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Öğe Bingöl ili Adaklı ilçesi elma üreticilerinin tarımsal ilaç kullanımında bilgi tutum ve davranışlarının değerlendirilmesi ve ekonomik analizi(2017) Çelik, Ali; Karakaya, ErsinBu araştırma, Bingöl ili Adaklı ilçesinde elma üretiminde tarımsal ilaç kullanımında üreticilerin çevresel duyarlılıklarının belirlenmesi ve ilaç kullanımının ekonomik analizinin yapılması amacıyla hazırlanmıştır. Araştırmada kullanılan veriler 40 adet elma üreticisinden 2015 yılı üretim döneminde anket yöntemi ile toplanmıştır. Verilerin analizinde frekans, ortalama ve yüzde gibi tanımlayıcı istatistiklerden yararlanılmıştır. Ayrıca nominal ölçekli değişkenlerden oluşan önemli görülen bazı verilerin birbiriyle ilişkisi olup olmadığını öğrenmek için Ki-Kare bağımsızlık testi yapılmıştır. Araştırma sonuçlarına göre; yetiştiricilerin tamamı (%100) tarım ilaçlarını zirai ilaç bayilerinden temin ettiklerini ifade etmişlerdir. Yetiştiricilerin %50.9’u tarım ilacı seçiminde etki derecesine dikkat ederken, tarım ilacı seçiminde %30.4 oranında tarım il ve ilçe müdürlükleri teknik elemanlarının etkili olduğu sonucu saptanmıştır. Üreticilerin %50’si kullanılan tarım ilaçlarını ahır veya barınakta, %35’i özel bir dolapta ve %15’i ise evin herhangi bir yerinde depo ettiklerini, üreticilerin %50’si boşalan ilaç kutularını bir yerde depolayıp daha sonra yakarak imha ettiklerini belirtirken, %30’u genel çöp kutusuna attıklarını ve %20’si ise bahçenin bir kenarına attıklarını ifade etmişlerdir. Toplam ilaçlama masrafları arazi büyüklüğü ≤ 4 dekar olan işletmelerde 100.50 TL, 5-8 dekar olan işletmelerde 155.75 TL ve ≥ 8 dekar olan işletmelerde ise 205.85 TL olarak saptanmıştır. Sonuç olarak; üreticilerin örgütlenmeleri sağlanmalı, devlet destekleri konusunda yeni politikalar belirlenerek üreticilerin sorunlarının çözülmesi hedeflenmelidir.Öğe Bitlis İli Ceviz Yetiştiriciliği Yapılan Tarım Alanlarında Görülen Ceviz Antraknozu (Ophiognomonia leptostyla) Hastalığının Morfolojik ve Moleküler Karakterizasyonu(2020) Koç, Ibrahim; Çelik, Ali; Durak, Emre Demirer; Demir, Ibrahim; Bayman, Serkan; Mirtagioğlu, Hamit; Demir, SemraBitlis, ceviz üretiminde ülkemizde öne çıkan illerimiz arasında yer almaktadır. Ceviz insan beslenmesi açısından oldukça yüksek besin değerlerine sahiptir. Ceviz antraknozu (Ophiognomonia leptostyla) hastalığı dünyada olduğu gibi ülkemizde de cevizin en önemli fungal hastalıkları arasında yer almaktadır. Bu çalışmada Bitlis il genelinde (Adilcevaz, Ahlat, Güroymak, Hizan, Merkez, Mutki ve Tatvan) sürveyler yapılmış ve gözle görülür simptomların çıkış zamanının Haziran sonu (Temmuz başı) olduğu gözlenmiştir. Bahsi geçen ceviz üretimi yapılan alanlardan hastalık etmeninin kültür ortamına izolasyonu yapılmış olup, besi ortamında meydana getirdiği kolonial özelliklere göre hastalık etmeni morfolojik olarak doğrulanmıştır. Ayrıca gelişen kolonilerden DNA izolasyonu yapılarak etmene ait ITS (Internal Transcribed Spacer) bölgeleri PCR ile çoğaltılmıştır. PCR sonucu elde edilen yaklaşık 560 bp uzunluğundaki amplikonlar dizilenmiştir. Etmenin ITS bölgesine ait diziler diğer dünya izolatları dikkate alınarak “Blastn” analizine tabi tutulmuş ve Genbank veri tabanına erişim numaraları (MK685678 ve MK685679) altında kaydedilmiştir. Çalışma ülkemizde hastalık etmeninin moleküler düzeyde incelendiği ilk araştırma özelliğindedir.