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Öğe Construction of a high-density genetic linkage map and QTL analysis using an interspecific F1 population in pistachio(Springer Science and Business Media Deutschland GmbH, 2023) Islam, Md Rashedul; Tevfik, Habibullah; Topçu, Hayat; Karcı, Harun; Kafkas, SalihPistachio (Pistacia vera L.) is one of the commercially important cultivated nut tree species in Turkey. Pistachio nuts have many beneficial properties to human health and are widely used in the food industry. Cultivar breeding programs in pistachio take a long time, huge labor, high cost, and large land areas due to the alternate bearing and the long juvenile period of pistachio. Molecular breeding approaches are widely used to shorten long-term breeding programs in pistachio. In this study, we aimed to (i) construct the first SNP-based high-density genetic linkage maps using an interspecific F1 population derived from a cross between P. vera cv. ‘Ohadi’ and P. atlantica cv. ‘Pa-18’ (‘Ohadi × Pa-18’), and (ii) perform QTL analysis in leaf, shoot, and inflorescence traits in pistachio. To obtain the SNP markers, the DArT-Seq™ genotyping-by-sequencing method was used. A total of 1407 SNPs were mapped in the ‘Ohadi’ female, whereas the ‘Pa-18’ male map consisted of a total of 2518 SNP markers. The total length of the ‘Ohadi’ map was 1122.2 cm with an average length of 74.8 cM, while the ‘Pa-18’ map was 1307.2 cM in length with an average length of 87.1 cM. The marker density was 1.2 and 1.9 markers per cM in ‘Ohadi’ and ‘Pa-18’ linkage maps, respectively. The ‘Ohadi’ map had an average of 93.8 markers per linkage group (LG), while the ‘Pa-18’ map had an average of 167.9 markers per linkage group. A total of four significant QTLs that are related to terminal leaflet base, leaf width, tree vigor, and inflorescence rachis length were detected in three linkage groups in the ‘Ohadi’ genetic linkage map. While the detected QTLs can be used for marker-assisted breeding and genetic studies, the generated SNP-based genetic linkage maps in this study will be used for QTL analysis of other important agronomic traits in pistachio. © 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Öğe Development of a high-density genetic linkage map and identification of quantitative trait loci (QTLs) associated with Botrytis cinerea resistance in strawberry (Fragaria × ananassa Duch.)(2024) Sönmez, Duygu Ayvaz; Karcı, Harun; Topçu, Hayat; Bilgin, Ömer Faruk; Günaçtı, Hale; Tevfik, Habibullah; Özgören, BurakOver the centuries, strawberry fruit quality has greatly improved through various selection studies. The discovery of genes and genomic positions related to traits such as fruit quality and resistance to diseases and pests has been accelerated by new biotechnological methods. The objectives of this study are (i) to construct single nucleotide polymorphism (SNP) Fana array-based high-throughput genetic linkage groups for the ‘Fortuna × Rubygem’ F1 population, and (ii) to detect quantitative trait loci (QTL) regions associated with Botrytis cinerea resistance in leaf and fruit traits of strawberry. A total of 945 and 984 SNPs were mapped in the ‘Fortuna’ maternal and the ‘Rubygem’ paternal maps, respectively. The lengths of the linkage groups (LGs) and the average length of ‘Fortuna’ were calculated to be 1814 cM and 55.0 cM, respectively. The total length of ‘Rubygem’ was determined to be 2170 cM, with an average length of 65.7 cM. The average marker densities for the‘Fortuna’ and ‘Rubygem’ linkages per cM were recorded as 0.58 and 0.53 markers, respectively. The ‘Fortuna’ female produced a mean of 28.64 markers per LG, while the ‘Rubygem’ male linkage groups had approximately 30 markers per LG. Five significant QTLs associated with resistance to B. cinerea in the leaves were identified in both parents. QTLs associated with resistance in strawberry fruits were found within a total of three LGs in different positions. The compressive genetic linkage maps developed in ‘Fortuna × Rubygem’ population can be used in genetic and QTL studies for important agronomical traits. The identified QTLs associated with Botrytis cinerea resistance may be preferred for use in future strawberry breeding programs to carry out marker- assisted selection.