Atilla DURSUN

Correction | 2021 | Scientific Reports11 ( 1 )

Correction to: Scientific Reports https://doi.org/10.1038/s41598-021-86991-9, published online 13 April 2021.In the original version of this Article the Acknowledgments section was incomplete.“We are very grateful to The Atatürk University, Scientific Research Projects Foundation for generous financial support (Project Number FBA-2019-7219).”Now reads: “We are very grateful to The Atatürk University, Scientific Research Projects Foundation (Project Number FBA-2019-7219) and Humintech GmbH for generous support.”

İsmail ERPER | Sezim COLDOŞBEKOVA

Note | 2023 | Journal of Plant Pathology105 ( 3 )

Keywords; penicillium fruit rot; postharvest; pyrus communis; RPB2

Tinatin DOOLOTKELDİEVA

Chapter of Books | 2018 | Agricultural Research Updates22 ( Chapter 2 )

Erwinia amylovora as a fire blight pathogen and Venturia inaequalis as a scab pathogen were isolated from the blossoms, exudates, infected fruits, leaves and bent branches of diseased apple, pear and hawthorn trees, selected in the Chy, Osh and Jalal Abad regions. Biochemical and pathogenicity tests, alongside PCR analyses were conducted to identify the local isolates of Erwinia amylovora and Venturia inaequalis. The alternative antagonistic microorganisms which combat bacterium E. amylovora and fungus Venturia inaequalis were tested within in vitro and in vivo conditions. The results revealed the ability of Streptomyces antagonisti . . .c bacteria to decrease fire blight severity on pear and apple trees during the first stage of the fire blight disease in leaf tissues. Streptomyces strain C1-4 suppressed E. amylovora disease symptoms in the leaf tissues and excised apple and pear shoots. The incidence of fire blight on leaves was reduced by about 70 with two applications of bacterial antagonists. Streptomyces sp strains were tested for apple scab control in vitro and field conditions. Two applications of Streptomyces strain C1-4 within 35 days completely stopped the scab disease in seedling leaves. Within 40 days, the seedlings were recovered; the new leaves have blossomed on branches. Seedlings grew new shoots and leaves around 50 days after the second treatment. Orchard experiment results provide great hope that a biological product based on Streptomyces could work as an effective agent to suppress the development of the pathogen in the early spring, when leaves start to show scab disease symptoms. Further studies at different locations in Kyrgyzstan, using large scale application, would allow for stronger recommendations to be made, including studies and recommendations on their ability to prevent diseases and to use them as main components in an integrated pest management program More less

Tair Esenalı Uulu

Article | 2021 | Phytoparasitica49 ( 3 )

This study was conducted in Meram district of Konya province (Turkey) in 2018 and 2019 to evaluate the efficacy of mating disruption against the tomato leafminer, Tuta absoluta in an open-field tomato growing area. Three pheromone-treated fields and three control fields were used to evaluate the effectiveness of mating disruption in both years. In pheromone-treated fields, mating disruption pheromone was applied once at a rate of 2500 g/ha with a caulking gun. In control fields, only pheromone traps were hung for monitoring and comparing the pest population. Male captures in monitoring pheromone traps and infestation rates of tomato . . . plants by T. absoluta were recorded weekly. The mean number of males captured in the traps per week in pheromone-treated fields in 2018 and 2019 was 120.86 /- 16.82 and 69.90 /- 15.70, respectively. In control fields, the mean number of males captured in the traps per week in 2018 and 2019 was 299.73 /- 16.82 and 230.75 /- 15.70, respectively. The mean percentage of infestation of the pest was 4.40 /- 0.56?n pheromone-treated fields, while it was 11.80 /- 0.56?n control fields in 2018. In 2019, the mean percentage of infestation of the pest was recorded in pheromone-treated and control fields as 1.88 /- 0.52?nd 7.39 /- 0.52?respectively. As a result of the study, it was determined that the mating disruption application against T. absoluta was successful in all three pheromone-treated fields when compared to control fields in both years. This technique was tested for the first time against the tomato leafminer in Turkey with this project More less

