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Öğe Alternaria alternata causing inner black rot of lemon (Citrus limon) fruits in Turkey: Genetic diversity and characterisation(Academic Press Ltd- Elsevier Science Ltd, 2023) Güney, İnci Güler; Tekin, Fatih; Günen, Tacettin Utku; Özer, Göksel; Derviş, SibelThe market sales of symptomless lemons in 2020 revealed a persistent and severe internal black rot with browning of the membrane wall and juice sac. To investigate the causal agent, externally symptom-free lemons from Mediterranean locations were sampled from supermarkets, local markets, and bazaars in three southeastern Turkish provinces. Internal black rot symptoms were observed in 13.69% of the 1300 externally symptomless fruits, and Alternaria was isolated from 96.63% of those exhibiting these symptoms. Morphological analysis confirmed the identity of Alternaria alternata in 26 representative isolates collected from various markets and bazaars. To examine genetic diversity or polymorphisms, start codon targeted (SCoT) markers were used. Species identification was based on the sequences of translation elongation factor 1-alpha (TEF 1-alpha), RNA polymerase second largest subunit (RPB2), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). SCoT 29 exhibited the highest amount of polymorphic amplicons, with 18 polymorphic bands scored when compared to the other six scoreable markers. The 26 representative isolates from various markets and bazaars were divided into four clades by SCoT 29. However, multilocus sequence analyses confirmed the identification of a single species, A. alternata. In terms of virulence and the impact of temperature on growth, representative isolates from four SCoT clusters were evaluated. Data suggests that SCoT markers can be used to evaluate virulence-based polymorphism in A. alternata; nonetheless, all clades showed comparable temperature responses, with 25 degrees C being the optimum. There was also no association between individual morphotypes and SCoT clade membership. Due to the lack of obvious signs on lemon fruits, producers, merchants, and consumers are unable to identify black rot, and the widespread presence of A. alternata in lemons may pose a significant risk that must be avoided at all costs.Öğe Alternaria burnsii'nin gelişimi üzerine farklı kültürel koşulların etkisi ve rDNA-ITS sekansına dayanan filogenetik analizi(2017) Bayraktar, Harun; Yılmaz, Olgac; Özer, GökselAlternaria burnsii'nin neden olduğu kimyon yanıklığı birçok ülkede kimyon üretimini sınırlandıran önemli bir fungal hastalıktır. Patojen ülkemizde de hemen hemen tüm kimyon ekim alanlarında yaygın olup önemli ekonomik kayıplara neden olmaktadır. Bununla birlikte, Alternaria burnsii' nin morfolojik, fenotipik ve filogenetik özellikleri hakkında çok fazla bilgi bulunmamaktadır. Bu çalışmada Alternaria burnsii'nin miseliyal gelişimi ve sporulasyonu üzerine farklı besi ortamları ve çevresel faktörlerin etkisi araştırılmıştır. Ayrıca patojen izolatları arasındaki morfolojik farklılıklar değerlendirilmiştir. Bu amaçla patojen izolatlar, yedi farklı besi ortamı (Patates Dekstroz Agar , Patates Havuç Agar, Mısır Unu Agar, Czapek Dox Agar, Sukroz Agar, Su Agarı, Domates Suyu Agarı, V88) üzerinde iki farklı inkubasyon koşulu altında geliştirilmiştir. Değerlendirilen kültür ortamları arasında en yüksek sporulasyon değişken sıcaklık ve ışık koşularına maruz bırakılan V88 ortamı üzerinde elde edilmiştir. Ayrıca kültür ortamı ve gelişme koşullarına bağlı olarak konidi uzunluğu, genişliği ve septa sayısı bakımından istatiksel olarak önemli farklılıklar gözlemlenmiştir. Sıcaklık patojen gelişimini etkileyen önemli bir sınırlayıcı faktör olup en iyi gelişme oranı 25 °C' de gözlemlenmiştir. Ayrıca, UPGMA metodu ile gerçekleştirilen ITS sekansının filogenetik analizi ise test edilen tüm izolatların aynı grup içerisinde yer aldığını ve bu izolatların GenBankasından elde edilen ve farklı seksiyonları temsil eden Alternaria tür gruplarına ait izolatlardan filogenetik olarak farklı olduğunu göstermiştir. Bu sonuçların gelecekteki araştırmalar için patojen inokulumunun hazırlanmasının yanısıra patojen tespit ve tanılanması için farklı metotların geliştirilmesinde faydalı bilgiler sağlayacağı düşünülmektedirÖğe Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers(Springer, 2022) Yeken, Mehmet Zahit; Emiralioğlu, Orkun; Çiftçi, Vahdettin; Bayraktar, Harun; Palacıoğlu, Gülsüm; Özer, GökselBackground Breeding strategies to improve modern varieties having high yield, high nutritional value and resistance to biotic and abiotic stress, etc. is very important to make up for the food deficiencies. Molecular studies as a tool in breeding programs for the characterization of germplasm have been performed with several