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Öğe Comparison of Chemical Composition in Lupin (Lupinus spp.) Species(Revista Chimie Srl, 2015) Yilmaz, Saban; Atak, Mehmet; Erayman, MustafaThe aim of this study was to investigate the chemical characteristics of seeds in two cultivated bitter landraces of Lupinus albus and two wild Lupinus angustifolius types in Mediterranean environment (Hatay, southern Turkey). Fat quantity and fatly acid quality were considerably different depending on the genotype. L. albus showed the higher oil content (74.0-85.1 g/kg), saturated fatty acids (16.88-19.3 g/100 g), monounsaturated fatty acids (55.80-57.62 g/100 g) and polyunsaturated fatly acids (24.8-25.5 g/100 g) than did L. angustifolius with oil content of 38.8-46.69 g/kg; saturated fatty acids of 23.40-25.12 8/100 g, monounsaturated fatty acids of 51.48-52.98 g/100 g and polyunsaturated fatty acid of 23.4-23.6 g/100 g. The data obtained suggest L. albus as the most interesting lupin species for aiding the crop-livestock food chain and wild L. angustifolius type as a promising crop due to its high nutritive traits for the Mediterranean environment.Öğe Demarcating the gene-rich regions of the wheat genome(2004) Erayman, Mustafa; Sandhu, Devinder; Sidhu, Deepak; Dilbirligi, Muharrem; Baenziger, P.S.; Gill, Kulvinder S.By physically mapping 3025 loci including 252 phenotypically characterized genes and 17 quantitative trait loci (QTLs) relative to 334 deletion breakpoints, we localized the gene-containing fraction to 29% of the wheat genome present as 18 major and 30 minor gene-rich regions (GRRs). The GRRs varied both in gene number and density. The five largest GRRs physically spanning <3% of the genome contained 26% of the wheat genes. Approximate size of the GRRs ranged from 3 to 71 Mb. Recombination mainly occurred in the GRRs. Various GRRs varied as much as 128-fold for gene density and 140-fold for recombination rates. Except for a general suppression in 25-40% of the chromosomal region around centromeres, no correlation of recombination was observed with the gene density, the size, or chromosomal location of GRRs. More than 30% of the wheat genes are in recombination-poor regions thus are inaccessible to map-based cloning. © Oxford University Press 2004; all rights reserved.Öğe Diversity analysis of genetic, agronomic, and quality characteristics of bread wheat (Triticum aestivum L.) cultivars grown in Turkey(2016) Erayman, Mustafa; İlhan, Emre; Eren, Abdil Hakan; Güngör, Hüseyin; Akgöl, BatuhanTurkey is an important bread wheat producer. The objective of this study was to dissect the diversity of genetic, agronomic, and quality characteristics of bread wheat cultivars grown on 25% of the total wheat area in Turkey. A total of 24 wheat cultivars and 5 wild progenitors of wheat were examined using 24 simple sequence repeat (SSR) primers with a known physical locus on the A, B, and D genomes of hexaploid wheat. A total of 72 bands produced 939 alleles on the wheat cultivars and wild progenitors. Markers were efficient in discriminating the species and the highest genetic diversity information was obtained from the markers Xgwm312 and Xgwm372. Microsatellite markers clearly separated cv. Pandas from all other cultivars although it was closely related to most of them in terms of agronomic and quality traits. Four agronomic characteristics including yield component traits and eight bread quality analyses were used for the diversity analyses. A significant association between morphological and bread wheat quality traits was observed while the correlation was weak with the genetic data. Cultivars were also classified with respect to release year and origin. Molecular variance between old (released before the year 2000) and new cultivars accounted for 1% of the total variation and the variance was 3% between national and foreign cultivars. Results showed that the number of alleles was lower in national and new cultivars compared to foreign and old cultivars. Therefore, breeding sources do not appear to improve the genetic base of wheat cultivars in Turkey. Introducing new variation sources may be needed to broaden the narrowed gene pool of bread wheat.