Browsing by Author "Ilhan, Emre"

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Ameliorative Effects of SL on Tolerance to Salt Stress on Pepper (Capsicum Annuum L.) Plants
(Elsevier France-Éditions Scientifiques Médicales Elsevier, 2025) Yuce, Merve; Aydin, Murat; Turan, Metin; Ilhan, Emre; Ekinci, Melek; Agar, Guleray; Yildirim, Ertan
Salinity is one of the most important problems that threaten agricultural production, especially in arid and semiarid areas. Strigolactones (SLs) are important in providing tolerance to various abiotic stresses in plants. The study was carried out in a hydroponic system to determine the effects of external GR24 (were applied as a foliar spray; 0, 10, and 20 mu M) applications at different doses on plant growth and some physiological, biochemical, and gene expression in two pepper genotype (Yalova and Maras,) grown under salt stress (0 and 100 mM NaCl). Plants were harvested and measured 10 days after the NaCl treatments. At the end of the research, it was determined that salt stress negatively affected plant growth in both genotype. Still, SL applications positively affected plant development both under normal and salt stress. While salt stress increased the amount of hydrogen peroxide (H2O2) and malondialdehyde (MDA), SL application caused a decrease in these parameters. Salt stress negatively affected the amount of chlorophyll and photosynthetic properties in both genotype, whereas SL applications mitigated this negative effect. SL applications caused a significant increase in antioxidant enzyme activities under both normal and salt stress conditions. SL content, which decreased with salt stress, increased with exogenous SL application. The content of other plant nutrients except sodium (Na) and chloride (Cl) decreased significantly in pepper seedlings grown under salt stress. External SL applications increased the uptake of these nutrients, especially under salt stress. In addition, the expression levels of CIPK3, CBL2, CCD7, DMAX2, PsbA, PsbB, PsbP1, TIP1;2, TIP5;1, SOS1, SOS2 and HKT2;2 genes were investigated in this study. It was observed that the expression levels of CCD7, DMAX2, SOS1, SOS2, and HKT2;2 genes increased with salinity stress, especially in the Maras, genotype, while SL applications decreased these expression levels. In the study, it was determined that especially exogenous 20 mu M SL application could significantly reduce the negative effects of salt stress in pepper.
Bitkilerde Yeni Nesil Dizileme Teknolojisi ile Mirna Analizi
(2016) Ilhan, Emre; İnal, Behcet; Eren, Abdil Hakan
MiRNA'lar (mikroRNA), genlerin intron bölgelerinde bulundukları için proteine dönüşemezler ve kendi gen bölgelerinden üretilirler. Bitkilerde 21-24 nükleotitden oluşan miRNA üretimi çekirdekte başlar ve sitoplazmada koordineli bir şekilde devam eder. Bitkilerde gelişim ve stres ile ilişkili genlerin ifade seviyelerinin belirlenmesinden dolayı genom bütünlüğünün korunmasına yardımcı olur ve böylelikle ökaryotik genomların %30'unu kontrol ettiği savunulur. Bitkilerde küçük RNA'lar: miRNA; siRNA'lar, phasiRNA'lar ve NAT-siRNA gibi birçok ana sınıfa ayrılır. Bunları belirlemek ve fonksiyonlarını ortaya çıkarmak için çeşitli analiz yöntemleri geliştirilmiştir. Bu yöntemler Northern Blot, Flow Sitometri, Klonlama, qRT-PCR, Sekanslama ve Mikroarray analizleri ve RNA-seq (transkriptom profillemesi) şeklinde gruplandırılabilir. miRNA-Seq olarak adlandırılan ve Yeni Nesil Dizileme (YND) yöntemlerinden olan bu metotla türe ve dokuya spesifik miRNA'lar kolayca saptanabilmektedir. miRNA çalışmalarında; miRDeep-Seq, miRanalyzer, miRCat, miRExpress, miRTRAP gibi belirli algoritmalar kullanılabilmektedir. Bu derlemede bitkilerde yeni nesil dizileme teknolojilerinin miRNA dizileme (miRNA-seq) çalışmalarındaki uygulama alanı ile ilgili güncel çalışmalar irdelenmiştir.