Öğe Burdur ilinde Plum pox virus’un tespiti ve kısmi kılıf protein geninin moleküler karakterizasyonu(Kahramanmaraş Sütçü İmam Üniversitesi Rektörlüğü, 2021) Morca, Ali Ferhan; Coşkan, Sevgi; Çelik, AliPlum pox virus (PPV), sert çekirdekli meyvelerde önemli verim kayıplarına sebep olan Şarka hastalığının etmenidir. PPV, Türkiye’nin farklı bölgelerinde sınırlı olarak tespit edilmesine rağmen, bugüne kadar Burdur iline ait herhangi bir kayıt bulunmamaktadır. Bu çalışmada, 2016-2019 yılları arasında Burdur ilinde PPV’nin varlığının belirlenmesine yönelik serolojik ve moleküler yöntemler kullanılarak yapılan araştırmanın sonuçlarına yer verilmiştir. Sürveyler süresince toplanan 47 adet sert çekirdekli meyve yaprak örneği ilk olarak Double antibody sandwich enzyme linked immunosorbent assay (DAS-ELISA) ile analiz edilmiş ve 2 adet şeftali örneğinin PPV ile enfekteli olduğu belirlenmiştir. Çalışmada, PPV’nin kılıf protein bölgesi için 767 nükleotid büyüklüğünde bir bölgeyi çoğaltan bir adet dejenere primer çifti tasarlanmıştır. Yeni primerler ile gerçekleştirilen Reverse transcription-polymerase chain reaction (RT-PCR) ve sekans analizleri sonucunda elde edilen diziler GenBank’a kaydedilmiştir. Yapılan BlastN analizi neticesinde Burdur PPV izolatları en yüksek benzerlik oranını (%99.86-%98.49), PPV-M ırkı ile göstermiştir. Neighbour-joining yöntemiyle yapılan filogenetik ağaçta Burdur izolatlarının, Türkiye ve farklı ülkelere ait PPV-M izolatı ile kümelendiği belirlenmiştir. Bu çalışma ile elde edilen 2 adet PPV-M izolatı Akdeniz Bölgesi’nin PPV açısından ari alanı konumunda olan Burdur ilinde ilk kayıt niteliğindedir. Çalışma sonucunda enfekteli olduğu tespit edilen ağaçlar eradike edilerek 1 km çapında tampon bölge oluşturulmuş ve 3 yıl boyunca Prunus türlerinin yetiştiriciliğinin yasaklanmasına ve sürvey çalışmalarınnın devam edilmesine karar verilmiştir.Öğe Bursa ve Bilecik illeri şeftali yetiştiriciliği yapılan alanlarda prune dwarf virus (PDV) yaygınlığı ve genetik çeşitliliği(2020) Çelik, Ali; Ertunç, FilizPrune dwarf virus (PDV), sert çekirdekli meyve ağaçlarının önemli viral patojenleri arasında yer almaktadır. Bu çalışmada Türkiye’nin önemli şeftali üretiminin yapıldığı Bursa ve Bilecik illerinde ilk kapsamlı PDV enfeksiyonu araştırılmıştır. 460 viral simptom şüphesi ile toplanan şeftali yaprağı DAS-ELISA testine tabi tutulmuş ve 19 örneğin (%4.13) PDV ile enfekteli olduğu tespit edilmiştir. Yapılan RT-PCR çalışmaları sonucunda virüsün kılıf protein bölgesine ait 862 bp uzunluğunda nükleotid dizileri elde edilmiş, elde edilen diziler GenBank’ta kayıtlı Türkiye ve dünya PDV referans izolatları ile karşılaştırılmıştır. Yapılan BLASTn analizi sonucunda PDV şeftali Türkiye izolatları, referans PDV sekans verileri ile nükleotid düzeyinde %87.77-97.56 arasında benzerlik göstermiştir. Nükleotid dizi bilgisi elde edilen izolatların filogenetik analiz çalışmaları ile, dünya ve Türkiye izolatları ile ilişkisi belirlenmiştir. Araştırma bulguları coğrafik orijin ve farklı Prunus türlerinden izole edilen PDV izolatları arasında herhangi bir filogenetik ilişkinin olmadığını göstermiştir. Çalışma sonucunda ilk kez ülkemizde şeftali PDV izolatlarının kılıf protein bölgesine ait nükleotid dizileri elde edilmiştir.Öğe Comparison of some morphological and physiological characters of apple scab pathogen (Venturia inaequalis) in two different agricultural ecology of Turkey(Springer, 2021) Kavak, Hamit; Çelik, AliBingol and Isparta are two remote regions with significant differences in terms of apple production in Turkey. In this study, some morphological and physiological characteristics of the apple scab (Venturia inaequalis) were measured and compared between these two regions. Colony colors and boundary lines, mycelial structures, colony growth rates, conidial numbers and sizes of the isolates were measured and compared in controlled conditions. With respect to colony morphologies of Bingol and Isparta isolates, important differences were observed. On the other hand, coloni development rate of Bingol isolates in PDA, MEA and CMA media were statistically significant, exhibiting an average of 30% faster