Şenol YILDIZ

Article | 2023 | Plant Biology25 ( 6 )

center dot Citrus plants are host to several plant parasitic nematodes (PPNs), which are microscopic organisms. Among PPNs, the citrus root nematode, T. semipenetrans (Cobb 1913) (Tylenchida: Tylenchulidae), causes significant damage to citrus plantations worldwide. Understanding citrus nematode populations, precise identification, host preference among citrus species, and damage threshold are crucial to control T. semipenetrans. The minutiae of citrus plant-nematode interactions, nematode density and molecular nematode identification are not well understood. In this study, nematode species and density in citrus orchards, host speci . . .alization, molecular and morphological characteristics of nematodes were assessed. center dot Molecular and morphological methods, host- nematode interactions, host (citrus species) preference, damage economic threshold (ET), and economic injury level (EIL) were determined using laboratory methods and field sampling. Citrus plantations in different provinces in the Mediterranean region of Turkey were investigated. center dot Nematode species were identified molecularly and morphologically. ITS sequences revealed that samples were infected by citrus root nematode T. semipenetrans. The lowest nematode density was in C. reticulata in Mersin (53 2nd stage juveniles (J2s) 100 g(-1) soil), while the highest density was from Hatay in C. sinensis (12173 J2s 100 g(-1) soil). Highest citrus nematode population density was on roots of C. reticulata, followed by C. sinensis, C. limon, and C. paradisi. center dot The citrus nematode is more common than was thought and population fluctuations change according to specific citrus species. Environmental conditions, host and ecological factors, such as temperature, soil pH, and soil nutrients, might influence nematode populations in citrus orchards. Investigating nematode density in diverse soil ecologies and the responses of different resistant/tolerant citrus species and cultivars to nematode populations is essential in future studies. Keyword: citrus nematode; host preference; ITS sequence; molecular characterizatio More less

Tinatin DOOLOTKELDİEVA

Chapter of Books | 2012 | Diversity of biodegradative gene populations in aquatic sediments examined by gene-targeted metagenomics ( Chapter 3 )

Previous studies in our lab and elsewhere showed that different microbial gene groups are obtained from geographically distant sites. Alkane monooxygenases activate terminal carbon-carbon bonds in the first step of alkane degradation with the addition of an oxygen to the compound, resulting in an alcohol product. The aim of this study was to test the hypothesis that unique microbial populations and alkane monooxygenase (alkB and Cytochrome P450) genes can be recovered from geographically distinct sites, with varying degrees of anthropogenic impact. Sediment was collected from six river and stream sites with various levels of human i . . .mpact located in Bishkek, Kyrgyzstan as well as Dushanbe and Khorog, Tajikistan, in Central Asia. The sites included rural and mountain streams, as well as rivers near or in cities. All sediments were enriched in media containing hexadecane as a carbon source and subcultured into fresh media with the alkane two times. DNA was extracted from each enrichment culture at various points throughout the enrichment for 16S rRNA and alkB clone library construction. The enrichment cultures were also analyzed by terminal restriction fragment length polymorphism (TRFLP) analysis of both 16S rRNA and alkB genes. The alkB and P450 genes, as well as 16S rRNA, were targeted with 454 pyrosequencing to obtain an estimate of microbial and alkane hydroxylase diversity at the sample locations and enrichments. The data show that distinct populations of alkB and P450 genes can be enriched from different locations and countries in Central Asia confirming that there is a wide diversity of alkane degrading genes in the environment More less