Characterization of Two-Component System Gene (TCS) in Melatonin-Treated Common Bean Under Salt and Drought Stress
(Springer, 2023) Kasapoglu, Ayse Gul; Ilhan, Emre; Aydin, Murat; Yigider, Esma; Inal, Behcet; Buyuk, Ilker; Agar, Guleray
The two-component system (TCS) generally consists of three elements, namely the histidine kinase (HK), response regulator (RR), and histidine phosphotransfer (HP) gene families. This study aimed to assess the expression of TCS genes in P. vulgaris leaf tissue under salt and drought stress and perform a genome-wide analysis of TCS gene family members using bioinformatics methods. This study identified 67 PvTCS genes, including 10 PvHP, 38 PvRR, and 19 PvHK, in the bean genome. PvHK2 had the maximum number of amino acids with 1261, whilst PvHP8 had the lowest number with 87. In addition, their theoretical isoelectric points were between 4.56 (PvHP8) and 9.15 (PvPRR10). The majority of PvTCS genes are unstable. Phylogenetic analysis of TCS genes in A. thaliana, G. max, and bean found that PvTCS genes had close phylogenetic relationships with the genes of other plants. Segmental and tandem duplicate gene pairs were detected among the TCS genes and TCS genes have been subjected to purifying selection pressure in the evolutionary process. Furthermore, the TCS gene family, which has an important role in abiotic stress and hormonal responses in plants, was characterized for the first time in beans, and its expression of TCS genes in bean leaves under salt and drought stress was established using RNAseq and qRT-PCR analyses. The findings of this study will aid future functional and genomic studies by providing essential information about the members of the TCS gene family in beans.
Chrysin Mitigates Copper Stress by Regulating Antioxidant Enzymes Activity, Plant Nutrient and Phytohormones Content in Pepper
(Elsevier, 2024) Yuce, Merve; Ekinci, Melek; Turan, Metin; Agar, Guleray; Aydin, Murat; Ilhan, Emre; Yildirim, Ertan
Copper (Cu) has an important role in physiological processes. High concentrations of Cu can cause toxic effects for plants. To evaluate the effect of Cu and chrysin (Chr) on the seedling growth, some physiological and biochemical properties of pepper, a factorial experiment in a completely randomized design was carried out. The treatments were T1= Control, T2= 0.1 mM Chr, T3= 0.5 mM Chr, T4= 50 mM Cu, T5= 50 mM Cu+ 0.1 mM Chr and T6= 50 mM Cu+ 0.5 mM Chr. Plant morphological characters were significantly affected by Cu and Chr treatments. The results showed a significant decrease in plant growth parameters due to Cu stress while Chr alleviated negative impacts of Cu on growth these parameters. The hydrogen peroxide (H2O2), malondialdehyde (MDA), prolin and sucrose content increased in pepper seedlings grown under Cu stress conditions. The MDA and H2O2 content showed a decrease with the effect of Chr treatment. Chr treatments also increased prolin and sucrose content of pepper plants under non-stressed conditions. Catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) enzyme activity elevated considerably compared to the control plants under Chr treatments. Moreover, higher values were observed for Chr treated plants under Cu stress. The findings of the study showed that Cu stress lowered all plant nutrient elements except for Cu content. 0.1 and 0.5 mM Chr treatments increased plant nutrient elements content of pepper seedlings under normal and Cu stress conditions. In conclusion, Chr mitigates Cu stress by regulating antioxidant enzymes activity, plant nutrient and phytohormones content in pepper.