Öğe Effects of seeding rates on competition indices of barley and vetch intercropping systems in the Eastern Mediterranean(2015) Yılmaz, Şaban; Özel, Ali; Atak, Mehmet; Erayman, MustafaForage mixtures are common agricultural practices for the energy and protein needs of animals. In this study, common vetch (Vicia sativa L.), Hungarian vetch (Vicia pannonica L.), and barley ( Hordeum vulgare L.) mixtures in diferent seeding rates were investigated in terms of forage yield and quality. In order to evaluate the efect of vetch, cereal intercropping and the competition/ economic indices of 8 diferent legume–barley mixtures, along with their pure stands, were assessed during the 2008–2009 and 2009– 2010 growth seasons in the Eastern Mediterranean region of Turkey. Te feld experiment was arranged as a randomized complete block design with 3 replications for each year. Intercropping indices were calculated by means of land equivalent ratio (LER), aggressivity (A), crowding ratio (CR), and actual yield loss (AYL). Competition indices revealed that both the common vetch–barley and the Hungarian vetch–barley intercroppings at a seeding ratio of 80%:20%, respectively, were advantageous due to their high yield, land use efciency, and economic value compared to other mixtures or pure stands. All samples were analyzed for quality parameters such as dry matter (DM), crude protein (CP), neutral detergent fber (NDF), and acid detergent fber (ADF) content. While digestible dry matter (DDM) content did not difer among treatments, CP, NDF, ADF, TDN (total digestible nutrients), DDM, RFV (relative feed value), and NE1 (net energy for lactation) content signifcantly difered among the diferent vetches–barley mixtures (P < 0.01). Te results emphasize that both vetch species combined with barley and using the seeding ratio of 80% vetch:20% barley should be proftable for farmers in terms of implementation and maximum yield per unit area under Eastern Mediterranean conditions.Öğe Evaluation of seedling characteristics of wheat (Triticum aestivum L.) through canonical correlation analysis(Cereal Res Inst, 2006) Erayman, Mustafa; Abeyo, Bekele Geleta; Baenziger, P. Stephen; Budak, Hikmet; Eskridge, Kent M.To examine the seedling characteristics of nine different bread wheat (Triticum aestivum L.) varieties, several variables regarding seedling size and germination characteristics were analyzed using canonical correlation analysis. Significantly correlated first canonical variate pairs indicated that the variables within each set such as coleoptile length, shoot length and fresh weight within the size set, and emergence rate index and germination percentage can be regarded as main factors for vigorous wheat seedlings. The variables such as root number, root weight and dry weight did not seem to have predictive power on seedling size measurements of wheat. Both emergence rate index and somewhat germination percentage within the first canonical variate of germination set appeared to be the correct factors for vigorous germination of wheat seed. Our analysis revealed that compared to other variables, coleoptile length and emergence rate index are powerful determinants of reliable germination, and in turn for better wheat stand establishment. Selecting for these traits in early generation is expected to increase the seedling vigor of wheat. Canonical correlation analysis was shown to be suitably sensitive to detect relationships between seedling variables in bread wheat.Öğe Genome-wide fungal stress responsive miRNA expression in wheat(Springer, 2014) Inal, Behcet; Turktas, Mine; Eren, Hakan; Ilhan, Emre; Okay, Sezer; Atak, Mehmet; Erayman, MustafaMicroRNAs (miRNAs) are small non-coding class of RNAs. They were identified in many plants with their diverse regulatory roles in several cellular and metabolic processes. A number of miRNAs were involved in biotic and abiotic stress responses. Here, fungal stress responsive wheat miRNAs were analyzed by using miRNA-microarray strategy. Two different fungi (Fusarium culmorum and Bipolaris sorokiniana) were inoculated on resistant and sensitive wheat cultivars. A total of 87 differentially regulated miRNAs were detected in the 8 x 15 K array including all of the available plant miRNAs. Using bioinformatics tools, the target transcripts of responsive miRNAs were predicted, and related biological processes and mechanisms were assessed. A number of the miRNAs such as miR2592s, miR869.1, miR169b were highly differentially regulated showing more than 200-fold change upon fungal-inoculation. Some of the miRNAs were identified as fungal-inoculation responsive for the first time. The analyses showed that some of the differentially regulated miRNAs targeted resistance-related genes such as LRR, glucuronosyl transferase, peroxidase and Pto kinase. The comparison of the two miRNA-microarray analyses indicated that fungal-responsive wheat miRNAs were differentially regulated in pathogen- and cultivar-specific manners.