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    Asma ve narlardan izole edilen grapevine leafroll-associated virus-1 izolatlarının kısmi sekanslarının karşılaştırmalı genomik analizleri
    (2017) Elçi, Eminur; Gazel, Mona; Çağlayan, Kadriye
    Asma yaprak kıvırcıklık (grapevine leafroll) hastalığı geçmişten bu yana bağ virüs hastalıkları içerisinde ekonomik önem derecesi yüksek olan dünya çapında yayılım gösteren bir hastalıktır. Closterovirus cinsine ait virüs üyeleri içerisinde, Asma yaprak kıvırcıklık virüsü 1 (Grapevine leafroll-associated virus 1) (GLRaV-1) en eski olanıdır. Bağlarda önemli verim kayıplarına neden olan bu virüs, özellikle yapraklarda kıvrılma simptomu ile tanımlanır. Nar bitkisi, ekonomik değeri yüksek bitkiler arasında yer almakta olup henüz az sayıda virüs hastalıkları tanımlanmış ancak son yıllarda yürütülen çalışmalarda bu bitkinin de GLRaV-1'in konukçusu olabileceği bildirilmiştir. Bu çalışmanın amacı, bağ ve narlardan elde edilen GLRaV-1 izolatlarının genomik olarak kıyaslanmasıdır. Bu amaçla, 2014 yılında Hatay ve Niğde illerinden toplanan asma ve nar örneklerinden total RNA ve dsRNA izolasyonları yapılmış, virüs genomuna özgü 2 farklı bölgenin (hareket (movement) proteini (p24) ve ısı şok (heatshock) proteinini (HSP70h) çoğaltan primerler kullanılarak RT-PCR ile analizleri yapılmış elde edilen ürünler klonlanmış ve sekans analizleri yapılmıştır. Ayrıca Closterovirüs'ün HSP70h genine özgü dejenere primer kullanılarak DOP-PCR analizleri yapılmıştır. DNA dizi analizlerinin sonunda elde edilen kısmi genomun, BLAST analizleri yapıldıktan sonra filogenetik analizleri yapılmıştır. Bu çalışma sonunda, yeni bir konukçu olduğu düşünülen nardan izole edilen GLRaV-1 izolatlarının asma izolatları ile kıyaslamalı olarak analiz edilmesi sağlanmış ve izolatlar arası yüksek oranda benzerlik olduğu tespit edilmiştir.
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    (Elsevier, 2023) Elçi, Eminur; Sajid, Qurat-ul Ain; Çağlayan, Kadriye
    Common fig (Ficus carica L.) has several identified viruses, and fig mosaic disease (FMD) is a well-known disease infecting fig plants around the world. The causal agent of FMD has been identified as fig mosaic emaravirus (FMV), which has an extensive dispersal rate. The vector of FMD has been indefinable, as no evidence was found until 1955, though the eriophyid mite Aceria ficus (Cotte) was known as an efficient vector for FMV. It has been detected in many countries, like Turkey, England, the United States, Algeria, Spain, Tunisia, Syria, China, New Zealand, Israel, Italy, Greece, Jordan, Lebanon, and Australia. Its major symptoms comprised of mosaic, spotting, and mottling, foliar discoloration, size reduction and mosaics of fruits, and irregular leaf distortion. FMV is the one with the highest association with FMD, and beside this virus; numerous viruses have been reported belonging Caulimoviridae, Closteroviridae, Flexiviridae, Partitiviridae, and Tymoviridae families, including fig leaf mottle-associated viruses-1 and 2, Arkansas fig closteroviruses-1 and 2, fig latent virus-1, fig mild mottle-associated virus (FMMaV), fig cryptic virus, fig fleck-associated virus, fig badnavirus-1. Scouting and removal of infected trees can be the best management for this disease to avoid profit loss. © 2024 Elsevier Inc. All rights reserved.
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    Genetic diversity of Turkish commercial cotton varieties revealed by molecular markers and fber quality traits
    (2014) Elçi, Eminur; Akışcan, Yaşar; Akgöl, Batuhan
    To assess the genetic diversity and relationships among commercial Gossypium species released in Turkey between 1964 and 2014, 96 cotton varieties were analyzed using morphological and molecular markers. Morphological analysis was performed based on 4 fber quality traits including fber length, strength, fneness, and uniformity, and the mean values of each trait for each genotype were calculated using 2-year data. Te results showed that most of the genotypes have long fber length, very high fber strength, coarse (45 genotypes) or average (50 genotypes) fber fneness, and high uniformity. Twenty-six simple sequence repeat (SSR) markers and 14 markers linked to quantitative trait loci (QTLs) for fber quality traits produced a total of 103 alleles, with an average of 2.57 alleles per locus ranging from 80 bp to 300 bp products, with an average polymorphism information content (PIC) value of 0.233. Markers DPL513 and DPL431 (among 26 SSR markers) and markers CIR246 and BNL4108 (among 14 molecular markers) were found to be very informative, with 0.724, 0.663, 0.749, and 0.583 PIC values, respectively. Te combined morphological and molecular data analysis resulted in more than 8 clades using the unweighted pair group method with arithmetic average (UPGMA). Te upland cotton varieties were distinctly separated from the lowland cotton variety Maydos Yerlisi (Gossypium herbaceum L.). Within the upland cotton varieties, the Egyptian cotton variety Giza 70 (G. barbadense L.) was distinctly separated from commercial cotton varieties of Turkey ( G. hirsutum L.), as revealed by both morphological and molecular dendrograms. Principal component analysis (PCA) derived from combined data was in agreement with UPGMA analysis. It is concluded that commercial Turkish cotton varieties have a good genetic diversity with high fber quality, considering the upland cotton’s narrow genetic structure. Tese results can provide a useful guide for selecting specifc germplasm with distinct genetic backgrounds in cotton breeding programs.