DNA marker systems. Materials and methods In the present study, the genetic diversity of 53 common bean landraces and 22 registered varieties from Turkey, and 12 genotypes from USDA was investigated using start codon targeted (SCoT) markers for the first time worldwide. The 8 primers having stronger and more polymorphic bands were used for PCR amplification. Results The mean polymorphic band of all primers was found as 13.13. The average of polymorphic information content and resolving power values was 0.34 and 7.55, respectively. Analysis of molecular variance (AMOVA) explored the existence of higher genetic diversity within populations accounting for 92% compared to among populations variations. According to cluster analysis (UPGMA) and genetic structure based on SCoT data, accessions were separated into Andean (PopA) and Mesoamerican PopB) gene pools. Moreover, accessions were mostly placed in the same groups/subgroups according to their geographical origin. Conclusions A high level of genetic diversity was observed between the investigated accessions in this work. The findings will help to plant breeders to characterize common bean accessions.Öğe Assessment of variation in seed morphological traits in Phaseolus sp. landraces from western Anatolia(Banats Univ Agricultural Sciences & Veterinary Medicine Timisoara, 2019) Cancı, Hüseyin; Yeken, Mehmet Zahit; Kantar, Faik; Bozkurt, Murat; Çiftçi, Vahdettin; Özer, GökselSeed size, seed shape and seed colour are easily discernible phenotypic traits of beans in the market. Consumers often have specific preferences to different combinations of seed size, shape and colour. Local landraces are usually grown for their desired organoleptic and seed properties by consumers. This study investigated the variability in seed size attributes, seed shape, visual seed colour properties and seed luminosity/chromaticity properties of the germplasm of 255 landraces representing major local bean types grown in 20 provinces in Western Anatolia Region of Turkey. Measurements were made on seeds from representative single plants for seed size index, 100 seed weight, seed length, seed width, seed thickness, seed width in cross section, seed shape, seed degree of curvature in kidney types, seed shape in cross section, number of seed colors, main seed color, secondary seed colour, distribution of secondary seed color, seed veining, colour of hilum ring and values of L (Luminosity), chromaticity a*, chromaticity b*, chroma (C) and hue angle. Data were statistically analysed, principle component analysis was carried out, the germplasm was classified by UPGMA dendograms and selections were made on the bases of GGE biplot analysis. Landraces showed a considerable diversity for seed size, seed shape and seed colour trait measured. All seed size variables ranged by 2-10-fold within the germplasm. 100-seed weight ranged ten-fold from very small seeded Meso-American types (18.4 g, e.g. AYD-8, KTH-30, MGL-1, DNZ-1 and BRD-24) to very large seeded Andean types (182.3 g, e.g. MGL-37, PKS-1, ANT-33, MGL-31 and ANT-16). Seed shape also varied as kidney-shaped (96 landraces), circular to elliptic (73), circular (58), elliptic (27) and rectangular (1) shapes. Main and secondary seed colours had considerable variation within the germplasm with 151 landraces had white, 31 grey, 31 beige, 23 brown, 8 violet, 5 red and 4 black main seed colour whereas 24 landraces had violet followed by 17 black and 14 red secondary seed colour. Landraces exhibited a large variation for chromaticity and luminosity variables. L value ranged between 20.3 and 90.1 representing a 4.5-fold variation. The landraces in the germplasm were assessed and characterised on the bases of diversity in seed morphological traits. Selections were made using UPGMA dendogram and GGE-biplot for production and breeding bean cultivars for preferences of changing consumer demands.Öğe Batı Anadolu fasulye genetik kaynaklarının biyolojik çeşitliliğinin araştırılması ve karakterizasyonu(2019) Çancı, Hüseyin; Bozkurt, Murat; Kanta, Faik; Yeken, Mehmet Zahit; Özer, Göksel; Çiftçi, VahdettinBu çalışmada, Batı Anadolu Bölgesi'nde 10 ilde üretilen 156 önemli yerel fasulye ekotipi 2015 yılında toplanmış ve ekotipler arasındaki biyolojik çeşitliliği araştırmak ve karakterize etmek için 2016 yılında Akdeniz Üniversitesi Ziraat Fakültesi'nde tarla denemesi yürütülmüştür. İncelenen karakterler açısından en belirgin değişim kuru sap ve tane veriminde kaydedilirken bunu bitkide bakla sayısı, baklada tane sayısı, bitki boyu ve yüz tane ağırlığı takip etmiştir. En yüksek bitki başına tane verimi MGL-30 (145.6 g), MGL-38 (101.7 g), ANT-43 (87.8 g) ve MGL-26 (81.9 g) genotiplerinden elde edilmiştir. Temel bileşen analizinde, 17 bileşen yerel fasulye genetik kaynaklarındaki varyasyonun %74.9’unu izah etmiştir. Bakla rengi, bitki tipi ve sarılma özelliği en fazla katkı sağlayan özellikler olmuştur. Bitki boyu ve olgunlaşma gün sayısı, biplot analizinde tane verimi ile aynı yönde ve en dar açıya sahip vektörler olmuştur. Morfolojik özellikler kullanılarak üretilen benzerlik dendogramı genotipleri iki ana gruba (A ve B) ve dört alt gruba (A1, A2, B1 ve B2 ) ayrılmıştır. Morfolojik özellikler açısından en uzak gruplarda yer alan MGL-01, KTH-01, MNS-01 ve ANT-13 ile UŞK-01, ANT-01, MGL-05 ve AYD-02 ekotipleri kullanılarak melezleme ıslahı ile yeni çeşitler geliştirilebilir.