Öğe Fatty acids composition in Pistachio(EDP Sciences, 2024) Gündüz, Leyla Nurefşan; Kazan, Murat; Topçu, Hayat; Kafkas, SalihPistachio (Pistacia vera L.), is an important food source for human health. It has nutritional content rich in protein, fat, fatty acids, fiber, vitamins and minerals. Such as other nuts, pistachio oil is rich in unsaturated fatty acids. Pistachio is rich in omega fatty acids such as n-3, n-6, n-9, it is known to be beneficial in decreasing cholesterol by increasing HDL level in blood plasma. Oleic acid (C18: 1) and palmitoleic acid are the main component of unsaturated fatty acids in pistachio. It has fatty acids such as linoleic acid and alpha linoleic acid among polyunsaturated fatty acids and myristic acid, palmitic acid, stearic acid among saturated fatty acids. Gas chromatography-flame ionization detector (GC-FID) is generally used for the analysis of fatty acids in foods. The main component of unsaturated fatty acids contained in pistachio is oleic acid (C18: 1) and the variety varies between 51.6% and 81.17% according to the origin. Linoleic acid (C18:2) content, which is a polyunsaturated fatty acid, varies between 15% and 30%. Stearic acid content of saturated fatty acids varies between 0.8% and 3.5%. This review provides information about the properties and curent status of the fatty acids in pistachios. © The Authors, published by EDP Sciences.Öğe In vitro salinity stress mediates grass pea genotypes' (Lathyrus sativus L.) responses(Tubitak Scientific & Technical Research Council Turkey, 2022) Khosravi, Zahra; Pourmohammad, Alireza; Aliloo, Ali-Asghar; Shahabivand, Saleh; Hassanpouraghdam, Mohammad Bagher; Topçu, HayatThis study was carried out to determine the tolerance of grass pea genotypes to salinity stress at callus and seedling stages under in vitro conditions. The calli and seedlings of six selected tolerant genotypes based on the primary screening in the field were separately exposed to salinity treatments (0, 125 mM) in vitro. Salinity was imposed with NaCl during in vitro culture, and it significantly affected all seedling traits. Genotype of Iran had the lowest seedling dry weight and therefore was more sensitive to salinity stress. According to salinity tolerance indices for seedlings, genotype Greece-III was characterized as high-yield and relatively high-salt-tolerant genotype. Salinity significantly affected callus size, callus RWC, callus RGR, and callogenesis index. Calli fresh and dry weights were not affected by the treatments. For callus dry weight, genotype Greece-III had the highest mean; and the lowest mean belonged to Greece-I. The stress tolerance indices showed that the highest values belonged to genotype Greece-III, which showed high yield and yield stability and so reasonable salinity tolerance. Cluster analysis divided the genotypes into two separate groups. The first cluster consisted of Iran, Greece-II, and Greece-III genotypes, and the second cluster consisted of Bangladesh, Canada, and Greece-I genotypes. Cluster analysis potentially separated the tolerant and sensitive genotypes to salinity in terms of callus dry weight. Grass pea callus and seedlings were able to survive at 125 mM salinity. Salinity did not affect callus dry and fresh weights, but its effect was remarkable on seedling dry and fresh weights (55% less than control). Therefore, calli were reasonably salinity tolerant. The present study suggests that grass pea was reasonably tolerant to salinity and can survive under salinity conditions during the seedling and callus stages.Öğe Optimal Propagation and Rooting Mediums in Rubus spp. by in Vitro Micropropagation(2022) Topçu, HayatRubus spp. is a shrub-form plant known for its fruits called blackberries. Blackberries are plants with high commercial value, delicious taste, nice aroma, and high nutritional value. Turkey has wealthy genetic origins of Rubus species. Conventionally, the trading propagation of Rubus plants is done as vegetatively, utilizing truncation, rooting, or stratuming. However, these traditional methods are time-consuming and inefficient in virus-free plant production. Cloning of plant grown in the tissue culture also enables to obtain virus-free plants and to provide fast replicating high standard plants. Rubus obtained by micropropagation is used for the formation of commercial fruit plantations as well as source plant formation. In this work, the aim is the development of in vitro micropropagation process of the wild Rubus in the Trakya Region. Proliferation from axillary buds was made by adding BAP (6- Benzylaminopurine), NAA (Naphthalinacetic acid) and GA3 (Gibberellic acid) in various combinations and concentrations to the MS medium. Rooting was successfully realized with 83.3% rooted plants in 1 IBA medium. No roots were seen in 0 MS. The survival rate of plants transferred to ex vitro conditions was 100%.