Eucalyptus Grandis Yabby Transkripsiyon Faktörlerinin Genom Bazında Analizi
(2018) Ilhan, Emre
YABBY gen ailesi bitki transkripsiyon faktörlerinden biridir. Bu çalışmanın amacı Eucalyptus grandis bitkisinde insiliko olarak YABBY gen ailesinin üyelerini genom çapında belirlemek ve karakterize etmektir. Bu çalışmada çeşitli in silikoyöntemler kullanılmıştır. Ökaliptus genomunda 6 Egra-YABBY proteini tespit edilmiştir. Bu proteinler 18.39 ile 32.38 kDaağırlığına sahip olup, 168-290 arasında değişen amino asitten oluşmuştur. İzoelektrik noktaları 5.54 (Egra-YABBY- 2) ile9.92 (Egra-YABBY- 6) arasındadır. Egra-YABBY genleri arasında tahmini belirlenen ekzonların sayısı en düşük 6, en yüksek7 olarak elde edilmiştir. Filogenetik analizler sonucunda Egra- YABBY proteinleri ile Arabidopsis thaliana ve Vitis viniferatürlerinin proteinleri 5 ana grupta (FIL, INO, CRC, YAB2 ve YAB5) kümelenmiştir. Egra-YABBY-4/Egra-YABBY-5 genleriarasında segmental duplikasyon tespit edilmiştir. Egra-YABBY genlerinin ifade profilleri bu genlerin farklı dokularda ifadeolduğunu ortaya çıkarmış ve bitkinin gelişim süresince çeşitli fizyolojik işlevlerde görev alabildiklerini de göstermiştir. Buçalışmanın sonuçları, ökaliptus bitkisinde YABBY gen ailesinin moleküler temellerinin daha fazla anlaşılması için potansiyelbiyoteknolojik kaynak ve ilave bilgiler sağlayacaktır.
Evaluation of Genetic Diversity Using IPBS-Scot Marker Methods in Native Hawthorn Genetic Resources and Species Identification by Using DNA Barcoding Method
(C M B Assoc, 2023) Sagbas, Halil Ibrahim; Ercisli, Sezai; Aydin, Murat; Ilhan, Emre; Aydinyurt, Recep; Kasapoglu, Ayse Gul; Polat, Yakup
Hawthorn is an important medicinal plant that spreads around the world and is used in traditional Chinese medicine. Its flowers and leaves contain flavonoids, vitamins, organic acids and essential oils. Its fruit is consumed as fresh and dried and is an important plant for human health. In this study, iPBS (Inter Primer Binding Site) and SCoT (Start Codon Target Polymorphism) markers were used to analyze genetic variation among 101 hawthorn genotypes collected from coruh Valley, Turkiye and ITS markers were used for DNA barcoding. Ten iPBS primers were used and a total of 400 alleles were identified from ten iPBS primers with an average of 40 alleles. PIC values ranged from 0.239 (iPBS 2387) to 0.272 (iPBS 2244). Twenty SCoT pri-mers were used and have an average of 50.05 alleles. The PIC values of the primers ranged from 0.251 (SCoT 2) to 0.297 (SCoT 34). For the DNA barcoding study, it was confirmed that the correct region was amplified and sequenced. The genotypes we used in the study matched 14 different accession numbers by searching a BLASTN in the NCBI. NCBI similarity rates of hawthorn genotypes are between 90.83% and 100%. The study emphasizes the genetic diversity of hawthorn grown from seed and the importance of preserving plant genetic resources.
Evaluation of Sodium Azide as a Chemical Mutagen in Developing Cold-Tolerant Quinoa (Chenopodium Quinoa Willd.) Lines
(Springer Int Publ Ag, 2023) Ilhan, Emre; Kasapoglu, Ayse Gul; Turkoglu, Aras; Aygoren, Ahmed Sidar; Muslu, Selman; Aydin, Murat; Haliloglu, Kamil
Quinoa (Chenopodium quinoa Willd.) is an allotetraploid grain crop belonging to the Amaranthaceae family. With a nutritionally well-balanced nature and rich oil, protein, vitamin, carbohydrate, and amino acid content, it has various health benefits. Hybridization programs to induce genetic variation are difficult processes in quinoa plants; however, the introduction of variations through mutation to obtain promising genotypes is much easier. In this research, quinoa cultivar Atlas seeds were exposed to different doses and application durations of sodium azide (NaN3) were cultivated in pots. The present findings revealed distinctive differences in all studied traits between native and mutant plants. NaN3 mutagenesis caused genetic variations that were categorized based on studied traits and RAPD data, which led to two distinct groups during M-2. It was noted that 2 mM + 3 h NaN3 treatments had the greatest effects on genetic variations and germination parameters. Present findings were also confirmed by molecular analysis. This research will provide new insights into molecular breeding programs to be conducted to improve present quinoa genotypes and produce better genotypes.