Öğe Bipolaris sorokiniana’nın Buğday Bitkisi Dokularından Tespiti için Real-Time PCR Metodunun Geliştirilmesi ve Erken Enfeksiyon Aşamasında Patojenisite ile Alakalı Bazı Genlerin İfade Düzeylerinin Araştırılması(2020) Özer, GökselBugday insan beslenmesinde önemli enerji ve mineral kaynaklarından biri olup, birçok ülke için stratejik ürün olarak kabul edilmektedir. Bugday yetistiriciliginde biyotik ve abiyotik stres etmenlerin neden oldugu ürün kayıplarının önlenmesi veya en aza indirilmesi oldukça önemlidir. Dünyada ve ülkemizde bugday yetistiriciliginde karsılasılan en yaygın etmenlerden Bipolaris sorokiniana bugday bitkisinde olusturdugu önemli bir hastalıkta noktalı yaprak lekesi hastalıgıdır. Özelikle kıslık bugday ekimlerinde önemli ürün kayıplarına neden hastalıkla mücadelede dayanıklı çesit gelistirilmesine yönelik ıslah çalısmaları en çevreci ve en etkin bir strateji olarak ön plana çıkmaktadır. Proje kapsamında elde edilen Bipolaris sorokiniana izolatları elde edilmis ve genetik ve patojenik olarak karakterize edilmistir. Etmene karsı ülkemizde yaygın yetistirilmekte 55 bugday çesidinin konukçu duyarlılıgı ortaya konmustur. Çesitlerin gösterdikleri reaksiyonlar arasında istatistiki olarak önemli farklılıklar gözlenmis olup Kırik, Lancer, Dogu-88, Nenehatun ve Damla çesitleri sırasıyla en hassas çesitler olarak görülmüs iken Anafarta, Koç-2015, Abide, Yakamoz ve Gelibolu sırasıyla en dayanıklı çesitleri olarak tespit edilmistir. Real-Time PCR dayalı olarak etmenin DNA?sının konukçu dokulardan tespitine yönelik çalısmalarda ribozomal DNA?nın Small Subunit (SSU) ve Internal Transcribed Spacer (ITS) bölgeleri ile Glyceraldehyde 3-phosphate Dehydrogenase (GAPDH) geninin oldukça uygun tespit edilmistir. Bu bölgeler sırasıyla etmen DNA?sının varlıgını 0.1 pg, 0.01 pg ve 1 pg düzeyinde tespitine olanak vermistir. PCR çalısmasının özgüllügü, enfekte olmamıs bitki dokuları ve iliskili diger fungus türlerine karsı test edilerek dogrulanmıstır. Teknik inokulasyonu takip eden ve örnekleme yapılan 3. 5. ve 8. günlerde hassas ve dayanıklı çesitler arasında istatistiksel farkı ortaya koymustur. Gelistirilen teknik görsel hastalık degerlendirmesine bir alternatif olarak enfeksiyonun erken bir asamasında dayanıklı ıslah materyalinin seçimi için faydalı bir yaklasım saglayacaktır. Ayrıca bugday çesitlerinde hastalık stresi altında patogenez ile iliskili protein genlerinin karsılastırmalı ifadesini degerlendirmis dayanıklı olan Anafarta çesidinde patogenez ile iliskili olan PAL, PR2, PR3, PR5, PR10 genlerinin ifade düzeyinde artıs görülmesine karsın hassas Nenehatun çesidinde SOD, APX, CAT, PR1 genlerinin ifade düzeylerinde daha fazla miktarda artısa sahip oldugu tespit edilmistir. Bu çalısmalar ile hastalıgın olusumu ve dayanıklılık mekanizmalarını inceleyenler için önemli bilgiler içermekte olup ve dayanıklı çesit ıslahı çalısmalarına da önemli katkılar saglayacaktır.Öğe Bitki Patojeni Fungusların Tespitinde Polimeraz Zincir Reaksiyonu’na Dayalı Bazı Moleküler Teknikler(2021) Palacioğlu, Gülsüm; Özer, Göksel; Bayraktar, HarunKültür bitkilerinde ciddi kayıplara neden olan hastalık etmenleri içerisinde bitki patojeni funguslarönemli bir grubu oluşturmaktadır. Bu patojenlere karşı etkin mücadele yöntemlerinin geliştirilmesi ve nedenoldukları ürün kayıplarının en aza indirilmesi için doğru ve hızlı bir şekilde tespit edilmesi en önemli adımdır.Bu kapsamda fungal patojenlerin klasik tespitinde kullanılan morfolojik karakterlere dayalı yöntemlerdeğişkenlik göstermekle birlikte uzun zaman almakta ve taksonomik açıdan deneyimli personel gerektirmektedir.Bu nedenle bitki patojenlerinin tespiti için çok sayıda moleküler teknik geliştirilmiş ve epidemiyolojikçalışmalarda, karantina uygulamalarında, tohum sertifikasyonunda, ıslah programlarında ve fungisit direncitespitinde yaygın olarak kullanılmaktadır. Bu çalışmada da bitki patojeni fungusların tespitinde yaygın olarakkullanılan polimeraz zincir reaksiyonuna dayalı bazı moleküler teknikler (Loop aracılı izotermal amlifikasyon,manyetik yakalama hibridizasyon, floresan in situ hibridizasyon, yeni nesil dizileme, Real Time PCR) hakkındabilgi verilmesi amaçlanmıştır. Bitki patojeni fungusların neden olduğu ekonomik kayıpları azaltmak amacıylafitopatolojik çalışmalarda moleküler yöntemlerin daha etkin kullanılmasına katkı sağlayacağı düşünülmektedir.