Öğe Phytochemical analysis of leaves and stems of Physalis alkekengi L. (Solanaceae)(De Gruyter Poland Sp Z O O, 2022) Popova, Venelina; Ivanova, Tanya; Stoyanova, Magdalena; Mazova, Nadezhda; Dimitrova-Dyulgerova, Ivanka; Stoyanova, Albena; Ercisli, Sezai; Topçu, HayatPhysalis alkekengi L. (Solanaceae) is encountered in different regions of Bulgaria as a wild growing or ornamental plant. The objective of this work was to characterize the phytochemical composition (macro and micro components) of the leaves and stems of two local phenotypes (PA-SB and PA-NB), with the view of revealing their use potential. The dry leaves contained (DW) protein (16.25 and 19.27%), cellulose (25.16 and 25.31%), and ash (18.28 and 16.16%) and the stems contained protein (6.83 and 7.35%), cellulose (39.34 and 38.25%), and ash (15.01 and 7.48%) for PA-SB and PA-NB, respectively. The dominant amino acids (by HPLC) in the leaves of both phenotypes were arginine (21.3-22.3 mg/g) and aspartic acid (8.8-18.4 mg/g), and those in the stems were proline and aspartic acid for PA-SB (8.8, 7.7 mg/g); isoleucine and tyrosine for PA-NB (12.8, 6.6 mg/g). Mineral elements, determined by AAS (K, Ca, Mg, Na, Cu, Fe, Zn, Mn, Pb, Cr), also varied between phenotypes and plant parts. The leaves alone were further processed by extraction with n-hexane, for the identification of leaf volatiles (by gas chromatography-mass spectrometry). The analysis identified 28 components (97.99%) in the leaf extract of PA-SB and 32 components (97.50%) in that of PA-NB. The volatile profile of PA-SB leaves was dominated by diterpenes (49.96%) and oxygenated sesquiterpenes (35.61%), while that of PA-NB was dominated by oxygenated aliphatics (40.01%) and diterpenes (35.19%). To the best of our knowledge, the study provides the first data about the phytochemical composition of the leaves and stems of P. alkekengi from Bulgaria, in a direct comparison of phenotypes from two distinct wild populations, which could be of further scientific interest.Öğe Reference gene selection for RT-qPCR normalization of strawberry at various organs, different growing stages of fruits, and salt-stress treatment(Scientific And Technological Research Council Turkey, 2022) Topçu, HayatStrawberry (Fragaria x ananassa Duch.) is a favorite fruit of high economic value due to its good taste and high nutrition ingredients. Strawberry is a fruit grown around the world that has distinct genetic structures and indicates diverse levels of precision to different environmental circumstances. Plants respond differently to diverse physiological processes, organizing of biological events, control of hormones, different individuals of the same species, and internal and external factors in developmental stages. Quantitative real-time polymerase chain reaction (RT-qPCR) has become a very useful tool for the determination of plant genetic and physiological changes in gene expression. To obtain more securable gene expression outcomes, RT-qPCR data should be standardized with a control gene that shows homogeneous expression at diverse stages of growth in plants, in different organs, or under various environmental circumstances. We evaluated the gene expression of 8 reference genes, including StRefHISTH4, StRefGAPDH, StRefDBP, StRefActin1, UBQ, aTUB, 18SrRNA, and EF1a in different sets of 2 cultivars, four different organs, various fruit growing stages, and development period samples treated with salt. The genes expressions are greatly dissimilar in various organ samples examined. The expressions of StRefHISH4 and StRefActin 1 were very steady in all the different organs, fruits at various growth stages, and samples treated with salt analyzed. Furthermore, StRefHISH4 and StRefActin 1 showed the steadiest expression in plants cultivated under different development states. The expression of these reference (housekeeping) genes can be utilized for the standardization of real-time PCR outcomes for gene expression examination in many types of samples in strawberries.