Expression Analysis and Characterization of the CPP Gene Family of Melatonin-Treated Common Bean Cultivars Under Different Abiotic Stresses
(Elsevier, 2023) Rakhimzhanova, Akgul; Kasapoglu, Ayse Gul; Sapakova, Aigul; Ilhan, Emre; Zharmukhametova, Raushan; Turan, Murat; Ciltas, Abdulkadir
Cysteine-rich polycomb-like protein (CPP) transcription factors, which are prevalent in plants and animals but absent in prokaryotes and fungi, play a significant role in response to various abiotic stresses and the reg-ulation of cell division and development of reproductive tissues in plants. Plants can not avoid environmental challenges because they are soil-bound organisms. Therefore, they activate physiological, pharmacological, and molecular stress defence mechanisms. Among the molecular defence systems is the repression or stimu-lation of the expression of specific genes or gene families by particular transcription factors. Identification of these gene families is of great importance. The CPP gene family has been identified in some plants but not in beans. This study aimed to identify and characterize the CPP genes in the P. vulgaris genome and investigate them using various bioinformatics tools on a genome-wide scale. Expression levels of melatonin and stress factors PvCPP genes were determined by qRT-PCR analysis. Seven CPP genes have been identified in the Pha-seolus vulgaris genome. Except for the PvCPP7 gene, the other PvCPP genes contain two CXC domains. The CPP genes of Phaseolus vulgaris, Arabidopsis thaliana, and Glycine max were analyzed for their phylogenetic rela-tionships and were separated into three distinct groups. In qRT-PCR analysis, 5 CPP genes were studied and their expression levels in stress and melatonin applications were determined and differences in expression levels of PvCPP genes were observed in all treatments. The information generated from this study will serve as a foundation for future functional genomics research by understanding the structure and function of CPP genes in bean genotypes.& COPY; 2023 SAAB. Published by Elsevier B.V. All rights reserved.
Fasulye’de (Phaseolus Vulgaris L.) Ahl Gen Ailesinin Genom Çaplı Analizi ve Karakterizasyonu
(2024) Aydın, Murat; Ilhan, Emre; Yildirim, Ertan; Kasapoğlu, Ayşe Gül; Turan, Murat; Merve, Yüce; Yaprak, Esra
AT-hook motifi nükleer lokalize ailesi (AHL), küçük bir DNA bağlayıcı protein motifi olarak tanımlanmış ve bir transkripsiyon faktörü olarak görev yapmaktadır. Bu transkripsiyon faktörü ailesi, bitki büyüme ve gelişme süreçlerini ve çevresel streslere verilen yanıt mekanizmasını etkilemede önemli bir rol oynamaktadır. Phaseolus vulgaris (fasulye) genomunda 41 AHL geni tanımlanmıştır. İn silico biyoinformatik araçlar kullanılarak, AHL genlerinin karakteristik özellikleri, ekzon-intron yapıları, AHL genlerinin kromozomlardaki yerleşimleri, korunmuş motifleri, promotor bölgeleri, duplikasyon ilişkileri, AHL proteinlerinin protein özellikleri, protein-protein etkileşimleri ve kuraklık ile tuzluluk streslerine karşı AHL genlerinin ifade düzeyleri incelenmiştir. Ayrıca, P. vulgaris’in Arabidopsis thaliana ve Glycine max ile filogenetik ilişkisi belirlenmiştir. Bu proteinlerin amino asit uzunlukları 167 ile 422 ve moleküler ağırlıkları ise 18.19 kDa ile 45.13 kDa arasında değişmektedir. AHL proteinlerinin izoelektrik noktaları (pI) 4,5 ile 10,3 arasında değişmektedir. Pvul-AHL genleri fasulyenin bütün kromozomlarına yayılmış olup, en fazla gen 6 ve 8 numaralı kromozomlarda bulunmaktadır. P. vulgaris’te 14 duplike olmuş gen tespit edilmiş ve ardından yapılan Ka/Ks analizi, tümünün arındırıcı seleksiyona tabi olduğunu göstermiştir. Bu araştırmadan elde edilen bulgular, gelecekte yapılacak fonksiyonel çalışmaların fasulyedeki AHL genlerinin işlevlerini daha iyi anlamamıza yardımcı olacaktır.