Öğe Breeding of dry bean cultivars using phaseolus vulgaris landraces in Turkey(2018) Yeken, Mehmet Zahit; Kantar, Faik; Çancı, Hüseyin; Özer, Göksel; Çiftçi, VahdettinYield and yield components is one of the key objectives of the legume breeding program worldwide. Information on these traits is required for the selection of desirable types and efficient utilization of the genetic diversity in dry bean improvement program. Local landraces of dry beans grown over long time period are more resistant to low input growing conditions its genetic and morphologic properties and quality is more acceptable by the growers. From this perspective, 83 dry bean landraces were collected from different bean growing areas of Western Anatolia Region of Turkey in 2015-2016. The dry bean landraces were grown on the experimental farm of Abant Izzet Baysal University, Bolu during 2016 growing season. A single plant from each dry bean landrace was selected according to morphological characterization results and weighted scaling method, and twenty (8 climber and 12 bush types) dry bean lines were accepted as promising. In the present study, yield and yield components of 12 dry bean lines and 2 commercial cultivars were compared in Bolu province under western black sea ecological condition of Turkey. The experiment was arranged in a Randomized Block Design with three replicates in 2017 growing season on the experimental farm of Abant Izzet Baysal University. Emergence percentage (69.50-96.00%), days to flowering 50% (48.00-52.00 days), days to maturity (86.00-107.33 days), plant height (37.20-58.30 cm), height to first pod (12.50-19.00 cm), number of branches per plant (6.25-8.25), number of pods per plant (16.96- 41.50 pods), seeds per pod (4.00-6.40 seeds), seed yield per plant (25.41-96.83 g plant-1) and 100 seeds weight (29.82-55.35 g) were determined according to IPGRI and EU-CPVO criteria. As a result, lines ÇNK-2, ÇNK-4, YLV-28, YLV-32 and BLCK-7 had superior with respect to yield and yield components and hence selected advanced promising lines will be transferred to regional yield trials required for the official procedures of cultivar registration.Öğe Canker and leaf scorch on olive (Olea europaea L.) caused by Neoscytalidium dimidiatum in Turkey(Elsevier Science Ltd, 2022) Güney, İnci Güler; Özer, Göksel; Türkölmez, Şahimerdan; Derviş, SibelIn a recent survey of olive groves in the Southeast Anatolia Region of Turkey, a new and serious decline of olive trees, beginning with foliar scorching and then dieback of twigs, branches, and even whole trees, was observed for the first time. In more advanced stages of the disease, necrosis and cankers were observed on the bark of the trunk, branches, and twigs. Isolations from symptomatic tissues from multiple cultivars in diverse locations yielded Neoscytalidium dimidiatum, which were identified using ITS, tef1, and tub2 loci of genomic DNA, in combination with morphological data. In vitro studies showed that conidial germination, hyphal growth, and pycnidia formation of the pathogen were positively correlated with elevated temperatures. Wild type olive Delice, Edincik Su, and Memecik seemed like the most resistant cultivars on which disease severity values were the lowest among 14 screened olive cultivars in two experimental orchards under natural conditions. Pathogenicity tests showed that Gemlik was the most susceptible cultivar showing the largest cankers and extensive scorch lesions. Isolates caused canker but not leaf scorch on O. europaea cultivars Arbequina Halhall, Manzanilla, Nizip Yafglik, and Saurani. Neoscytalidium isolates are likely to have a negative impact on the health of diverse olive groves, which are primarily confined to Mediterranean-type climatic regions. These findings suggest an increased risk of infection in environments with increasing temperatures, as is common in the Southeast Anatolia Region of Turkey. The information gathered in this study will be used to examine the disease's epidemiology and establish disease control initiatives. This is also the first report of N. dimidiatum infecting O . europaea in the world.