2.01 pg) are consistent with the scarce previous data available, and point to a diploid and tetraploid ploidy level, respectively, for the analysed taxa. Despite a certain deviating individual inD. antarctica, whose higher genome size could suggest the existence of B-chromosomes, no significant genome size differences were found amongst the populations studied, for both species, which might be related with the recent colonisation history of the Antarctic continent.Öğe Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon(Ios Press, 2022) Sultana, Nusrat; Menzel, Gerhard; Seibt, Kathrin M.; Garcia, Sonia; Weber, Beatrice; Serce, Sedat; Heitkam, TonyBACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. OBJECTIVE: Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. METHODS: Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. RESULTS: We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsy in silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. CONCLUSIONS: We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.Öğe Heritability estimates and the variation of pomological traits, total phenolic compounds, and antioxidant capacity in two apricot progenies(Tubitak Scientific & Technological Research Council Turkey, 2020) Karaat, Firat Ege; Serce, SedatEven though pomological traits are important in fruit breeding for quality, antioxidant capacity and the total content of phenolic compounds have also gained importance, together with a rising awareness of their health benefits. As a result, this study was conducted to evaluate the variation and heritability levels of antioxidant capacity and total phenolic compounds, as well as pomological traits in 'Hacihaliloglu' x 'Stark Early Orange' and 'Cataloglu' x 'Stark Early Orange' apricot crosscombinations based on phenotypic assessments of fruit samples. The results indicated significant differences among F-1 progenies in the samples involved in the study. Broad-sense heritability coefficients ranged from 0.59 to 0.98 in the combinations examined. Parent-offspring regression coefficients for antioxidant capacity and total phenolic compounds were calculated to be 0.433 and 0.164, respectively. The results of the study can be useful in deciding selection strategies and choosing parents in relevant breeding programs.Öğe In vitro screening of octoploid Fragaria chiloensis and ragaria virginiana genotypes against iron deficiency(TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEY, 2014) Torun, Ayfer Alkan; Kacar, Yildiz Aka; Bicen, Belgin; Erdem, Nazife; Serce, SedatIron (Fe) deficiency is one of the common problems in strawberry (Fragaria x ananassa Duch.) growing regions. In vitro screening enables researchers to evaluate genotype performance under several concentrations of Fe in a relatively fast and economical way. Therefore, we evaluated the responses of several genotypes belonging to octoploid Fragaria chiloensis (L.) Mill. and Fragaria virginiana Mill. (the progenitors of cultivated strawberry) against Fe treatments under in vitro conditions. In the first experiment, HM 1, Pigeon Point, CFRA1267 (F. chiloensis subsp. pacifica), and CA1541 (F. chiloensis subsp. chiloensis) were tested with various Fe concentrations (0%, 10%, 15%, 25%, 50%, 65%, 80%, and 100%, where 100% = 27.8 mg L-1 FeSO4.7H(2)O). Different Fe concentration treatments resulted in differences in plant height, fresh and dry weight, as well as macro- and microelement concentrations among the tested genotypes. In the second experiment, 16 octoploid Fragaria genotypes were tested with 4 Fe concentration treatments (0%, 10%, 50%, and 100%, where 100% = 27.8 mg L-1 FeSO4.7H(2)O). Iron concentration and genotype interactions were significant for all studied characteristics except sulfur (S) and manganese (Mn) concentrations, and the 16 genotypes responded differentially to varying Fe treatments. The results of these experiments indicated that F. chiloensis and F. virginiana genotypes exhibited considerable variation under different Fe treatments in vitro, and the more resistant genotypes could be utilized to develop new strawberry cultivars with tolerance to low Fe concentrations.