Öğe Genome-wide identification of salinity responsive HSP70s in common bean(Springer, 2016) Buyuk, Ilker; Inal, Behcet; Ilhan, Emre; Tanriseven, Mehmet; Aras, Sumer; Erayman, MustafaThe present study is aimed to identify and characterize HSP70 (PvHSP70) genes in two different common bean cultivars under salt stress. For this purpose various in silico methods such as RNAseq data and qRT-PCR analysis were used. A total of 24 candidate PvHSP70 gene were identified. Except for chromosome 4 and 7, these candidate PvHSP70 genes were distributed on the remaining chromosomes. While the lowest number of PvHSP70 genes was determined on chromosomes 1, 3, 5, 7, 9, 10 and 11 (one HSP70 gene), the highest number of PvHSP70s was on chromosomes 6 and 8 (seven HSP70 genes each). Three genes; PvHSP70-5, -9, and -10 were found to have no-introns. In addition, four tandemly and six segmentally duplicated gene couples were detected. A total of 13 PvHSP70 genes were targeted by miRNAs of 44 plant species and the most targeted genes were PvHSP70-5 and -23. The expression profile of PvHSP70 genes based on publicly available RNA-seq data was identified and salt treated leaf tissue was found to have more gene expression levels compared to the root. qRT-PCR analysis showed that the transcript concentrations of upregulated PvHSP70 genes in leaves of Zulbiye (sensitive) were mostly higher than those of Yakutiye (resistant). The present study revealed that PvHSP70 genes might play an important role in salt stress response for common bean cultivars and variability between cultivars also suggests that these genes could be used as functional markers for salt tolerance in common bean.Öğe IDENTIFICATION OF SSR AND EST MARKERS ASSOCIATED WITH WATERLOGGING TOLERANCE IN BREAD WHEAT(Parlar Scientific Publications (P S P), 2015) Atak, Mehmet; Ilhan, Emre; Erayman, Mustafa; Dilbirligi, Muharrem; Eren, Abdil Hakan; Arslan, Mehmet; Celiktas, NafizCrop production is significantly limited by waterlogging especially in high rainfall and poorly drained regions in the world. Hence, breeding for waterlogging tolerance to increase production is one of the main objectives of breeders. Similar to other abiotic stress tolerances, the tolerance to waterlogging is a complex trait and difficult to select for in breeding programs. Marker assisted selection has been an effective method for crop improvement by utilizing markers closely related to target traits combined with accurate phenotyping of key factors. In the present study, two bread wheat (Triticum aestivum L.) F-2:3 populations ('Dogankent' x 'Ducula-4' and 'Ducula-1' x 'Seri-82') derived from susceptible cultivars ('Dogankent' and 'Seri-82') and tolerant ('Ducula-1' and 'Ducula-4') lines were treated with four weeks of waterlogging and screened in two different locations. Additionally, 32 expressed sequence tags and 210 microsatellite markers were screened for analysis of marker trait associations; of which less than %20 (45) of those markers were polymorphic between parents of both populations. Tolerance, yield and quality related traits including plant height index, tillering index, adventitious root formation, heading date, tolerance scoring index, total kernel number and thousand kernel weight were identified to be mostly affected by environment. Marker - trait analyses identified markers significantly associated with waterlogging tolerance as well as yield and quality component traits. In the 'Dogankent' x `Ducula-4' derived population, two markers explaining more than 10% of the total variance for adventitious root formation and thousand kernel weight were detected both on chromosomes 3DL (Xgwm645) and 4AL (Xgwm160). This is one of the first studies revealing markers linked to the tolerance related traits in spring wheat under waterlogging conditions.