Öğe Characterization and pathogenicity of pythium-like species associated with root and collar rot of kiwifruit in Turkey(American Phytopathological Society, 2022) Türkkan, Muharrem; Özer, Göksel; Karaca, Gürsel; Erper, İsmail; Derviş, SibelDuring the period of June to October in 2018, a widespread decline was observed on kiwifruit vines in the vineyards located in the Altinordu, Fatsa, and Persembe districts of Ordu province in Turkey. The symptoms were associated with reddish-brown rots expanding from the root to the collar with sparse off-color foliage. Based on the percentage of the total infected samples across 18 vineyards, the most common oomycete species were Globisporangium intermedium (37.1%), Phytopythium vexans (34.3%), Globisporangium sylvaticum (14.3%), Globisporangium heterothallicum (11.4%), and Pythium dissotocum (2.9%). The morphological identification of isolates was confirmed based on partial DNA sequences containing the nuclear rDNA internal transcribed spacer region gene and the mitochondrial cytochrome c oxidase subunit II gene. The optimum growth temperature and the optimum pH values of the five species ranged from 22.98 to 28.25 degrees C and 5.67 to 8.51, respectively. Pathogenicity tests on the seedlings of kiwifruit cv. Hayward revealed significant differences in virulence among isolates. Phytopythium vexans and Globisporangium sylvaticum isolates caused severe root and collar rot resulting in seedling death, while Globisporangium heterothallicum and Globisporangium intermedium isolates had relatively lower virulence. All Globisporangium spp. and Phytopythium vexans isolates significantly decreased plant growth parameters (plant height, shoot and root dry weights, and root length); however, Pythium dissotocum caused very mild symptoms and did not affect these parameters of growth. To our knowledge, this is the first study reporting Globisporangium sylvaticum, Globisporangium heterothallicum, and Globisporangium intermedium causing root and collar rot on kiwifruit not only in Turkey but also in the world.Öğe Characterization and sensitivity to fungicides of Rhizoctonia spp. recovered from potato plants in Bolu, Turkey(Wiley, 2015) Özer, Göksel; Bayraktar, HarunIsolates of Rhizoctonia spp. associated with stem canker and black scurf disease of potato were examined for their anastomosis group, sequence variations in the ITS-5.8S rDNA region, pathogenicity and sensitivity to fungicides. A total of 92 isolates were obtained from diseased tuber, stolon and sprouts of the potato plants, collected from five districts of Bolu province, Turkey. Based on the anastomosis group and the similarity of the nucleotide sequence of the ITS-5.8S rDNA, most of the isolates (81.5%) were identified as AG 3 PT. Other isolates belonged to AG 2-1 (1.08%), AG 2-2 IV (1.08%), AG 4 HG II (8.07%), AG 5 (2.17%), binucleate Rhizoctonia AG A (1.08%) and AG K (4.35%). Pathogenicity tests showed that isolates of AG 3 PT, AG 4 HG II and AG 5 caused similar degrees of disease severity on 45-day-old potato seedlings, whereas AG 2-1 was moderately virulent. AG 2-2 IV and binucleate Rhizoctonia spp. were weakly pathogenic or non-pathogenic on potato seedlings. In this study, anastomosis groups of Rhizoctonia spp. isolates associated with potato in Turkey were characterized for the first time using molecular techniques and classified at the level of subgroups. Furthermore, the effect of selected fungicides was evaluated on disease development caused by soil-borne inoculums of different anastomosis groups (AGs). Flutolanil and Bacillus subtilis QST 713 were found to be most effective against the Rhizoctonia isolates tested. These results revealed significant differences among the fungicides on disease development resulted from the different AGs.Öğe Characterization of cereal cyst nematodes in wheat using morphometrics, SCAR markers, RFLP, and rDNA-ITS sequence analyses(Springer, 2023) Dağlı, Deniz; Duman, Nagihan; Yüksel, Ebubekir; Yıldız, Şenol; Özer, Göksel; Dababat, Abdelfattah; İmren,MustafaIn this study, morphological and molecular characterizations of twenty-four Heterodera populations (cereal cyst nematodes, CCNs) collected from wheat production fields in Turkey were carried out. Light microscopy, species-specific markers, RFLP, and ITS sequencing were used to identify the nematode populations. The obtained CCN populations were identified as Heterodera avenae, H. filipjevi, and H. latipons according to the morphometric analysis, which was confirmed by the molecular techniques. The ITS region sequencing analysis confirmed the species identification, and phylogenetic analysis of this region grouped the populations with representative Heterodera populations from different origin countries deposited in GenBank. The simulation of four restriction enzymes, Alul, PstI, BsuRI (HaeIII), and Rsal, employed the ITS sequences of isolates to discriminate the Turkish Heterodera populations. ITS-RFLP patterns produced by endonuclease enzymes provided variations among Heterodera species. There was no intraspecific variation in populations of each Heterodera species in the ITS-RFLP analyses. The species-specific primers, AvenF-COI/AvenR-COI, HfF/HfR, and H-LatF/H-LatR, yielded 109 bp, 646 bp, and 204 bp products for H. avenae, H. filipjevi, and H. latipons populations, respectively. This is the first research to provide conclusive diagnostic tests for cyst nematode populations isolated from Turkey. These assays provide a sensitive, practical, and quick method for detecting Heterodera species and, therefore, have the potential to be utilized in the early identification of populations and monitoring of infestations without morphometric studies.