Öğe Lysophosphatidylethanolamine (LPE) Improves Fruit Size, Color, Quality and Phytochemical Contents of Sweet Cherry c.v. '0900 Ziraat'(KOREAN SOC HORTICULTURAL SCIENCE, 2015) Ozgen, Mustafa; Serce, Sedat; Akca, Yasar; Hong, Ji HeunLysophosphatidylethanolamine (LPE) affects the quality of flowers, fruits, and other horticultural products. Studies have provided evidence that LPE can accelerate ripening of fruits and prolong shelf-life at the same time. In this study, the influence of LPE on anthocyanin accumulation and phytochemical characteristics of sweet cherry was investigated. LPE (10 mg center dot L-1) was applied to a commercial sweet cherry c.v. '0900 Ziraat' orchard two and four weeks before harvest for two treatment years (2011 and 2012). Preharvest applications of LPE resulted in significant improvement in both pomological and phytochemical attributes at harvest. LPE treatment led to a 17% increase in fruit weight and a 6% increase in soluble solid content when averaged over two experimental years. Fruit phytochemical content and antioxidant capacity were increased significantly. The average total phenolic content of LPE-treated fruits for the two years was 703 mu g gallic acid equivalent (GAE)/g fresh weight (g FW) compared to 569 mu g GAE/g FW in the untreated control. Fruits treated with LPE had a 27% and 16% more anthocyanin than the control fruits in 2011 and 2012. Antioxidant capacity of fruits, as measured by TEAC (Trolox equivalent antioxidant capacity) assay, was 12.5 and 11.4 mu mol TE/g FW in LPE-treated and untreated control fruits, respectively, when averaged over two experimental years. Our results suggest that preharvest application of LPE may have the potential to increase anthocyanin accumulation, improve fruit quality and enhance phytochemical characteristics of sweet cherries.Öğe MOLECULAR CHARACTERIZATION OF SOME SELECTED PERSIMMON GENOTYPES AND CULTIVARS BY SRAP AND SSR MARKERS(Serbian Genetics Soc, 2017) Pinar, Hasan; Yildiz, Ercan; Kaplankiran, Mustafa; Toplu, Celil; Unlu, Mustafa; Serce, Sedat; Ercisli, SezaiIn this study, SRAP and SSR markers were employed to determine genetic relationships among 42 persimmon genotypes (Diospyros kaki Thunb) obtained from Hatay province and 3 persimmon cultivars, 2 of which belong to Diospyros kaki Thunb and one belongs to Diospyros oleifera Cheng. Genetic relationships were determined by using a total of 29 molecular DNA primers (SRAP and SSR). Of these primers, 21 SRAP primer combinations produced a total of 107 bands and 77.6% of them were polymorphic; 8 SSR primers produced 26 polymorphic bands with an average polymorphism ratio of 84.6%. The SRAP and SSR markers produced 4.6 bands as average and the number of bands produced per marker was calculated as 3.6. The lowest similarity was observed between MK-113 (Diospyros oleifera Cheng) and the other genotypes all belongs to Diospyros kaki Thunb (with similarity ratios of 0.41-0.69 for SRAP primers, between 0.25-0.67 for SSR primers). The genotypes/cultivars belongs to Diospyros kaki had similarity ratio between 0.98-1.00 according to SRAP and SSR markers. This synonym or similarity could be results of clonal propagation rather than autogamy.Öğe Morphological characterization of Cyclamen sp. grown naturally in Turkey: Part II(Wydawnictwo Akad Rolniczej W Lublinie, 2016) Curuk, Pembe; Sogut, Zerrin; Izgu, Tolga; Sevindik, Basar; Tagipur, Ehsan Mohammad; Teixeira da Silva, Jaime A.; Serce, SedatThe morphology of 279 accessions of Cyclamen sp. growing naturally in Tur-key, namely C. alpinum (syn. C. trochopteranthum), C. graecum, C. hederifolium (syn. C. neapolitanum) and C. mirabile, was characterized. Plants with intact tubers were collected from locations in Antalya, Isparta, Aydın, Muğla, İzmir and Denizli, determined by GPS, where they grow naturally in spring and autumn. The morphology of the four Cyclamen species was characterized using one year old regenerated plants based on 27 morphological traits (13 flower, 11 leaf, 2 plant, 1 tuber). There were distinct differ-ences among these accessions related to petal colour, pedicel length, leaf length and width, leaf shape, and tuber diameter. Even though principle component analysis con-firmed the grouping of characters into species-specific clusters, a wider range of morpho-logical data as well as molecular data are needed for more reliable conclusions to be drawn about the classification of these Cyclamen species. © by Wydawnictwo Uniwersytetu Przyrodniczego w Lublinie, Lublin 2016.Öğe Screening of Wild Strawberry Germplasm for Iron-deficiency Tolerance Under Hydroponic Conditions(Galenos Publ House, 2022) Alkan Torun, Ayfer; Erdem, Nazife; Serce, Sedat; Aka Kacar, Yildiz; Torun, BulentCultivated strawberry has been developed from hybridization between Fragaria chiloensis and F. virginiana. The progenitor species exhibit significant genetic diversity. Growth attributes of progenitor species and their responses to several stress factors have been studied. However, iron deficiency tolerance (FeDT) of different species have merely been tested under hydroponic conditions. This study evaluated FeDT of 23 genotypes belonging to super-seed collection under hydroponic conditions. Two genotypes (one Fe-deficiency tolerant and one sensitive) were selected from screening experiment and their physiological and morphological mechanisms playing role in FeDT were determined. Plant parameters associated with FeDT, i.e., pH of the growth medium, root Fe reductase activity, total and active Fe concentration of shoot were recorded. The Fe efficiency of strawberry subspecies varied between 51% and 98%. Fe efficiency values also varied among subspecies. AukeLake and RCP37 belonging to F. chiloensis were highly resistant and sensitive to Fe deficiency, respectively based on Fe efficiency values. A highly significant relationship was observed between Fe concentration and FeDT of the genotypes. Acidification of nutrient solution and root Fe reductase activity were closely related to high shoot iron concentration. Our findings indicated existence of a close relationship between root uptake and root to shoot translocation of Fe, which ultimately contribute greatly to FeDT among tested strawberry genotypes.