Genetic diversity of Turkish commercial cotton varieties revealed by molecular markers and fber quality traits

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.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

Genomic Variability and Recombination Analysis of Grapevine leafroll-associated virus-1 Isolates from Turkey

Grapevine leafroll-associated virus-1 (GLRaV-1), one of the causal agents of Grapevine leafroll disease (GLRD), is one of the most important viral diseases of grapevine worldwide. In this study, the prevalence of GLRaV-1, genetic variation and recombination events among GLRaV-1 isolates in Turkey were investigated. Initially, 197 grapevine samples from different provinces of the country were serologically tested. Of the total samples, 109 (55.32%) were identified as GLRaV-1 infected. Subsequently, 9 samples representing different geographic distribution were selected for further sequence analysis of the heat-shock protein 70 homolog (HSP70h), open reading frame 9 (p24), coat protein (CP) and coat protein duplicate 2 (CPd2). Among the four gene regions, CPd2 was found the most divergent region while HSP70h gene exhibited the lowest genetic diversity. The phylogenetic analysis of four genomic regions including GenBank records clustered all variants in two major groups and grouped Turkish isolates mostly together. However, the isolate clusters were not correlated to their geographic origin. Furthermore, several putative recombination events were detected with trace to moderate evidence support of algorithms implemented in Recombination Detection Program (RDP). Taken together, the results provide a better understanding on genetic variation of Turkish GLRaV-1 isolates in the country and worldwide and can help to improve sanitation of propagated material programs for the grape growers

Molecular Characterization and Germination Analysis of Cotton (Gossypium hirsutum L.) Genotypes under Water Deficit Irrigation

Pamuk bitkisi, ülkemiz için stratejik ve ekonomik öneme sahip olan bir üründür. Kuraklık stresi, dünyanın birçok ülkesinde olduğu gibi Türkiye'de de bitki büyüme ve verimini olumsuz yönde etkileyen en önemli çevresel stres faktörlerinden birisidir. Bu çalışmada, kuraklık stresine karşı toleranslı yeni yerli pamuk çeşitlerinin geliştirilmesi amacı ile tarımsal özellikleri bakımından seçilmiş olan 11 farklı pamuk çeşidinin kısıntılı sulama stratejileri altında çimlenme süresi ve çimlenme oranı incelenmiş ve mikrosatellit markörleri aracılığıyla moleküler olarak karakterize edilmiştir. Yapay ortamda % 25, % 50, % 75 ve % 100 sulama planı ile kısıntılı sulama uygulanarak kuraklık stresi uygulanmıştır. Bitkilerin % 50 ve % 25 sulama koşullarında strese girdikleri gözlenmiştir. Kısıntılı sulama koşullarında çimlenme süresi ve çimlenen bitki sayısı incelendiğinde; Tamcot Sphinx, Tamcot 94, Tamcot CamdEs ve BA525 çeşitlerinin diğerlerine oranla su stresine karşı daha toleranslı oldukları tespit edilmiştir. Moleküler karakterizasyon çalışmaları için ortalama 0.306 polimorfizm bilgi içeriğine (PIC, Polymorphism Information Content) sahip 28 adet markör kullanılarak Aritmetik Ortalama Kullanılarak Ağırlıksız Çift Grup Metodu (UPGMA) analizleri yapılmıştır. UPGMA analizleri sonucunda çeşitler iki grup altında sınıflanmıştır. Elde edilen bu verilerin, kuraklığa karşı toleranslı yeni çeşitlerin geliştirilmesinde önemli bir bilgi sağlayacağı düşünülmektedir.Cotton is an important crop in terms of economic and strategic impacts. Drought stress is one of the most important environmental stress factors which negatively affects growth and yield of plants in Turkey as occurred in many countries in the world. In this study, 11 different cotton cultivars selected based on their agronomical characters were tested under water deficit irrigation strategies. Thus, it was aimed to select and/or determine appropriate new varieties for breeding new national materials resistant to drought stress, and to characterize with the molecular microsatellite markers. According to the different irrigation levels (25%, 50%, 75% and 100%) plants were observed under the stressed conditions at the irrigation levels of 50% and 25%. Among the tested varieties, Tamcot Sphinx, Tamcot 94, Tamcot CamdEs and BA525 varieties were found to be more water stress tolerant than others in terms of germination time and germinated plant. The UPGMA (Unweighted Pair-Group Method Using Arithmetic Averages) analysis was carried out using 28 markers with average 0.306 polymorphism information content (PIC) for molecular characterization studies. Based on the UPGMA results, the varieties were clustered into two groups. It is expected that the results obtained from this study might provide considerable data for improving new drought tolerant varieties