Öğe Identification of SSR and EST markers associated with waterlogging tolerance in bread wheat(Parlar Scientific Publications, 2015) Atak, Mehmet; Ilhan, Emre; Erayman, Mustafa; Dilbirli?i, Muharrem; Eren, Abdil Hakan; Arslan, Mehmet; Çeliktas, NafizCrop production is significantly limited by waterlogging especially in high rainfall and poorly drained regions in the world. Hence, breeding for waterlogging tolerance to increase production is one of the main objectives of breeders. Similar to other abiotic stress tolerances, the tolerance to waterlogging is a complex trait and difficult to select for in breeding programs. Marker assisted selection has been an effective method for crop improvement by utilizing markers closely related to target traits combined with accurate phenotyping of key factors. In the present study, two bread wheat (Triticum aestivum L.) F23 populations ('Dogankent' x 'Ducula-4' and 'Ducula-1' x 'Seri-82') derived from susceptible cultivars ('Dogankent' and 'Seri-82') and tolerant ('Ducula-1' and 'Ducula-4') lines were treated with four weeks of waterlogging and screened in two different locations. Additionally, 32 expressed sequence tags and 210 microsatellite markers were screened for analysis of marker trait associations; of which less than %20 (45) of those markers were polymorphic between parents of both populations. Tolerance, yield and quality related traits including plant height index, tillering index, adventitious root formation, heading date, tolerance scoring index, total kernel number and thousand kernel weight were identified to be mostly affected by environment. Marker - trait analyses identified markers significantly associated with waterlogging tolerance as well as yield and quality component traits. In the 'Dogankent' x 'Ducula-4' derived population, two markers explaining more than 10% of the total variance for adventitious root formation and thousand kernel weight were detected both on chromosomes 3DL (Xgwm645) and 4AL (Xgwm160). This is one of the first studies revealing markers linked to the tolerance related traits in spring wheat under waterlogging conditions. © by PSP.Öğe Molecular and ecological investigations on the wild populations of Glycyrrhiza L. taxa distributed in the East Mediterranean Area of Turkey(Springer Japan Kk, 2016) Altay, Volkan; Karahan, Faruk; Ozturk, Munir; Hakeem, Khalid Rehman; Ilhan, Emre; Erayman, MustafaThis paper covers studies on the molecular and ecological aspects of G. glabra var. glandulifera, G. flavescens ssp. flavescens and G. echinata collected from Hatay (Turkey); with the aim to better understand their genetic variation and ecological requirements for possible conservation programs. The material including total genomic DNA was extracted by the CTAB, and for PCR reaction, a total of 14 SSR primers developed for Medicago truncatula were used. PCR amplifications were performed in a Multigen(A (R)) Thermal Cycler. Soil samples were analysed for their texture, pH, total soluble salts, calcium carbonate, total N content, total phosphorus and organic matter content. In order to see the association between genetic, ecological and geographical data, a similarity matrix was generated. Genetic similarity distances between genotypes were correlated with those of Eucledian distances obtained from ecological and geographical data. Analysis of molecular variance (AMOVA) was performed using GenAlEx 6.5 software to determine variation among and within genetic variations. The genetic analysis showed that the highest expected heterozygosity values were obtained from G. glabra while the lowest were obtained from G. echinata. In general heterozygosity values were low, especially for G. echinata. Therefore, variation appears to be lower within each species than among three species. The physical and chemical analysis of soil and plant samples indicates that mineral accumulation in plants is substantially affected by the soil characteristics. There is a need for identification of better strategies for the improvement of varieties, especially for small farmers managing marginal soils. More studies should be conducted in order to safeguard these taxa, especially G. glabra var. glandulifera which is collected intensively due to its economic value, the same is true for endemic taxon G. flavescens ssp. flavescens.