Öğe Characterization of potato golden cyst nematode populations (globodera rostochiensis) in Turkey(Friends Science Publ, 2020) Toktay, Halil; Evlice, Emre; İmren, Mustafa; Özer, Göksel; Ali, Muhammad Amjad; Dababat, AbdelfattahGolden potato cyst nematode, Globodera rostochiensis (Wollenweber) Behrens, is one of the most important soilborne pathogens causing economic losses in potato. The nematode is known to occurin several countries including Turkey and has a worldwide regulatory concern. In this study, identification and genetic diversity of G. rostochiensis specimens obtained from the main potato producing areas of Turkey were determined. Twenty -five of 35 soil samples collected from the provinces of Izmir, Nevsehir and Nigde were found to contain G. rostochiensis. The variation between G. rostochiensis populations was determined when examined according to ecological and pathogenic characteristics of nematode in Turkey. The cysts of G. rostochiensis were identified by measuring the morphological characters using perennial patterns, vulval cone, vulval basin and juveniles. Phylogenetic analysis of the Large Sub Unit (LSU) region of rDNA sequences was used to assess the inter or intra phylogenetic relationships between the nematode populations. The phylogenetic analyses demonstrated that the nematode specimens from Turkey cluster with Globodera spp. and signified the presence of single species of G. rostochiensis. As a result, morphological, morphometric and molecular methods were successfully combined for identification and characterization of G. rostochiensis. The frequency of G. rostochiensis in regulatory samples frompotato -producing areas is becoming increasingly important. The morphological characterization has several complications in the detection of this quarantine nematode, using of this combination is beneficial for a reliable and quick diagnostic for these nematodes which is crucial for regulatory services and growers. The results might help to investigate different ecotypes of G. rostochiensis for comprehensive understanding about physiology, ecology , and biology of the genus Globodera for its effective management in Turkey. (C) 2020 Friends Science PublishersÖğe Clonostachys rosea strain ST1140: An endophytic plant-growth-promoting fungus, and its potential use in seedbeds with wheat-grain substrate(Springer, 2023) Türkölmez, Şahimerdan; Özer, Göksel; Derviş, SibelIn this study, Clonostachys rosea strain ST1140, a naturally occurring endophyte in healthy roots of a pistachio tree, was identified morphologically and molecularly through DNA sequencing, and its endophytic ability and growth effect in/on three solanaceous plant species were tested. Three different organic substrates (bread wheat-grain, sawdust, and leonardite) were also investigated for their utility in cultivating and multiplying the strain. In-tray and pot experiments, the rates of seed germination and vegetative development of pepper, tomato, and eggplant inoculated with C. rosea at planting were compared to those of non-inoculated controls. In pot experiments, inoculating seedbeds with increasing doses of C. rosea strain ST1140 with wheat-grain substrate resulted in higher plant height values for all plant species, and the strain endophytically colonized the roots of all plant species. In-tray experiments revealed that ST1140 inoculation resulted in 2-4 days earlier and 10% higher germination rates for all plant species, as well as more vigorous and accelerated seedling growth (10-13 days earlier for seedlings at the 4-5 true leaf stage) on all inoculated plant species. Among three different organic substrates, wheat-grain was found to be the most effective for long-term cultivation and multiplication of the fungus, which could be of interest for its development as a commercial product. These results promised the strain ST1140's use as a biofertilizer in seedbeds with a wheat-grain substrate.Öğe Comparison of phenotypic and marker-assisted selection in Turkish cultivars and global genotypes of chickpea for resistance to pathotypes of Ascochyta rabiei (Pass.) Labr.