growth compared to Isparta isolates. In addition, conidial numbers in 1 cm(2) area of PDA were to be higher and significant in Bingol isolates. However, it has not been determined differences for the dimensions of the conidial isolates developed in PDA belonging to two districts. As a result, it is considered that the morphological and physiological privileges determined by the comparison of the two district isolates of apple black spot is important. These results may be due to the genetic or fungicidal pressure due to the new race formation and the phenotypic characteristics due to different agricultural applications.Öğe Comprehensive surveillance and population study on plum pox virus in Ankara Province of Turkey(Springer Science and Business Media Deutschland GmbH, 2022) Coşkan, Sevgi; Morca, Ali Ferhan; Akbaş, Birol; Çelik, Ali; Santosa, Adyatma IrawanAnkara Province with its sizeable stone fruits outputs and its geographic location in the middle of Turkey might be one of the diversity centers of plum pox virus (PPV) in the country, yet the epidemiological data from there were rather limited. Multi-year extensive surveillance in all 25 districts of Ankara sampled 8131 Prunus spp. plants to be tested against PPV. DAS-ELISA detected 609 PPV positive samples (7.49%), which were all also confirmed by RT-PCR using two primer pairs to amplify P3-6K1-CI and partial NIb-CP regions. The partial genomes of 80 isolates were sequenced, then the sequences were subjected to phylogenetic and population analyses together with 170 isolates which complete genome sequences available in NCBI GenBank. The phylogenetic study showed that 73 new isolates were PPV-T, six isolates were PPV-M, and one isolate was PPV-D. The subsequent population study confirmed the interesting features of PPV with very high genetic diversities at the species level, thus it should be divided into strains that each retained much lower divergence among isolates. The obtained data also could provide new evidence to separate M, and MIs isolates into two distinct strains. Although previous studies suggested that Turkish isolates have been endemic since a long time ago in the country, the results of demographic analyses of the present study indicated that the expansions of Turkey and Ankara populations were recent, driven by relatively new mutations in their genome. © 2022, The Author(s), under exclusive licence to Deutsche Phytomedizinische Gesellschaft.Öğe Development of colorimetric and real time loop-mediated isothermal amplification (cr-LAMP) assay for rapid detection of Wheat dwarf virus (WDV)(Elseiver Science Ltd, 2021) Çelik, Ali; Morca, Ali FerhanColorimetric and real-time loop-mediated isothermal amplification (cr-LAMP) assays were developed targeting the coat protein region of genomic DNA of Wheat dwarf virus (WDV). The method was optimized relating to primer selection, determination of isothermal temperature, and determination of incubation duration. The specificity of the assay was tested using potential hosts of WDV and Maize streak virus (MSV) from Mastrevirus genus. No cross-reaction took place with MSV or with the potential hosts tested. For the naked eye observation of positive LAMP reaction, WarmStart 2X Master Mix from NEB (New England Biolabs) was used, where the change in colour from pink to yellowish points out a positive result. The amplification was monitored in real-time by smart-DART platform (Diagenetix Inc, USA) that allows connecting to a tablet or smartphone via bluetooth. The detection sensitivity of the LAMP assay was 100-fold more sensitive than conventional PCR after optimization of the cr-LAMP reaction conditions. The novel LAMP assay showed a high specificity in distinction of WDV detection from potential hosts and MSV. The cr-LAMP is considered to be fast and effective assay since it only requires very basic equipment and the results can be evaluated easily by using colorimetric and real time approaches. The simple, low-power, handheld smart-DART platform and colorimetric detection both have a major powerful advantage of the LAMP reaction in that it can be enabled in agricultural industries, where laboratory capacity is often rudimentary.