Genetic Analysis of Maize (Zea mays L.) Hybrids Using Microsatellite Markers

Genetic purity is one of the most important quality criteria required for successful hybrid seed production. In this study, molecular markers were used for assessing the genetic purity and diversity of three commercially important maize F1hybrids (Pasha, Frida and PG1661) and their parental inbred lines. Fifty Simple Sequence Repeats (SSRs) markers were used to analyze samples, also the efficiency of the markers were compared. Twenty three primer pairs among the fifty markers were able to detect polymorphism between the different types of hybrids with an average of 0.69 polymorphism information content (PIC) value. Genetic purity analyses revealed more than 98% homogeneity in the hybrid seeds. The hybrids were grouped into three main clusters. It can be concluded that, molecular markers are efficient to study the genetic purity and diversity in maize hybrids and microsatellites are more accurate marker-type because of their co-dominanc

Comparative genomic analysis of partial grapevine leafroll-associated Virus-1 sequences isolated from pomegranate and grapevines

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.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

Asma ve Narlardan İzole Edilen Grapevine leafroll-associated virus-1 İzolatlarının Kısmi Sekanslarının Karşılaştırmalı Genomik Analizleri

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

First report on Grapevine leafroll associated virus 1 infecting pomegranate trees (Punica granatum L.) in Turkey

Pomegranate (Punica granatum L.) has been cultivated since ancient times through the Mediterranean region, Asia, Africa and some parts of Europe. The main production countries being mainly Mediterranean and Asian countries such as India, Iran, China and Turkey. Turkey is one of the leading producer and exporter for this fruit and total pomegranate production reached 315.000 tons in 2012 that corresponds to one of the largest pomegranate economies in the world. Hatay, located in Eastern Mediterranean region, is one of the most important centers of diversity in pomegranate in Turkey. Recently symptoms resembling virus infection in&nbsp; local pomegranate cultivars were observed in late summer-autumn periods in Hatay province. Pomegranate leaves showing yellowing, chlorotic spots, vein clearing and oak-leaf symptoms were sampled to verify possible virus association with these symptoms. DAS-ELISA and RT-PCR analysis were used for the detection of suspecious viruses infecting fruit trees, grapevines and potatoes such as Plum pox virus, Prunus necrotic spot virus, Apple mosaic virus, Apple chlorotic ring spot virus, Apple stem grooving virus, Arabis mosaic virus, Grapevine leafroll associated virus 1, 2, 3, 4-9, 6, 7, Grapevine virus A, Cucumber mosaic virus, Pepino mosaic virus, Potato virus X, Potato virus Y (PVYN), Potato virus M and Potato leafroll virus. Plant sap extraction for ELISA and Nucleic acid extraction for PCR analysis were performed from leaf and shoots of three strong symptomatic and twenty suspecious plants. Due to high content of metabolic compounds such as polyphenols and anthocyanins in pomegranate tissues, nucleic acid extractions did not result in high quality RNA in most of the conventional procedures used in this study, except modified CTAB based method. One set of primer F5&#39;-GTTACGGCCCTTTGTTTATTATGG-3&#39; and R5&#39;-CGACCCCTTTATTGTTTGAGTATG-3&#39; was used to amplify coat protein gene (397 bp) of GLRaV-1. According to ELISA and RT-PCR analysis only three symptomatic plant samples yielded positive results for Grapevine leafroll associated virus-1 (GLRaV-1) among tested viruses whereas all other samples were negative for all tested viruses. Up to now, there are only a few reports on Cucumber mosaic virus and Hop stunt viroid in pomegranates. To the best of our knowledge, this is the first report to show GLRaV-1 in pomegranate trees.&nbsp;</p

Identification and Characterization of a Novel <i>Robigovirus</i> Species from Sweet Cherry in Turkey

High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5&#8242; UTR and 3&#8242; UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43&#8722;53%, 44&#8722;60%, 39&#8722;43%, 38&#8722;44% and 45&#8722;50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies