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    Bread wheat responds salt stress better than einkorn wheat does during germination
    (2016) Aslan, Didem; Zencirci, Nusret; Etöz, Murat; Ordu, Bülent; Bataw, Sara
    Salt stress during germination degenerates crop establishment and declines yield in wheat (Triticum subsp.). Against salt (NaCl) stress, we investigated 12 bread (Triticum aestivum L.) and 10 einkorn wheat (T. monococcum subsp. monococcum) entries for germination rate, germinating power, coleoptile length, shoot length, root length, shoot/root length ratio, root fresh weight, root dry weight, and root fresh/dry weigh ratio. An effective blocking in variance analysis improved statistical significance and differentiation between germination stages and wheat entries. Salt total and salt ranking tolerance indices grouped the wheat entries into tolerant (Bayraktar 2000, Gerek 79, İkizce 96, Gün 91, Demir 2000, and Momtchil) and susceptible ones (Population-4, Population-14, Population-15, Population-9, Population-11, and Population-10). The best coleoptile length and root fresh weight developments occurred between 0 and 0.15 M and root length between 0 and 0.10 M salt doses. Coleoptile length, root fresh weight, and root dry weight started decreasing at 0.20 M. Pearson linear correlation coefficients were significant at different levels for coleoptile length, root fresh weight, and root dry weight. Spearman correlation coefficients were not significant between the worst salt affected characters of coleoptile length, shoot length, root length, root fresh weight, and root dry weight characters under the control treatment but were significant under salt stress. A significant PC value of 0.356 was recorded for root dry weight, 0.335 for root length, 0.310 for shoot root length ratio, and 0.309 for root fresh weight in PC 1. The first three PCs accounted for 90.52% of total variation. The highest PC was PC1 (71.946%), followed by PC2 (11.098%), and PC3 (7.481%). The dendrogram of all wheat entries clearly differentiated bread and einkorn wheats as both salt indices did. Here, it seemed, then, that those bread wheat cultivars were more salt tolerant than einkorn populations, most likely because of their geographic origin differences.
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    Identification and characterization of conserved micrornas in wheat (Triticum monococcum ssp. monococcum) by high-throughput sequencing and computational analysis
    (Bolu Abant İzzet Baysal Üniversitesi, 2016) Bataw, Sara; Zencirci, Nusret; Ünlü, Ercan Selçuk
    Buğday; yıllık 615.8 milyon metre küp tonun üzerindeki yıllık hasatıyla, zirvedeki üç ana tahılın en önemli ikinci tarım ürünüdür. Kuraklık ve tuzluluk buğday çeşitlerinin verimini ve kalitesini en fazla etkileyen olumsuz çevresel stres faktörleridir. Bitkiler, öte yandan, bu abiyotik streslerle mücadele etmek için kendi savunma sistemlerini geliştirmişlerdir. Savunma mekanizmalarından biri microRNA'lar (miRNAlar) yoluyla gen açıklanmasının değiştirilmesidir. miRNAlar spesifik mRNAların 3'-dönüştürülmemiş bölgesine (3'-UTR) bağlanarak post transkripsiyonel seviyelerde gen ifadelerini düzenleyen ortalama 22 nükleotit uzunluğuyla kodlamayan RNAların geniş bir sınıfıdır. miRNA genetik modifikasyonlarI, bu nedenle kurak ve tuz stresine karşı olan tepkiyi anlama ve buğdayın kurak ve tuz toleransını geliştirme potansiyeline sahiptir. Son yıllarda miRNAların çeşitli bitki türleri ve buğday genomlarında tuz ve kuraklık stresine tabi tutulduğu çalışmalar rapor edilmesine krşın siyez (Triticum monococcum ssp. monococcum) buğdayında henüz herhangi bir çalışma yapılmamıştır. Bu çalışma; korunmuş miRNAları kurak ve tuz stresi altında, gelecek generasyon dizilemesi ve simulasyon analizinin bir kombinsayonu ile incelemişitr. Bu yaklaşımın kullanılmasıyla 15,139,448 ham okumadan 75,164 özgün okuma elde edilmiş ve 142 belirgin miRNA familyasından 167 olgun miRNA dizisi tanımlanmıştır. Aynı şekilde; Triticum urartu tabanı kullanılarak ikincil yapı tahminleri microRNA prekursorları elde edilmiştir. Sonuçta; ve Triticum urartu genomunun %100 homologu olan 111 prekursor dizileri Mfold bilgisayar programı ile analiz edilmiştir. Bu çalışmadan elde edilen veriler; siyez buğdayının epigenetik düzenlenmesindeki transkriptlerin rolüne ilişkin bir araştırma başlatılabilmesi için gerekli kritik bilgilerin elde edilmesi ve miRNAlarla bunların dahil oldukları biyolojik süreçlerin daha iyi anlaşılabilmesi için uygun bir zemin sağlayacaktır.
