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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 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 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 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.Öğe Development of conventional and real-time PCR assays to detect alternaria burnsii in cumin seed(Springer, 2019) Özer, Göksel; Bayraktar, HarunAlternaria burnsii is the causal agent of cumin blight, a seed-borne disease of economic concern for all cumin growing areas. Current detection and identification methods for the pathogen are based on visual examination of morphological features, which are time-consuming and laborious. The present study describes conventional and real-time PCR assays for rapid and accurate detection of A. burnsii in cumin seeds. Based on sequence differences in Alternaria allergen a1 (Alt a1) gene, two primer pairs, Ab35/326 and AB177/403, were designed for conventional and real-time PCR assays, respectively. Both primer pairs amplified the expected target PCR fragment from A. burnsii genomic DNA. The sensitivity of conventional PCR with primer pairs Ab35/326 was 1x202f;pg of genomic DNA and allowed the detection of pathogen in cumin seeds samples with 0.2% infestation rate. Real-time PCR assay was highly sensitive and allowed the quantification of 0.1x202f;pg pathogen DNA. Also, this assay confirmed the presence of pathogen in cumin seeds up to 0.1% infestation level. The standard curve (r(2)x202f;= 0.99) showed a good correlation between fungal DNA quantities and Cq values. The specificity of primer pairs was confirmed by the absence of amplified product with DNA of related fungi species and healthy plant tissue. The assays developed in this study provide a rapid and sensitive tool for the detection and quantification of Alternaria burnsii in cumin seed.Öğe Evaluation of Ascochyta resistance in chickpea genotypes with quantitative polymerase chain reaction assay(Wiley, 2023) Özer, Göksel; Palacıoğlu, Gülsüm; Aydoğan, Abdulkadir; Bayraktar, HarunAscochyta blight caused by Ascochyta rabiei is a globally important chickpea disease. Host resistance to Ascochyta blight is considered the most practical and effective means of control, but breeding has been hindered by a lack of effective resistance sources, and time-consuming, labour-intensive traditional methods to screen the resistance level of chickpea genotypes. This paper evaluated the progression of pathogen infection and the disease reaction of chickpea genotypes to Ascochyta blight by traditional and molecular methods. The resistance level of 84 chickpea genotypes was assessed by a quantitative polymerase chain reaction assay (qPCR) using a standard curve produced by various known amounts of pathogen DNA and compared with disease scores based on visual assessments 8 days after inoculation. Disease assessments revealed statistically significant differences between the resistance levels of chickpea genotypes, while the quantity of target DNA in the samples inoculated with the pathogen ranged from 0.004 to 83.37 ng. Our results showed a close relationship between the visual assessment of disease severity and the quantification of the target DNA in chickpea genotypes. The genotypes Tub-35, Tub-47, Tub-26, Tub-82, Tub-65 and Tub-69 were classified as highly resistant to Ascochyta blight based on the results of both assays used for screening chickpea genotypes. This qPCR analysis could be used to quantify disease progression in plant tissues and screen chickpea genotypes as a potential alternative to visual assessment of resistance levels in breeding programmes.Öğe Expression comparisons of defense-related genes in resistant and susceptible chickpea cultivars in response to Ascochyta rabiei(Academic Press Ltd- Elsevier Science Ltd, 2023) Palacıoğlu, Gülsüm; Özer, Göksel; Bayraktar, HarunAscochyta blight caused by Ascochyta rabiei is a destructive disease affecting chickpea crops worldwide. Numerous studies have sought to identify resistance genes involved in the defense response against Ascochyta blight, but the function of potential resistant genes across different chickpea genetic backgrounds remains poorly understood. This study evaluated the potential role of 16 genes involved in defense responses in partially resistant (ILC482) and susceptible (Sari98) chickpea cultivars. The leaf samples were collected from 2-week-old seedlings at 6, 12, 24, 48, and 72 h post-inoculation (hpi) with A. rabiei and