Öğe EXPLORING I, bc-12 AND bc-3 GENE LOCUS IN PROMISING COMMON BEAN LINES(2023) Emiralioğlu, Orkun; Yeken, Mehmet Zahit; Çelik, Ali; Çiftçi, VahdettinCommon beans (Phaseolus vulgaris L.), known as the \"poor man's meat\", is an internationally important legume crop that appeals to farmers as well as consumers. Many biotic stressors such as bean common mosaic virus (BCMV), bean common mosaic necrosis virus (BCMNV) cause significant yield and quality losses in common bean. The most efficient and cost-effective way to lessen of these factors is to develop resistant cultivars. Local genotypes have been cultivated in many areas for years and have varied distinguishing characteristics as a result of spontaneous mutations. Identifying bean germplasm harboring gene sources is critical for developing resistant cultivars against BCMV and BCMNV. For this purpose, a total of 43 promising common bean lines selected from local genotypes cultivated across various regions of Türkiye were subjected to screening using diverse molecular markers (ROC11, SBD-5 and SW-13) to investigate gene sources associated with BCMV and BCMNV. The findings revealed that 21 lines had both I and bc-12 gene locus. In addition, the bc-12+bc-3 gene loci were discovered to be present in the 8 common bean lines. The combination of I+bc-3 resistance genes, which guarantees immune reaction to BCMV and BCMNV, was found in only one line; YLV-32. These gene sources can be evaluated in marker-assisted breeding to develop modern cultivars resistant to BCMV and BCMNV by breeders.Öğe First complete sequences and genetic variation of plum pox virus T strain in Prunus dulcis and Prunus cerasus(Springer Heidelberg, 2023) Akbaş, Birol; Morca, Ali Ferhan; Çoşkan, Sevgi; Santosa, Adyatma Irawan; Kılıç, Handan Çulal; Çelik, AliThe complete genome of plum pox virus strain T isolates from five different Prunus spp., including almond (P. dulcis) and sour cherry (P. ceracus) isolates, was fully sequenced using the primer pairs designed in this study. The five isolates were aligned with other 50 PPV-T isolates whose complete genome sequences were available in GenBank and then subjected to phylogenetic and diversity analyses. Recombination analysis showed no significant signal detected in the five newly sequenced isolates while confirming four recombinant isolates reported in a previous study. Nucleotide and amino acid phylogenetic trees clustered the tested isolates into three major groups: Balkan 1, 2, and 3. Strain T isolates shared high nucleotide and amino acid identities among them. Diversity analysis applied different parameters to found that the sequences of P3 and 6K1 genes were more conserved over other genes. In accordance, the highly variable P1 and CP genes were found to experience weaker purifying pressures, ? = 0.127 and 0.219, respectively, than other genes. The three neutrality tests gave negative values to all genes, suggesting that strain T populations have expanding or bottleneck selections. Genetic make-up of the only known sour cherry isolate is highly identical to isolates from other Prunus spp. Therefore, this study has updated our knowledge of T strain diversity in new hosts and provided a clear picture of genetic variation and host relationships.