Öğe NUCLEAR DNA CONTENT VARIATION AMONG GLYCYRRHIZA TAXONS COLLECTED FROM EAST MEDITERRANEAN(Parlar Scientific Publications (P S P), 2017) Ilhan, Emre; Ozgur, Sevda; Tuna, Gulsemin Savas; Eren, Abdil Hakan; Karahan, Faruk; Tuna, Metin; Erayman, MustafaIn this study, we performed nuclear DNA content determination of three different licorice species (G. flavescens Boiss, G. glabra L. var. glandulifera and G. echinata L.) collected from three different geographical regions of Hatay Province (Arsuz, Kirikhan, and Antakya) in the East Mediterranean Region. Previous cytogenetic studies in Glycyrrhiza genus is limited to chromosome counts by classical methods and no information was available on nuclear DNA content of the species included within the genus. Nuclear DNA content information is constant among individuals of one species, therefore, it is species specific. This makes nuclear DNA content information very useful for taxonomic, evolutionary, and genetic studies. Nuclear DNA content information (pg) can be converted to genome size (bp) by using a simple equation and it is critical for genome sequencing projects. In this study, nuclear DNA content of three different Glycyrrhiza species were comparatively analyzed for the first time by using flow cytometry method. Based on the results of the study G. flavesences (1.138 0,013 pg, 1112.96 Mbp) had larger nuclear DNA content than those of G. glabra (0.967 0,009, 945.73 Mbp) and G. echinata (0.946 0,008 pg, 925.19 Mbp). These results indicate that G. flavescens have different genomes than G. glabra and G. echinata, which have more similar genomes. The results of this study will be useful for taxonomic identification of Glycyrrhiza species and to understand their geno-mic structures and relations.Öğe Physiological and gene expression differences of wheat varieties under different waterlogging treatments(Elsevier Sci Ltd, 2011) Erayman, Mustafa; Ergun, Nuray; Yilmaz, Ebru Sebnem; Ilhan, Emre; Ozcubukcu, Serhat; Eren, Abdil Hakan; Hancer, Tugce[Abstract Not Available]Öğe Prospective analysis of antibiotic susceptibility patterns of MRSA in a Turkish university hospital(2005) Savaş, Lütfü; Duran, Nizami; Önlen, Yusuf; Savaş, Nazan; Erayman, MustafaMethicillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen. The prevalence of MRSA in many countries is increasing and, in some hospitals, more than half of all S. aureus disease isolates are MRSA. MRSA strains are becoming increasingly multiresistant, and have recently developed resistance to vancomycin, which has been used successfully to treat MRSA for more than 30 years. In-vitro determination of resistance patterns of S. aureus is critical in terms of administering suitable antimicrobial treatments. The objective of this study was to identify the frequency of MRSA from various clinical samples and resistance patterns against various antibiotics used broadly for treatments. All isolated S. aureus strains were identified using standard procedures and tested for oxacillin resistance according to methods of the National Committee for Clinical Laboratory Standards. A total of 345 coagulase-positive Staphylococci and 187 MRSA were isolated. We found that the incidence of MRSA in intensive care units (ICUs) and burn center was 23.4% (145/620) and 29.6% (32/108), respectively. This rate was 7% (10/143) in the other units. Resistance rates of MRSA were 29.9% for trimethoprim-sulfamethoxazole, 60.8% for clindamycin, 71.8% for erythromycin, 7.7% for teikoplanin, 90.1% for gentamycin, 88.8% for ofloxacin, 88.1% for norfloxacin and 100% for penicillin. All isolates were found to be sensitive against vancomycin. In our region, although methicillin resistance increased in S. aureus strains, teicoplanin resistance remained low in MRSA, suggesting an effective alternative treatment for Staphylococcus aureus infections. These results indicated that vancomycin seemed to be the only antimicrobial agent effective against MRSA and it could be the choice of medicine in treating multidrug resistant MRSA infection.