analyzed for differential expression of defense genes using qRT-PCR. Twelve out of 16 genes were differentially regulated between chickpea cultivars. The qRT-PCR analysis indicated that the expression of defense genes was significantly higher in the partially resistant cultivar than that in the susceptible cultivar. The time point of the highest upregulation ratio for defense genes was variable between the cultivars. The expression of glutathione S-transferase, serine/threonine-protein kinase, WRKY gene (CaWRKY16), and wall associated-receptor kinase genes reached maximum levels in the resistant cultivar at 6 hpi, while antimicrobial peptide precursor (SNAKIN2), polymorphic antigen membrane protein, ethylene receptor-like sequences (CaETR1), and two nucleotide-binding site-leucine-rich repeat genes showed the highest activity at 24 hpi. In particular, CaWRKY16, CaWRKY50, glutathione S-transferase, CaETR1, and wall-associated-receptor kinase genes provided valuable information for assessing chickpea cultivars with different resistance levels. The results indicated that the expression changes of these genes involved in defense pathways play a crucial role in enhanced resistance of chickpea plants against Ascochyta blight and, therefore could be potential candidate genes for future breeding studies.Öğe Fasulyede Rhizoctonia Solani’nin neden olduğu kök çürüklüğüne karşı tohuma bazı fungisit uygulamalarının etkinliği(2019) Palacıoğlu, Gülsüm; Cankara, Beyza; Bayraktar, Harun; Özer, GökselFasulyede Rhizoctonia solani’nin neden olduğu kök çürüklüğüne karşı bazı fungisitlerin çıkış oranı, hastalık şiddeti ve bitki gelişimi üzerindeki etkisi bu çalışma kapsamında değerlendirilmiştir. Tohum ilacı olarak kullanılan fungisitler arasında sedaxane en etkili fungisit olup, patojenle inokuleli kontrol uygulamalarına göre çıkış oranını %93.33 seviyesinde artırdığı, hastalık şiddetini ise %44 oranında engellediği tespit edilmiştir. Benzer şekilde fludioxonil ve azoxystrobin etkili maddeli fungisit uygulamalarındaki çıkış oranının sırasıyla %86.67 ve %73.33 olduğu, hastalık şiddetinin ise %32.00 ve %30.67 oranlarında azaldığı belirlenmiştir. Trifloxystrobin ve difenocanozole etkili maddeli fungisitler ise orta derecede etkili olup, hastalık şiddetini sırasıyla %18.67 ve %20.00 oranlarında engellemişlerdir. Bununla birlikte thiram, acibenzolar-s-methyl ve propineb etkili maddeli fungisitlerin çıkış oranı ve hastalık şiddeti üzerinde etkili olmadıkları tespit edilmiştir. Bitki gelişimi açısından da sedaxane, fludioxonil ve azoxystrobin etkili maddeli fungisitlerin kontrole yakın bir gelişim sağladıkları gözlemlenmiştir. Bu kapsamda bu fungisitlerin tek başına yada kombinasyon uygulamalarının fasulyede bu hastalığın neden olduğu kayıpların azaltılması açısından faydalı olacağı düşünülmektedir.Öğe First report of botrytis cinerea on cornelian cherry(CSIRO, 2014) Özer, Göksel; Bayraktar, HarunBotrytis blight of cornelian cherry (Cornus mas) was reported for the first time from Bolu, Turkey. The pathogen caused flower, leaf and twig blights. The disease was widely observed on cornelian cherry stands in Central and Yeniçag districts of Bolu province. The fungus was identified as Botrytis cinerea based on mycological characteristics and molecular data.Öğe First report of crown rot caused by fusarium algeriense on wheat in Azerbaijan(Amer Phytopathological Soc, 2020) Özer, Göksel; İmren, Mustafa; Paulitz, T. C.; Bayraktar, Harun; Muminjanov, H.; Dababat, A. A.Fusarium algeriense Laraba & O’Donnell has been recently described as a novel crown rot pathogen of wheat within F. burgessii species complex (Laraba et al. 2017). To our knowledge, there are no reports of the existence of this pathogen outside of Algeria. In June 2017, 14 fields in Ismailli and Oguz provinces, Azerbaijan, were surveyed. Diseased wheat plants exhibiting symptoms of crown rot including brown discoloration on the first two or three internodes of the stem were collected before maturity, at maturity, and/or after harvest.Öğe First report of crown rot caused by rhizoctonia solani AG-4 HG-I on asparagus officinalis in Turkey(2012) Özer, Göksel; Bayraktar, HarunIn 2011, crown rot symptoms were observed on the base, root and spears of asparagus plants in Balikesir province (north-eastern Turkey). Surface-disinfected tissues were placed on potato dextrose agar medium and incubated at 22±1°C. Rhizoctonia cultures were obtained and identified based on vegetative hyphae, nuclear staining, and anastomosis typing with known tester isolates of Rhizoctonia solani (Sneh et al., 1991).