Öğe First report of prunus necrotic ringspot virus infecting apple in Turkey(Springer, 2019) Çelik, Ali; Ertunç, FilizApple (Malus domestica) is a widely grown fruit in various climate types of the world. Turkey is an important country for apple farming with 1.7 million da and 3.2 million tons of apple production in 2017. Apple is exposed to infection from many viruses during the growing period. In May 2017, a survey was conducted for plum pox virus (PPV) and prunus necrotic ringspot virus (PNRSV) of peach in the Bursa Province of Turkey. Leaves showing symptoms (mosaic, chlorosis, line patterns, ringspot and leaf curl) were collected from an apple garden near the peach growing areas.Öğe Fındık Kabuklarından Elde Edilmiş Odun Sirkesi’ nin In-Vitro Şartlarında Antifungal Etkisinin Belirlenmesi(2018) Koç, İbrahim; Yardım, Erdal Necip; Çelik, Ali; Mendeş, Mehmet; Mirtagioğlu, Hamit; Namlı, AytenBu çalışma fındık kabuklarından elde edilen odun sirkesi’nin, in-vitro şartlarında Aspergillus niger ve Penicillium digitatum’a karşı antifungal etkisini saptamak amacıyla yapılmıştır. Odun sirkesi’nin %1, %3, %5, %7 ve %10 mL’lik konsantrasyonlarının dâhil edildiği Patates Dekstroz Agar (PDA)’a, mikrofungusların 5 mm çapındaki miselyum diskleri inoküle edildikten sonra 24±1 oC’de 7 gün boyunca inkübasyona bırakılmıştır. İnkübasyonun sonunda mikrofungusların koloni çapları ölçülmüş ve kontrollere göre odun sirkesinin % engelleme oranları hesaplanmıştır. Yapılan varyans analizi sonucunda dikkate alınan uygulamalar arasında istatistiksel olarak önemli farkların bulunduğu görülmüştür (P=0.000). Varyans analizi sonucunda uygulanan Dunnett testi sonucunda ise kontrol grubu ile %1 mL odun sirkesi hariç, odun sirkesinin diğer dozları arasında istatistiksel olarak önemli farkların bulunduğu görülmüştür. Sonuç olarak; odun sirkesinin küf mantarlarını engellemede kullanılabileceği sonucuna varılmıştır.Öğe Gediz deltası kuş türlerinin ekoturizm potansiyeli(Bolu Abant İzzet Baysal Üniversitesi, 2021) Çelik, Ali; Kumbaşlı, MeriçEkoturizm, yerel halk ile işbirliği içerisinde hareket ederek kırsal bölgelerin sürdürülebilir gelişimini amaçlayan, turizmin önemli bir çıktısıdır. Bu çalışmada İzmir ilinin Karşıyaka, Çiğli, Menemen ve Foça ilçelerinin çevrelediği Gediz Deltası'nda yer alan kuş türlerinin ekoturizm potansiyeli araştırılmıştır. Araştırma alanında görülen kuş türlerini tespit etmek adına daha önceki çalışmalar incelenmiş ve saha gözlemleri yapılmıştır. Araştırmalar neticesinde 269 kuş türünün Gediz Deltası'nda görüldüğü belirlenmiş ve bunlardan 153'ü saha gözlemlerinde de kaydedilmiştir. Gediz Deltası'nda görülen kuş türleri farklı ölçütlere göre değerlendirilerek 60 türden oluşan yeni bir liste hazırlanmış ve ankete sunulmuştur. Katılımcılar kuş gözlemiyle ilgilenen kişilerden seçilmiş ve listedeki türleri ekoturizm potansiyellerine göre değerlendirmeleri istenmiştir. Bu değerlendirmeler ile Gediz Deltası'nın kuş türleri içerisinden en yüksek ekoturizm potansiyeline sahip olanlar belirlenmiştir. Ekoturizm potansiyeli yüksek olduğu tespit edilen kuş türleri için Gediz Deltası'nda yoğun olarak görüldükleri kısımlara ve dönemlere göre alan kullanımı haritaları hazırlanmıştır. Yöre halkı, ülkemiz ve uluslararası kamuoyunda Gediz Deltası ve sahip olduğu kaynakları tanıtma amaçlı yapılacak çalışmalar büyük önem arz etmektedir. Gediz Nehri üzerindeki sanayi bölgelerine ait atıklar ve tarım kimyasalları, deltanın biyolojik çeşitliliği için tehdit oluşturmaktadır.