(TUBITAK Scientific & Technical Research Council Turkey, 2021) Kabakcı, Hüseyin; Özer, GökselThe pathotypes of Ascochyta rabiei, which causes ascochyta blight, show a high pathogenic variation. Forty-four chickpeas, including 26 cultivars commonly cultivated in Turkey and 18 global genotypes, were characterized for resistance status to ascochyta blight following inoculation with four pathotypes of A. rabiei. The pathogenicity experiments were conducted using the whole-plant inoculation method and completely randomized designs with three replicates. The pathogenicity tests revealed that 32, 17, 3, and 1 chickpea showed resistance reactions to pathotypes I, II, III, and IV, respectively. These chickpeas were genotyped with STMS (GAA47, TA146, and TA194), SCAR (SCK13(603), SCAE19(336), and SCY17(590)), and an allele-specific (CaETR) MAS markers closely linked to QTLs located on linkage groups 2 and 4 for ascochyta blight resistance. QTL(AR1) predicted blight resistance to pathotype I with a rate of 65.9%. Strong correlations at P < 0.01 were found between resistance reactions of chickpeas to pathotype II and QTL(AR2), which made it possible to predict resistance in 79.55%-81.82% of studied chickpeas. A significant association was found between QTL(AR3) and resistance to pathotypes Ill and IV, which are the most aggressive groups among A. rabiei isolates. 'three chickpea genotypes (ICC 3996, ICC 12004, and ICC 4475) showed a high level of resistance to pathotypes I, II, and III. ICC 3996 was the only genotype with resistance to pathotype IV. This study is the most comprehensive phenotypic study yet for determining the resistance status of chickpeas against pathotype IV, and the first study showing a significant association between a MAS marker linked to QTL(AR3) and blight resistance to pathotypes III and IV. Breeders should include the isolates in pathotype III and IV groups into pathogenicity tests due to the increase in their prevalence. The markers linked to QTLs determining the resistance to these pathotypes should be emphasized, and the efficiency of the use of these markers in breeding programmes should be increased.Öğe CRISPR/Cas9-mediated immunity in plants against pathogens(Caister Academic Press, 2017) Sameeullah, Muhammad; Khan, Faheem Ahmed; Özer, Göksel; Aslam, Noreen; Gürel, Ekrem; Karadeniz, TuranGlobal crop production is highly threatened due to pathogen invasion. The huge quantity of pesticides application, although harmful to the environment and human health, is carried out to prevent the crop losses worldwide, every year. Therefore, understanding the molecular mechanisms of pathogenicity and plant resistance against pathogens is important. The resistance against pathogens is regulated by three important phytohormones, viz. salicylic acid (SA), jasmonic acid (JA) and ethylene (ET). Here we review the possible role of CRISPR technology to understand the plant pathogenicity by mutating genes responsible for pathogen invasion or up-regulating the phytohormones genes or resistant genes. Thus hormone biosynthesis genes, receptor and feeding genes of pathogens could be important targets for modifications using CRISPR/Cas9 following multiplexing tool box strategy in order to edit multiple genes simultaneously to produce super plants. Here we put forward our idea that the genes would be either mutated in case of plant receptor protein targets of pathogens or up-regulation of resistant genes or hormone biosynthesis genes will be better choice for resistance against pathogens.Öğe Crispr/cas9-mediated immunity in plants against pathogens(Caister Academic Press, 2018) Sameeullah, Muhammad; Khan, Faheem Ahmed; Özer, Göksel; Aslam, Noreen; Gurel, Ekrem; Waheed, Mohammad Tahir; Karadeniz, TuranGlobal crop production is highly threatened due to pathogen invasion. The huge quantity of pesticides application, although harmful to the environment and human health, is carried out to prevent the crop losses worldwide, every year. Therefore, understanding the molecular mechanisms of path-ogenicity and plant resistance against pathogens is important. The resistance against pathogens is regulated by three important phytohormones, viz. salicylic acid (SA), jasmonic acid (JA) and ethylene (ET). Here we review the possible role of CRISPR technology to understand the plant pathogenicity by mutating genes responsible for pathogen invasion or up-regulating the phytohormones genes or resistant genes. Thus hormone biosynthesis genes, receptor and feeding genes of pathogens could be important targets for modifications using CRISPR/Cas9 following multiplexing tool box strategy in order to edit multiple genes simultane-ously to produce super plants. Here we put forward our idea that the genes would be either mutated in case of plant receptor protein targets of pathogens or up-regulation of resistant genes or hormone bio-synthesis genes will be better choice for resistance against pathogens. © 2018, Caister Academic Press. All rights reserved.