Tinatin DOOLOTKELDİEVA | Saykal BOBUŞOVA | Mahabat KONURBAYEVA

Article | 2023 | Applied and Environmental Soil Science2023

Soil bacterial and fungal communities were investigated in relation to soil type and farm management practices after vegetation harvesting in autumn. Soils from fields cultivated with Phaseolus vulgaris (bean) and Pyrus comminus (pear) and nonarable, natural areas were studied. Microbial diversity was analysed using cultivation-dependent methods (isolation of pure cultures) and cultivation-independent methods (direct extraction of DNA from soil, followed by PCR amplification of the 16S rRNA and 18S rRNA genes). The use of cultivation-dependent methods revealed that there were no differences in the biodiversity of the soil bacterial . . .and fungal communities between fields cultivated with bean plants and pear trees. However, the use of cultivation-independent methods showed that there were clear soil and crop type-specific effects on the composition of the soil bacterial and fungal communities. The density of the bacterial population was two times higher in northern mountain-valley serozem (NMVS) soil samples than in light chestnut (LC) soil samples. In contrast, the densities of the fungal communities were almost equal in the studied soil types. The density of the actinomycetes community was almost two times higher in LC soil than in NMVS soil under bean plants. The Shannon index values showed that the bacterial biodiversity in the NMVS soil samples was greater than that in the LC soil samples. Soils under fallow appeared to have diverse bacterial communities that mainly consisted of local autochthonous microflora and a small amount of zymogenic microflora (since fresh plant residue does not enter the soil). The Shannon index results revealed two interesting facts: (1) the soil bacterial community was highly diverse in soils that supported bean plants and (2) the soil fungal biodiversity was high under pear trees in both soil types. Keyword: gradient gel-electrophoresis; bacterial communities; land-use; cropping systems; plant diversity; carbon; rhizosphere; management; proteobacteria; chrysanthemu More less

Hossein ZEİNALZADEH TABRİZİ

Article | 2023 | PLOS ONE18 ( 11 )

The genus Agropyron has an important role in soil protection and forage production in rangelands. The investigation utilized 37 ISSR primers, resulting in the detection of 956 loci within the A. elongatum genome and 705 loci within the A. cristatum genome. The findings revealed a high level of polymorphism, with 97 of loci in A. elongatum and 84 of loci in A. cristatum exhibiting variability. Notably, the primer (AC)8GCT emerged as a promising candidate for evaluating genetic diversity due to its ability to amplify numerous loci in both species. Using both the UPGMA algorithm and Bayesian analysis, the examined Agropyron accessions . . .were categorized into two subgroups based on their respective species. The Q values associated with these subgroups suggested that certain accessions, namely G16, G19, G20, G21, G22, G23, G24, and G25, displayed potential admixture genomes. An analysis of molecular variance (AMOVA) underscored the significance of within-species variability, which accounted for 69 of the overall diversity, compared to between-species variability at 31. Various genetic diversity parameters, including Na, Ne, I, He, and the number of private loci, were found to be higher in A. elongatum when compared to A. cristatum. Furthermore, Jaccard similarity coefficients ranged from 0.33 to 0.66 in A. cristatum and from 0.25 to 0.7 in A. elongatum, indicating the extent of genetic relatedness among these species. Intriguingly, the study identified two and three heterotic groups in A. cristatum and A. elongatum, respectively, which could be harnessed in the development of synthetic varieties to exploit heterosis. The results also indicated that a small proportion of ISSR loci pairs (5.2 in A. elongatum and 0.5 in A. cristatum) exhibited significant levels of linkage disequilibrium (LD) (P≤0.05), suggesting the potential utility of LD-based association mapping in Agropyron species. In conclusion, this research sheds light on the genetic diversity of Agropyron species and provides valuable insights into their potential applications in soil protection and forage production, as well as the prospects for enhancing genetic variability and heterosis in these species. Keyword: agropyron; algorithm; article; bayes theorem; consanguinity; controlled study; forage; gene linkage disequilibrium; gene pool; genetic variability; genetic variation; heterosis; Iran; nonhuman; rangeland; gene pool; genetics; Iran; poaceae; soi More less