Öğe Global population structure of apple mosaic virus (ApMV, Genus Ilarvirus)(MDPI, 2023) Çelik, Ali; Morca, Ali Ferhan; Coşkan, Sevgi; Santosa, Adyatma IrawanThe gene sequence data for apple mosaic virus (ApMV) in NCBI GenBank were analyzed to determine the phylogeny and population structure of the virus at a global level. The phylogenies of the movement protein (MP) and coat protein (CP) genes, encoded by RNA3, were shown to be identical and consisted of three lineages but did not closely correlate with those of P1 and P2, suggesting the presence of recombinant isolates. Recombination Detection Program (RDP v.4.56) detected significant recombination signal in the P1 region of K75R1 (KY883318) and Apple (HE574162) and the P2 region of Apple (HE574163) and CITH GD (MN822138). Observation on several diversity parameters suggested that the isolates in group 3 had higher divergence among them, compared to isolates in groups 1 and 2. The neutrality tests assigned positive values to P1, indicating that only this region experiencing balanced or contracting selection. Comparisons of the three phylogroups demonstrated high Fixation index (F-ST) values and confirmed genetic separation and the lack of gene flow among them. Additionally, & PLUSMN;500 bp of partial MP + 'intergenic region' + partial CP coding regions of two Turkish isolates from apple and seven from hazelnut were sequenced and determined that their phylogenetic positions fell within group 1 and 3, respectively.Öğe Impact of coat protein on evolution of ilarviruses(Academic Press Inc., 2024) Çelik, Ali; Santosa, Adyatma IrawanThe genomic sequences attributed to the coat protein play a pivotal role in the evolutionary trajectory of plant viruses. The coat protein region, particularly scrutinized in the genus of Ilarvirus phylogroups, actively shapes the regional and host-specific dispersion. Within this chapter, assorted insights pertaining to the roles undertaken by coat proteins of frequently encountered Ilarviruses in their evolutionary processes are consolidated. Nonetheless, it is discerned that the availability of genomic data for RNA1 and RNA2 remains markedly limited, impeding the provision of lucid elucidations in this domain. Hence, to comprehensively delineate the evolution of Ilarviruses, a requisite exists for supplementary nucleotide sequence data, with a particular emphasis on taxa that have received lesser attention in research endeavors. © 2024Öğe In vitro antifungal activity of mint, thyme, lavender extracts and essential oils on verticillium dahliae kleb.(Parlar Scientific Publications (P S P), 2016) Erdoğan, Oktay; Çelik, Ali; Zeybek, AhmetMint, thyme and lavender of Lamiaceae family were chosen as experimental materials. The aim of study was to investigate the antifungal effects of 3 medicinal plants extracts and essential oils obtained by water stem distillation method, against two pathotypes (defoliating-D and nondefoliating-ND) of Verticillum dahliae Kleb. The inhibition of the fungus mycelium growth was evaluated under in vitro conditions at the doses of plant extract in 1 %, 3 %, 5 %, 7 % and 10 % and essential oils in 2, 4, 8, 16 and 32 1 Experiment was set up at randomized plot design with 3 replications. After the end of 7 days incubation period, colony diameters were measured and % inhibition zone ratios were calculated compared to the controls. The reduction effects of mint, thyme and lavender essential oils were greater than the extracts of the same plants. Mint, thyme and lavender extracts reduced the mycelium growth of D and ND in varying degrees, however; the highest antifungal effect was observed at 10 % dose of thyme extract. 8, 16 and 32 mu 1 mL(-1) doses of thyme essential oil inhibited 100 % the mycelium growth of both pathotype and showed a significant fungicidal effect on them. Antifungal effect of mint essential oil was found to near the thyme essential oil depending on the pathotype and the applied dose.