Genetic Diversity Analysis of Lesser Burnet (Sanguisorba Minor Scop.) Genotypes Collected from Erzurum Province, Türkiye Using Inter-Simple Sequence Repeat (ISSR) Markers
(Springer, 2025) Karatas, Rufayi; Kasapoglu, Ayse Gul; Gullap, Mehmet Kerim; Ilhan, Emre; Aydin, Murat
This research was conducted over a three-year period from 2021 to 2023, utilizing the ISSR marker system to determine the kinship relationships among populations obtained from seeds of lesser burnet (Sanguisorba minor Scop.) collected from the natural pasture areas of the Erzurum region. The study revealed genetic diversity among 42 burnet genotypes, including 40 genotypes and 2 control cultivars (B & uuml;nyan 80 and Alt & imath;nova). The work with ISSR primers yielded PIC values ranging from 0.24 to 0.34, with an average of 0.30. The highest PIC value (0.34) was obtained from the UBC811 primer, while the lowest value (0.24) was from the UBC812 primer. Among the ISSR primers, UBC811 showed the highest Na, Ne, I, and h values with 2, 1.63, 0.54, and 0.37, respectively, whereas the UBC812 primer displayed the lowest Na, Ne, I, and h values with 2, 1.40, 0.42, and 0.26, respectively. When the results were evaluated as a whole, it was determined that there was no relationship among the collected lesser burnet (S. minor Scop.) populations solely in terms of geographical isolation. Additionally, we recorded that almost all of the 40 collected genotypes significantly differed from the commercial cultivars used as controls, indicating potential for the development of new cultivars.
Genetic Diversity and Population Structure of Barley Cultivars Released in Turkey and Bulgaria Using IPBS-Retrotransposon and SCOT Markers
(Ankara Univ, Fac Agriculture, 2022) Gungor, Huseyin; Ilhan, Emre; Kasapoglu, Ayse Gul; Filiz, Ertugrul; Hossein-Pour, Arash; Valchev, Dragomir; Dumlupinar, Ziya
To improve quantitative traits, it is essential to acknowledge genetic structure and diversity of the crop plants. In this study, 54 barley cultivars released from 1963 to date by different institutes in both Turkey and Bulgaria were screened with 18 iPBS and four SCoT markers to evaluate population structure and genetic diversity. According to the results, while total polymorphic band numbers was identified as 560, the polymorphic ones were found as 530 (438 and 92 amplified bands for iPBS and SCoT markers, respectively). In addition, the average polymorphic band number was found as 24.09. While the average polymorphism information content (PIC) value was 0.48, the average PIC value was 0.48 for iPBS and 0.48 for SCoT markers. The highest PIC value was determined as 0.50. The highest effective number of alleles, Shannon's information index, and Nei's genetic diversity were detected from the iPBS2271 marker at 1.61, 0.52 and 0.35, respectively among the iPBS markers while the highest values were obtained from SCoT-71 marker as 1.55, 0.32 and 0.48, respectively. As a result of a distribution of the 530 amplified bands in 54 barley cultivars, structure analysis showed that the subpopulations in the barley cultivars as a value of k=5. The average expected heterozygosity and fixation indices were identified as 0.234 and 0.322, respectively. Based on DICE similarity index, Marti and Zahir cultivars were found the most similar barley cultivars with 75% genetic similarity, whereas Ozdemir and Karatay 94 and Tosunpasa and Konevi cultivars were found 73% similar. On the other hand, Bayrak and Avci-2002 were found the most diverse cultivars with 19.9% genetic similarity. As a result, the barley cultivars released in Turkey and Bulgaria were found varying and, the genetic diversity and statistics index analysis indicated that iPBS and SCoT markers are powerful markers to perform genetic diversity analysis.