Öğe First report of dill blight caused by Itersonilia perplexans in Turkey(Springer, 2019) Palacıoğlu, Gülsüm; Özer, Göksel; Bayraktar, HarunDuring January 2018, when temperatures average around 5.8–14.8 °C, blight symptoms were observed on leaves, petioles and stems of dill (Anethum graveolens) plants grown in a greenhouse of 2 decares located in Antalya province of Turkey. The disease affected less than 2% of the total area. The symptoms appeared on all aerial parts of plant as small, greyish necrotic lesions. Seriously affected parts became completely dry and died over time.Öğe First report of Fusarium hostae causing crown rot on wheat in Azerbaijan(Amer Phytopathological Soc, 2019) Özer, Göksel; İmren, Mustafa; Bayraktar, Harun; Paulitz, Timothy C.; Muminjanov, Hafiz; Dababat, Abdelfattah A.In June 2017, 76 fields were surveyed in the main bread wheat (Triticum aestivum L.) and durum wheat (Triticum durum Desf.) growing regions of Azerbaijan to identify the fungi causing crown and root rot. Diseased plants were collected at just prior to maturity, at maturity, and/or after harvest. About 20 to 30 tillers of wheat were randomly sampled from each field (about 5 ha), put in paper bags, and transported to the laboratory. The crown, root, and stem base tissues of each plant were rinsed with tap water to remove soil particles and examined for lesions. Sections (3 cm) of symptomatic tissues were surface disinfested with 1% NaOCl for 1 min, rinsed with sterile distilled water, and air dried on sterilized filter paper in a laminar flow.Öğe First report of Fusarium proliferatum causing crown and root rot of Asparagus officinalis in Turkey(Edizioni Ets, 2011) Özer, Göksel; Bayraktar, Harun; Öksal, ErçinIn 2011, crown and root rot symptoms appeared on 3- to 8-month-old asparagus plantations in different production areas located in the Gönen district of the Balıkesir province (Turkey). The symptoms included a decrease in the yield of spears and brown lesions, vascular discoloration and rot of roots, rhizomes, and stems. The disease emerged on new plantings which were established with propagation materials from infected fields.Öğe First report of gray mold on sweet basil caused by Botrytis cinerea in Turkey(Springer, 2018) Özer, Göksel; Göre, Mehmet Erhan; Bayraktar, HarunSweet basil (Ocimum basilicum L.) is an aromatic plant in the family Lamiaceae. In August 2016, a disease was observed in sweet basil fields of Bolu, after the first cutting harvest, characterized by masses of gray-brownish spores on leaves and stems of the plants. Infected plant tissues were cut into small pieces, placed on potato dextrose agar after surface sterilization and incubated at 22 °C for 3 to 4 days. The identification of pathogen was carried out according to Ellis and Waller (1974) and the fungus determined as Botrytis cinerea based on morphological characteristics of conidia, conidiophores and cultural specifications.Öğe First report of phytopythium litorale associated with dieback disease of kiwifruit in Turkey(Springer, 2023) Polat, Zühtü; Kaymak, Suat; Gültekin, Mehmet Akif; Bayraktar, Harun; Özer, GökselEditorial MaterialÖğe First report of powdery mildew, caused by Arthrocladiella mougeotii, on Goji berry in Turkey(Edizioni Ets, 2016) Özer, Göksel; Bayraktar, HarunLycium barbarum, known as Goji berry or wolfberry, is a Chinese medicine plant in the family Solanaceae, and has been recently cultivated in Bolu, Turkey. During autumn 2015, severe powdery mildew symptoms were observed on Goji berry plantation area. White to grayish white fungal mycelia were shown on leaves and stems. Also, brownish discolorations and defoliation were exhibited. Microscope examination showed that conidia were formed in chains, hyaline, short-cylindrical and their length and width ranged from 19 to 31(mean=26.2)µm and from 10 to 14.5(mean=13.2)µm, respectively. Apothecial structures were not observed. The fungus was identified as Arthrocladiella mougeotii on the basis of morphological characteristics and the host specialization (Braun, 1987).Öğe First report of purple spot disease of asparagus officinalis in Turkey(2012) Özer, Göksel; Bayraktar, HarunIn the course of a survey to determine the fungal pathogens of asparagus in Balikesir province (north-western Turkey) brown sunken lesions with dark purple margins were observed on the spears. Pseudothecia and ascospores were looked for in overwintering plant debris.