Öğe Incidence and coat protein characterization of apple stem pitting virus isolates from Isparta province of Turkey(2022) Çelik, AliTurkey is one of the major countries in the world in terms of fruit growing due to its climate diversity and geographical features. Apple, which is one of these fruits, is grown intensively in Turkey, and especially the Mediterranean Region is important for apple agriculture. Today, viral diseases are considered as an important yield loss factor in apple farming. This study investigated the incidence and molecular characterization of apple stem pitting virus (ASPV) in Isparta province, a significant apple-producing region in Turkey. By using the DAS-ELISA and RT-PCR methods, ASPV infection was found in 7 out of 70 collected apple leaf samples. The partial nucleotid sequences of ASPV were obtained and registered in GenBank for accession numbers. The generated similarity matrix by using the representative isolates revealed that the new ASPV isolates shared 79–93% of their nucleotide sequences with GenBank reference acessions. The isolates collected in this research were clustered in group 1 of the phylogenetic tree that was created by selecting a specific number of isolates from GenBank and thought to be reliable in the phylogenetic differentiation of ASPV. This is the first study to examine the prevalence of ASPV in the Isparta region and its phylogeny. It is possible that the results of the research will contribute to a better understanding of the situation of ASPV in Turkey.Öğe Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus(MDPI, 2022) Çelik, Ali; Coşkan, Sevgi; Morca, Ali Ferhan; Santosa, Adyatma Irawan; Koolivand, DavoudA total of 112 symptomatic tomatoes (Solanum lycopersicum L.) and 83 symptomatic pepper (Capsicum spp.) samples were collected in Ankara, Eskişehir, Bartın, and Zonguldak provinces of Turkey during 2020–2021. Six tomatoes and one pepper sample (3.6%) tested positive for tomato brown rugose fruit virus (ToBRFV, genus Tobamovirus) infection by DAS-ELISA and RT-PCR. ToBRFV-positive tomato and pepper plants were removed from greenhouses as soon as possible, and the greenhouses and tools were disinfected completely. Phylogenetic analysis on the complete CP sequences suggested the clustering of 178 GenBank isolates and 7 novel isolates into three groups. A study using DnaSP software showed very low genetic variation among current global ToBRFV isolates. All four ORFs of the virus genome were under strong negative evolutionary constraints, with a ? value range of 0.0869–0.2066. However, three neutrality tests indicated that most populations of the newly identified ToBRFV are currently expanding by assigning statistically significant negative values to them. The very low FST values (0.25 or less) obtained by all comparisons of the isolates from Europe, the Middle East, China, and America concluded that there is no clear genetic separation among currently known isolates from different geographic origins. The divergence time of ToBRFV was estimated to be in the middle of the course of the evolution of 11 tested tobamoviruses. The time to the most recent common ancestors (TMRCAs) of ToBRFV were calculated to be 0.8 and 1.87 with the genetically closest members of Tobamovirus. The results of this study could improve our understanding on the population structure of the emerging ToBRFV. © 2022 by the authors.