Genetic Structure and Diversity of Adonis L. (Ranunculaceae) Populations Collected from Turkey by Inter-Primer Binding Site (Ipbs) Retrotransposon Markers
(TÜBİTAK Scientific & Technological Research Council Turkey, 2019) Hossein-Pour, Arash; Karahan, Faruk; Ilhan, Emre; Ilcim, Ahmet; Haliloglu, Kamil
The genus Adonis L. is a member of Ranunculaceae and consists of perennial and annual herbaceous plants included in the tribe Adonideae under the subfamily Ranunculoideae. Botanically, Ranunculaceae comprises vital medicinal plants. Molecular markers are one of the most effective tools for exploring genetic variation that can enhance breeding efficiency. To identify the genetic diversity of 62 Adonis ecotypes collected from different regions in Turkey, the interprimer binding site (iPBS) retrotransposon system was used. Of the 83 iPBS primers used, 10 provided sufficient polymorphic data, generating a total of 204 alleles. The number of iPBS bands per individual was 3.29, and the number of alleles per polymorphic locus ranged from 8 to 35, with an average of 20.30. The average polymorphism percentage was 99.50%, and polymorphic information content ranged from 0.16 to 0.39. The highest average number of alleles, Nei's genetic diversity (h), and Shannon's information index (I) were obtained from A. volgensis species (1.64, 0.39, and 0.58, respectively), whereas the lowest values (1.41, 0.29, and 0.46, respectively) were found in A. flammea species. The analysis of molecular variance revealed significant variance within the population (71%), whereas no significant genetic variation was observed among the different species (29%). Cluster analysis according to unweighted pair-group mean average (UPG MA) divided 62 Adonis ecotypes into four major clusters. According to the principal coordinate analysis, the first three principal coordinates accounted for 81.51% of total variation. Genetic structure analysis of the studied germplasm using the Bayesian method revealed four subpopulations with an average of 0.2634 for expected heterozygosity and 0.2154 for population differentiation measurements. The results of this study suggested that iPBS markers could be used in the identification of genetic diversity among the Adonis species.
Genome-Wide Analysis and Characterization of Eucalyptus Grandis TCP Transcription Factors
(Ankara University, Faculty of Agriculture, 2023) Ilhan, Emre; Kasapoglu, Ayse Gul; Muslu, Selman; Aygoren, Ahmed Sidar; Aydin, Murat
Teosinte branched/Cycloidea/Proliferating cell factors (TCPs), a small transcription gene family, serve in developmental processes such as branching, flowering, and growth of plants. In this study, the TCP transcription gene family of eucalyptus, which is considered important for its medicinal and industrial uses, was bioinformatically investigated. A total of 16 Eucalyptus grandis TCP (Egra-TCP) genes were found to be distributed on chromosomes 1, 2, 4, 6, 7, 9, 10 and 11. Several segmentally-duplicated gene couples including Egra-TCP-7/ Egra-TCP-11,-13 and-16, Egra-TCP-6/Egra-TCP-12 and-15, Egra-TCP-12/ Egra-TCP-15 and Egra-TCP-11/Egra-TCP-13 were discovered. Egra-TCPs were divided into three main clades based on phylogenetic analysis, motif, and gene structure. While Egra-TCP-10 has the highest molecular weight with 47.19 kDa, the lowest was Egra-TCP-1 with 21.68 kDa. Twelve Egra-TCP genes were found to have no introns, while the Egra-TCP-7,-15, and-16 genes had a single intron. The orthologous relationships among E. grandis/Arabidopsis thaliana and E. grandis/Vitis vinifera were identified through a synteny analysis. Digital gene expression profiles of Egra-TCP genes in tissues such as xylem, phloem, shoot tips, young and mature leaf revealed a high expression pattern. The findings of this study contributes to existing knowledge in the biotechnology field by providing contributing to our understanding of the molecular basis of the TCP gene family in the eucalyptus plant.