Öğe Screening wheat orthologs of tomato fw2.2 gene and their expression analysis(Elsevier Sci Ltd, 2011) Ilhan, Emre; Demirel, Ufuk; Eren, A. Hakan; Atak, Mehmet; Erayman, Mustafa[Abstract Not Available]Öğe Serin iklim tahıllarında virüs kaynaklı gen susturma : BSMV kullanımı(2013) İlhan, Emre; Eren, Abdil Hakan; Erayman, MustafaBitkiler doğada canlılıklarını sürdürebilmek için çeşitli savunma mekanizmaları geliştirmişlerdir. RNA ortamlı antiviral savunma mekanizması olarak bilinen Virüs Kaynaklı Gen Susturma (VIGS) bu mekanizmalardan biridir. Virüsle enfekte olmuş bitkilerde, virüs genomuna karşı savunma mekanizması çalışmaktadır. Aynı zamanda hedef geni taşıyan virüs vektörleri homolog içgen mRNA’larını da bozabilmektedir. Bununla birlikte VIGS genin fonksiyonunu anlamada ve fonksiyonel genomik analizleri için kullanılmaktadır. Birçok bitki için virüs vektörleri geliştirilmiştir. Son zamanlarda tahıllar için Arpa Çizgili Mozaik Virüsü (Barley Stripe Mosaic Virus = BSMV) kullanılmaya başlanmıştır. BSMV geniş bir konukçu aralığına sahip pozitif polariteli bir RNA virüsü olup, Hordeivirüs genusunun bir üyesidir. Üç farklı genom RNA (?, ? ve ?)’ dan oluşmaktadır. Bu çalışmada BSMV vektörünün çalışma prensibi ve bazı tahıllarda BSMV – VIGS’in uygulamaları hakkında bilgi verilmiştir.Öğe Transcriptome analysis of wheat inoculated with Fusarium graminearum(Frontiers Media Sa, 2015) Erayman, Mustafa; Turktas, Mine; Akdogan, Guray; Gurkok, Tugba; Inal, Behcet; Ishakoglu, Emre; Ilhan, EmrePlants are frequently exposed to microorganisms like fungi, bacteria, and viruses that cause biotic stresses. Fusarium head blight (FHB) is an economically risky wheat disease, which occurs upon Fusarium graminearum (Fg) infection. Moderately susceptible (cv. Mizrak 98) and susceptible (cv. Gun 91) winter type bread wheat cultivars were subjected to transcriptional profiling after exposure to Fg infection. To examine the early response to the pathogen in wheat, we measured gene expression alterations in mock and pathogen inoculated root crown of moderately susceptible (MS) and susceptible cultivars at 12 hours after inoculation (hai) using 12X135K microarray chip. The transcriptome analyses revealed that out of 39,179 transcripts, 3668 genes in microarray were significantly regulated at least in one time comparison. The majority of differentially regulated transcripts were associated with disease response and the gene expression mechanism. When the cultivars were compared, a number of transcripts and expression alterations varied within the cultivars. Especially membrane related transcripts were detected as differentially expressed. Moreover, diverse transcription factors showed significant fold change values among the cultivars. This study presented new insights to understand the early response of selected cultivars to the Fg at 12 hai. Through the KEGG analysis, we observed that the most altered transcripts were associated with starch and sucrose metabolism and gluconeogenesis pathways.Öğe Transferability of SSR markers from distantly related legumes to Glycyrrhiza species(2014) Erayman, Mustafa; İlhan, Emre; Güzel, Yelda; Eren, Abdil HakanLicorice (Glycyrrhiza spp.) is an important medicinal plant and its distribution of natural habitats has been shrinking day by day due to extensive collection. Genetic diversity identifcation will likely assist in conserving the diferent Glycyrrhiza species. A total of 127 simple sequence repeat (SSR) markers from Medicago truncatula Gaertn., Phaseolus vulgaris L., and Cicer arietinum L. were used and 26 of them were amplifed on Glycyrrhiza genomes. Te highest transferability rate (33%) was obtained from M. truncatula markers, while the highest genetic diversity values were obtained in P. vulgaris markers. Te markers BM153 and PV-ag004 from P. vulgaris had the largest polymorphism information content. Te amplifed primers were also used to identify genetic diversity among three Glycyrrhiza species. Te gene diversity values among Glycyrrhiza species appeared to be similar; however, donor species mostly had lower diversity values than those of Glycyrrhiza species. Additionally, the genetic analysis showed that G. favescens Boiss. subsp. favescens is more distantly related to species G. glabra L. var. glandulifera and G. echinata L. Te number of alleles was mostly higher than in the donor species, possibly proposing a multiallelic and/or polyploid structure in Glycyrrhiza species.