Öğe Investigation of genetic diversity in apple scab (Venturia inaequalis) isolated from two different geographical areas of Turkey(Springer, 2019) Çelik, Ali; Kavak, HamitApple (Malus domestica) is a widely grown fruit in various climate types of the world and is exposed to the attack of many fungal disease agents during the growing period. One of them is Venturia inaequalis, which is probably the most important in terms of economic loss worldwide, which makes apple scab disease important in apple growing areas. In this study, the genetic diversity of apple scab in Bingol and Isparta provinces has been examined, which represent the two extremes of Turkey in terms of apple production. The 18 isolates obtained from these regions and were amplified by PCR using 7 RAPD primers. Polymorphic bands of the isolates were obtained by subjecting to agarose gel imaging. The average number of bands per primer was determined to be 3.91, with the highest polymorphic bands obtained from OPF04 encoded primer and the least polymorphic bands from OPG15 encoded primer. According to the clustering analysis, the total isolate population belongs to 5 different groups. Significant privileges were not observed between the two regions's isolates It is thought that RAPD primers have a certain level to determine the diversity but not high levels of intra- and interregional variation in the isolates of V. inaequalis.Öğe Molecular analysis of prune dwarf virus reveals divergence within non-Turkish and Turkish viral populations(Springer, 2023) Santosa, Adyatma Irawan; Çelik, Ali; Glasa, Miroslav; Serçe, Çiğdem Ulubaş; Ertunç, FilizPrune dwarf virus (PDV) infection affects the production of stone fruits (Prunus spp.) around the world, including in Turkey. In this study, we analyzed the available nucleotide (nt) and amino acid (aa) sequences of P1, P2, movement protein (MP), and coat protein (CP) genes to assess the molecular variability and structure of non-Turkish and Turkish PDV populations. Global isolates were clustered into three major groups in nt-based phylogenetic trees of MP and CP. Comparison of geographically different isolates showed that the MP aa sequences were more conserved than the CP aa sequences. The major aa changes in MP and CP showed the most effect on group 3 isolates. MP and CP-based analyses revealed the lowest number of variable sites (S), total number of mutations (eta), average number of nt differences between sequences (k), and nt diversity (per site) (pi) values in group 3 isolates, indicating high genomic similarities. The Turkish isolates manifested the highest S and eta, and the second highest k and pi values were observed in the comparison with CP, confirmed the high intra-group divergence of the Turkish isolates belonging to the three phylogroups. A stronger purifying selection pressure was observed in the MP region than in the CP region. Neutrality tests deduced negative values for all the MP and CP phylogroups and positive values for the P1, P2, Bulgarian, and Polish populations. MP and CP comparisons showed the divergence of the three phylogroups, as revealed by the results of the K-S*, K-ST*, Z*, and S-nn permutation statistical tests. The fixation index (F-ST) values suggested that non-Turkish PDV isolates had a higher genetic distance compared with Turkish isolates from group 3 and the Turkish isolates from the other two groups.Öğe Molecular analysis of the global population of potato virus S redefines its phylogeny, and has crop biosecurity implications(MDPI, 2023) Topkaya, Şerife; Çelik, Ali; Santosa, Adyatma Irawan; Jones, Roger A. C.In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Nigde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP's, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVSI, PVSII or PVSIII. All Turkish CP sequences were in PVSI, clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (? = 0.0603-0.1825). Considerable genetic variation existed amongst PVSI and PVSII isolates. Three neutrality test methods showed PVSIII remained balanced whilst PVSI and PVSII underwent population expansion. The high fixation index values assigned to all PVSI, PVSII and PVSIII comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVSII spread constitutes a biosecurity threat for countries still free from it.