İlker KEPENEKÇİ

Article | 2016 | Turkish Journal of Entomology / Türkiye Entomoloji Dergisi40 ( 1 )

One of the major pests of the vegetables, root knot nematodes (Meloidogyne spp.) (Tylenchina: Meloidogynidae) (RKNs) can cause economic losses by forming knots on the host plant roots. RKNs are more prevalent in the greenhouse vegetable growing areas of the coastal regions. In this study, the effects of plant extracts from five different plants; Capsicum frutescens, Hyoscyamus niger (Solanaceae), Melia azedarach (Meliaceae), Xanthium strumarium and Achillea wilhelmsii (Asteraceae) were evaluated against RKNs. In the first studies; the effects of plant extracts (0.5, 1.0, 1.5, 3.0, 6.0 and 12.0% concentrations) on eggs, egg masses an . . .d second stage juveniles (J2s) of the Meloidogyne incognita were evaluated in laboratory conditions (in vitro tests). Concentrations of 3.0, 6.0 and 12.0% for H. niger, X. strumarium and M. azedarach caused 100% inhibition of egg hatching and J2s mortality. Effects of the same plant extracts against M. javanica on egg mass of nematode (I), the plant height (II), the plant age (III) plant dry weight (IV), root fresh weight (V) and root dry weight (VI) were also evaluated in greenhouse-pot studies. Result of pot trials, 12.0% of H. niger and X. strumarium has shown high effect on hatching studies. In the toxicity studies, 6.0% and 12.0% of X. strumarium and M. azedarach were found effective.Three plant extracts (X. strumarium, H. niger and M. azedarach), against mixed populations of M. incognita and M. javanica on tomatoes under natural greenhouse conditions (in vivo) were evaluated. Treatmets were repeated 4 times by watering for each pot (extract were applied 1 ml plant-1). In greenhouse trials, root gal indicies (root knot) and crop yield (tomatoes) (kg plant-1) values and effect of root gal indicies and yield (%) were evaluated. In vivo studies, it could be concluded that, only the M. azedarach has effected the galling indicies and consequentelly crop yield significantly. - Keywords: Root knot nematode, Meloidogyne incognita, M. javanica, plant extracts, tomat More less

Hasan CAN | İbrahim İlker ÖZYİĞİT | Mustafa PAKSOY

Article | 2019 | Journal of Genetics98 ( 3 )

Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar . . . development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding, with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information on population dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods More less

Şenol YILDIZ

Article | 2023 | Tropical Plant Pathology48 ( 2 )

In 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 wit . . .h 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 More less

Hüseyin GÖÇMEN

Article | 2020 | Applied Ecology and Environmental Research18 ( 2 )

The cotton whitefly (Bemisia tabaci Genn.) is a major pest of cultivated plants in tropical and subtropical regions. In this study, the genetic diversity between populations and various biotypes of B. tabaci collected from Hatay, Adana, Icel, Antalya, Mugla, Aydin and Denizli provinces of Turkey were investigated using mitochondrial cytochrome oxidase subunit 1 (mtCOI) sequences. Thirty-two nucleotide variations were found in a 617 bp mtCOI sequence of the among the populations studied. Phylogenetic analysis divided the B. tabaci populations of Turkey into two groups clustering around the main Middle East-Asia Minor 1(MEAM1) and Med . . .iterranean (MED) groups, (i.e. the so-called B and Q biotypes respectively). Mediterranean species were also divided into two subgroups. The populations from Aydin and Denizli provinces identified as the Qw haplotype were closely related to populations of Greece, whereas the remaining samples were identified as the Qe haplotype. This study indicated that the biotype status of the B. tabaci populations might have changed from year to year depending on several factors, such as insecticide resistance, host plant preferences, and climate niches to understand the factors causing changes in the biotype structure, pest populations should be monitored, and surveys must be conducted at regular intervals More less