Öğe Determination of Antagonistic Activities of Endophytic Bacteria Isolated from Different Wheat Genotypes Against Fusarium culmorum(2024) Güney, Inci Güler; Derviş, Sibel; Özer, Göksel; Aktaş, Hüsnü; Keske, Mehmet AtaThis study aimed to evaluate the physiological and biochemical properties and enzyme activities of endophytic bacteria obtained from different wheat genotypes, as well as their effectiveness against Fusarium culmorum, which causes root and crown rot in wheat. The results obtained from double culture tests of isolates against F. culmorum showed that the inhibition rate varied between 80.56% and 13.90%. The inhibition rate against F. culmorum was 80.59% for Bacillus subtilis (MM11), 69.41% for Stenotrophomonas maltophilia (EY5), and 61.10% for Enterobacter sp. (MY3) under in vitro conditions, the most effective isolates. Pseudomonas putida (EM9) and Pseudomonas orientalis (MM21) isolates gave positive results in all tests in the production of amylase, cellulase, phosphatase, ACC deaminase, and siderophore. To identify six promising isolates, 16S rRNA gene-based sequence analysis was utilized. The efficacy of bacterial strains against F. culmorum, pot experiments were conducted in a growth room (in vivo). The results demonstrated that the combination of S. maltophilia, Enterobacter sp., and B. subtilis (MY3+EY5+MM11) yielded the most favorable outcomes in terms of disease severity, plant height, wet weight, dry weight, root wet weight, and root dry weight. The combination of Stenotrophomonas rhizophila, P. putida, and P. orientalis (EY1+EM9+MM21) exhibited promising results. Utilizing effective bacterial strains is anticipated to reduce the dependence on and costs associated with chemical fertilizers and pesticides while minimizing their environmental impact. Furthermore, these strains show potential for commercial applications pending further validation procedures. The findings from this study significantly contribute to the field of biological control strategies against F. culmorum by leveraging the diverse capabilities of endophytic bacteria.Öğe Determination of Ascochyta blight disease in chickpea using real-time PCR(Springer Heidelberg, 2016) Bayraktar, Harun; Özer, Göksel; Aydoğan, Abdulkadir; Palacıoğlu, GülsümAscochyta blight is a devastating disease of chickpea caused by Ascochyta rabiei. In this article, we described a real-time PCR assay for the determination and quantification of A. rabiei infection in chickpea tissues and accurate monitoring of disease progression in plant materials inoculated with different inoculation methods. The primer pairs HEF1/HEF2 were designed to anneal to conserved regions of translation elongation factor 1 alpha (EF) gene for specific amplification of 82-bp fragment of A. rabiei based on SYBR Green I technology. The detection limit of assay was determined as 0.1 pg DNA. PCR specificity was confirmed by testing against uninfected chickpea tissues and another fungal species associated with chickpea. The chickpea plants were inoculated by the methods of whole-plant and detached leaflet inoculation. Disease progression in resistant and susceptible cultivars was evaluated at certain time intervals after pathogen inoculation by real-time PCR. The results revealed a good correlation between visual assessments of disease reaction and pathogen quantification in infected chickpea tissues. The target DNA sequence was also amplified from the samples of DNA extracts from artificially infested seed. This technique could provide a useful approach for efficient selection of resistant breeding material in an early stage of infection as an alternative to the visual disease assessment and will be also used for the determination and quantification of A. rabiei infection.Öğe Determination of fungal pathogens associated with Cuminum cyminum in Turkey(Czech Academy Agricultural Sciences, 2015) Özer, Göksel; Bayraktar, HarunThe occurrence of fungal pathogens, associated with cumin production of Turkey, was determined during 2011 and 2012. A total of 379 isolates were classified as Fusarium oxysporum f.sp. cumini, F. solani, F. acuminatum, F. equiseti, F. sambucinum, F. avenaceum, Macrophomina phaseolina, Alternaria burnsii, A. alternata, A. infectoria, Embellisia sp., and Rhizoctonia solani. Pathogenicity tests showed that F. oxysporum f.sp. cumini, F. solani, F. equiseti, M. phaseolina, A. burnsii, and A. alternata were highly pathogenic. A. burnsii and F. oxysporum f.sp. cumini were the major risk factors for cumin cultivation in Turkey. To our knowledge, this is the first report on F. oxysporum f.sp. cumini, F. solani, F. equiseti, M. phaseolina, and A. alternata in Turkey.