Öğe Survey of Turkish Strawberry Production Areas for Soil-borne Fungal Diseases(Amer Soc Horticultural Science, 2015) Bildik, Mehmet Naci; Serce, Cigdem Ulubas; Dervis, Sibel; Turkolmez, Sahimerdan; Ciftci, Osman; Serce, Sedat[Abstract Not Available]Öğe Variation among highbush and rabbiteye cultivars of blueberry for fruit quality and phytochemical characteristics(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2015) Gunduz, Kazim; Serce, Sedat; Hancock, James F.Variability in soluble solids (SS), titratable acidity (TA), SS/TA, pH, total phenolic content (TPC), ferric reducing ability of plasma (FRAP), total monomeric anthocyanin content (TMAC) and levels of vitamin C were evaluated in a broad array of northern and southern highbush (Vaccinium corymbosum) and rabbiteye (Vaccinium virgatum) cultivars of blueberry, grown in different locations and years. When cultivars were grouped by decade of release, there were few significant overall trends observed over years in fruit quality and phytochemical content; however, individual cultivars varied significantly for all the traits analysed. Considerable overlap in most quality and phytochemical characteristics were found among cultivars of the three blueberry types, suggesting that genetic barriers do not exist among the various types of blueberries with regard to breeding cultivars with comparable sugar, acid and phytochemical properties. There were significant negative correlations observed between fruit weight and SS, TPC, FRAP and TMAC, suggesting that as breeders have been selecting for larger fruit, they have inadvertantly selected for tarter fruit with lower antioxidant capacity. However, SS was correlated positively with FRAP and TMAC, indicating that cultivars can be developed that have high antioxidant capacity and anthocyanin content, combined with high sugar content. (C) 2014 Elsevier Inc. All rights reserved.Öğe Vitamin C and fruit quality consensus in breeding elite European strawberry under multiple interactions of environment(Springer, 2022) Ali, Muhammad Nisar; Serce, SedatBackground Vitamin C is a life saving molecule. Vitamin C based breeding is need of the hour in order to provide humans an immunity boosting supplement in the form of fresh food. Methods and Results Multiple interactions of Anatolian Mediterranean environment were studied with cultivars ('Calinda', 'Rubygem', 'Sabrina', and 'Sahara') and fruit maturity stages. Genetic expression of six vitamin C related genes was estimated showing significantly higher expression in open field. Cultivar 'Calinda' performed better in organic acids but poor in firmness. Cultivar 'Sabrina' showed highest fruit firmness but lower commercially desired fruit quality characters. Cultivar 'Sahara' performed best for vitamin C and fruit redness, and was high in fruit size, weight, and organic acids. Chroma trends indicated simultaneous accumulation of vitamin C and anthocyanins in strawberry fruits. Transition stage of fruits was found most critical for metabolite regulation and sensitive to environmental changes. Fruits of cultivar 'Sahara' at 'Red' maturity stage expressed highest vitamin C levels (138.03 mg/100 g FW) whereas 'Turning' fruits of cultivar 'Sabrina' had lowest vitamin C content (27.80 mg/100 g FW). All studied vitamin C related genes indicate highest genetic expression for cultivar 'Sahara', except for genes FaVTC2 and FaMDHAR which exhibit highest genetic expression for cultivar 'Rubygem.' Conclusion Two-way and three-way interactions between cultivars, environments, and maturity stages were significant for vitamin C and fruit quality regulation under Mediterranean climate. This indicates an absolute requisite of studying combined influences in actual field, rather than single factor, controlled, or lab experiments. Correlation analysis showed that vitamin C content in a fruit is a complex subject and mainly depends on fruit color, size, and firmness. Principal Component Analysis validated that cultivar 'Sahara' is a promising candidate for vitamin C based breeding in strawberry.Öğe Wild Vaccinium Species in Turkey(Amer Soc Horticultural Science, 2015) Celik, Huseyin; Serce, Sedat[Abstract Not Available]