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    Identification of conserved microRNA molecules in einkorn wheat (Triticum monococcum spp. monococcum) by deep sequencing analysis
    (Wiley-Blackwell, 2016) Ünlü, Ercan Selçuk; Bataw, Sara; Kaya, Özge; Zencirci, Nusret
    Glucocorticoid receptor (GR) is one of the involved receptors and its gene has been recognized as a candidate gene for major depressive disorder and bipolar disorder. The involvement of the GR gene (NR3C1) locus on human chromosome 5q31-q32. The N363S (rs6195) is located within exon 2 and changes the second base of codon 363, leading to asparagine to serine substitution in the transactivation domain of GR. In this study, we aimed to examine the role of NR3C1 N363S polymorphisms in genetic susceptibility to MDD development in a Turkish population. A total of 100 consecutive unrelated adult patients with documented medical records of MDD were from outpatient Psychiatry Clinic in Gaziosmanpasa University Research and Training Hospital, Tokat, Turkey by referral from the treating physician, after obtaining initial verbal consent to participate in the study. In addition, 100 control subjects from the same area as the patients, and comprising blood donors, healthy volunteers were enrolled this study. DNA was isolated from peripheral blood samples and the N363S variant was screened by the RT-PCR technique. 99 out of the 100 MDD patients were found to be AA genotype at the N363S (AA genotype frequency 0.99; A-allele frequency 0.995). Also, 1 out of the 100 MDD patients was found to be AG genotype (AG genotype frequency 0.01; G-allele frequency 0.005). No homozygote for the rare G-allele was seen. Significantly more frequent occurrence of allele-A in N363S polymorphism was observed in the group of the patients with MDD in comparison with the control group (OR: 4.061, 95% CI: 0.449–36.660, v2 : 1.823, p: 0.177). For genotype AG versus AA, no significant correlation was demonstrated between patients and the control group with respect to the investigated SNP (OR: 0.242, 95% CI: 0.027–2.208, v2 : 1.846, p: 0.1742). This study was supported by the Gaziosmanpas a University Scientific Research Fund (GOU BAP2013/8).
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    Identification of conserved miRNA molecules in einkorn Wheat (Triticum Monococcum subsp. Monococcum) by using small RNA sequencing analysis
    (2018) Ünlü, Ercan Selçuk; Bataw, Sara; Şen, Didem Aslan; Şahin, Yunus; Zencirci, Nusret
    Triticum monococcum subsp. monococcum as a first cultivated diploid wheat species possesses desirable agronomic and quality characteristics. Drought and salinity are the most dramatic environmental stress factors that have serious impact on yield and quality of crops; however, plants can use alternative defense mechanisms against these stresses. The posttranscriptional alteration of gene expression by microRNAs (miRNAs) is one of the most conserved mechanisms. In plant species including wheat genomes, miRNAs have been implicated in the management of salt and drought stress; however, studies on einkorn wheat (Triticum monococcum subsp. monococcum) are not yet available. In this study, we aimed to identify conserved miRNAs in einkorn wheat using next generation sequencing technology and bioinformatics analysis. In order to include a larger set of miRNAs, small RNA molecules from pooled plant samples grown under normal, drought, and salinity conditions were used for the library preparation and sequence analysis. After bioinformatics analysis, we identified 167 putative mature miRNA sequences belonging to 140 distinct miRNA families. We also presented a comparative analysis to propose that miRNAs and their target genes were involved in salt and drought stress control in addition to a comprehensive analysis of the scanned target genes in the T. aestivum genome.