Öğe A researchon the detection of some phytochemical properties in the fruits of passiflora species(EDP Sciences, 2024) Ada, Mesut; Oğuz, İlbilge; Kafkas, Nesibe Ebru; Burgut, Ayşegül; Topçu, HayatPassiflora belongs to the Passifloraceae family and is native to South Africa. Thanks to its health benefits, it is now commonly grown in tropical and subtropical regions. This fruit gathers attention, especially for its rich nutritional content, aroma, and taste. Passiflora has gained popularity in the Mediterranean region of Turkey, particularly in recent years. It stands out for its ease of maintenance, yielding twice a year, and high economic returns. Additionally, passiflora is used as an ornamental plant in landscaping arrangements by means of its showy flowers and is often referred to as the "passionflower" or "clock flower". In this study, the fruits of P. edulis and P. caerulea species were examined for their phytochemical properties, such as DPPH, total phenol, sugar, and organic acid. DPPH (2,2?diphenyl?1-picryl?hydrazyl?hydrate) and total phenol were analyzed using a spectrophotometric method, while sugar and organic acid were analyzed using HPLC. © The Authors, published by EDP Sciences.Öğe Sugar, Invertase Enzyme Activities and Invertase Gene Expression in Different Developmental Stages of Strawberry Fruits(MDPI, 2022) Topçu, Hayat; Değirmenci, İpek; Ayvaz Sönmez, Duygu; Paizila, Aibibula; Karcı, Harun; Kafkas, Salih; Alatawi, AishahThe cultivated strawberry (Fragaria × ananassa) is octoploid (2n = 8x = 56) and has been the focused fruit species of which an increasing number of molecular and genetic research has been conducted in recent years. The aim of this study is to identify the relationships between sucrose metabolism, invertase enzyme activity and gene expression in four different fruit development periods (red, pink, green and white) of two commercially important strawberry varieties ‘Rubygem’ and ‘Fortuna’. The metabolite profiles (glucose, fructose, sucrose and total sugar content) of two varieties were discovered to be extremely similar. The highest amount of total sugar was found in red fruits, while the lowest was obtained from green fruits. Invertase represents one of the key enzymes in sucrose metabolism. The lowest invertase activity was obtained from the green fruits in ‘Rubygem’ and ‘Fortuna’ during four developmental periods. In these varieties, the amount of sucrose was found to be close to glucose and fructose and the lowest amount was detected in green period, while invertase activity was relatively high during red and pink periods and invertase gene expression was determined at high levels in both primers (St-4 and St-6) in the green period. The results of the study indicated that sugar content and invertase activity were positively correlated while enzyme activity and gene expression were negatively correlated. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.Öğe Using computational modeling to design antiviral strategies and understand plant-virus interactions(2024) Kamal, Hira; Zafar, Muhammad Mubashar; Razzaq, Abdul; Ijaz, Aqsa; Anwar, Zunaira; Topçu, Hayat; Elhındı, Khalid M.Using a bioinformatics approach to identify binding pockets between proteins is a preferable method before modifying the genome to delineate host interactions with viruses. Based on extensive proteomics data in numerous databases, several interaction prediction methods are available to identify binding sites between viruses and hosts at the individual residue level, but little is known about the interaction prediction strategy for plant viruses. Begomoviruses, belonging to the family Geminiviridae, constitute a group of circular single-stranded (ss) DNA viruses that encode multifunctional proteins responsible for viral replication, causing severe diseases in multiple host plants. These viruses usually escape through plant defense mechanism overcoming physical and chemical barriers to trigger the infection with all possible combinations of interaction in the target host protein partners. Here, we have applied our computational approach for plant virus interaction at domain level. Previous study showed that myristoylation-like motif in Begomovirus cotton leaf curl Multan associated betasatellite protein ?C1 (CLCuMB- ?C1) played an important role in interaction with ubiquitin conjugating enzyme protein (UBC3) in tomato. This kind of binding at residue level has been validated using in vivo and in vitro molecular approach. Here, an in silico approach was utilized which is a combinatorial source of previous and recent protein prediction methods to determine all possible identified interface sites between ?C1 and UBC3. This molecular interaction of CLCuMB- ?C1 was further verified in the actual host i.e. cotton using a bimolecular fluorescence complementation system and yeast two-hybrid assay. This computational and molecular data will help to identify the interaction between virus and host before using any expensive and time-consuming molecular techniques.