Genome-Wide Analysis and Characterization of Fba (Fructose 1,6-Bisphosphate Aldolase) Gene Family of Phaseolus Vulgaris L
(2024) Aydın, Murat; Ilhan, Emre; Kasapoğlu, Ayşe Gül; Turan, Murat; Dikbas, Neslihan; Alım, Şeyma; Polat, Aysun
Fructose-1,6-biphosphate aldolase (FBA) genes have important roles in plant stress responses. At the same time, these genes positively affect growth and development in plants. FBA is involved in gluconeogenesis, glycolysis, and the Calvin-Benson cycle, and it is an enzyme that plays an important role in signal transduction of these stages. This study aims to determine and characterize the FBA gene family in the bean genome. As a result of the study, 7 Pvul-FBA genes were determined in the bean (Phaseolus vulgaris L.) genome. The highest amino acid number of Pvul-FBA proteins was determined in the Pvul-FBA-1 gene (1374), and the highest molecular weight (43.03 kDa) was determined in the Pvul-FBA-7 gene. Again, the highest isoelectric point (8.03) was determined in the Pvul-FBA-3 gene. It has been determined that the Pvul-FBA-6/Pvul-FBA-7 genes are segmental duplicated genes. The main four groups were obtained according to the phylogenetic analysis consisting of FBA proteins of three plants (P. vulgaris, Glycine max, and Arabidopsis thaliana). As a result of interproscan analysis, Motif-1, 2, 3, 4 and 5 were found to contain the fructose-bisphosphate aldolase domain. According to in silico gene expression analysis, it was determined that the expression rates of Pvul-FBA genes increased or decreased under salt and drought stress conditions. Synteny analyses of FBA genes in common bean and A. thaliana plants showed that these three plants have a relationship in terms of FBA genes. The results of this research will allow a better designation of the molecular structure of the FBA gene family in common bean.
Genome-Wide Analysis and Characterization of Sabath Gene Family in Phaseolus Vulgaris Genotypes Subject to Melatonin Under Drought and Salinity Stresses
(Springer, 2023) Aygoren, Ahmed Sidar; Gunes, Ebru; Muslu, Selman; Kasapoglu, Ayse Gul; Yigider, Esma; Aydin, Murat; Ilhan, Emre
The SABATH gene family is a plant-specific class of small molecule methyltransferases. The first goal of this study was to conduct a genome-wide analysis and in silico characterization of SABATH gene family members in Phaseolus vulgaris. The second goal was to see how the members of the SABATH gene family react to salt and drought stress, as well as their expression patterns when melatonin is added to the mix. Within the scope of the study, 18 Pvul-SABATH proteins were discovered in the Phaseolus vulgaris genome using various in silico methods. These proteins ranged in size from 30.18 to 42.73 kDa and were made up of 268 to 387 amino acids. The Pvul-SABATH proteins had isoelectric points ranging from 4.95 (Pvul-SABATH-8) to 6.08 (Pvul-SABATH-2 and -3). The Pvul-SABATH genes were found to have at least three but no more than four exons. According to the results of the phylogenetic analysis, Pvul-SABATH proteins were found to be clustered in three major groups with Arabidopsis thaliana, Glycine max species, and various methyltransferase members. There was segmental duplication between the Pvul-SABATH-1 and Pvul-SABATH-5 genes, as well as the Pvul-SABATH-10 and Pvul-SABATH-14 genes. By comparing the expression level of Pvul-SABATH genes, their different expression levels depending on the bean cultivars were discovered. Moreover, these findings suggested that Pvul-SABATH genes may play a role in the growth and development process of the plants in response to various biotic and abiotic stresses. The findings of this study, which is the first to look at the SABATH gene family in Phaseolus vulgaris, are thought to be beneficial in plant biotechnology and molecular biology.
Genome-Wide Analysis and Characterization of the Pif Gene Family Under Salt and Drought Stress in Common Beans (Phaseolus Vulgaris L.)
(2022) Aydın, Murat; Ilhan, Emre; Kasapoğlu, Ayşe Gül; Turan, Murat; Aygören, Ahmed Sidar; Muslu, Selman; Isıyel, Murat
The purpose of this study was to identify and describe members of the phytochrome-interacting factors (PIFs) gene family including the basic helix loop helix (bHLH) binding site in Phaseolus vulgaris plants, as well as to investigate their responses to salt and drought stress. Various tools of in silico approaches were used to identify five Pvul-PIF gene families in the P. vulgaris genome. This gene family contained 324 to 726 amino acids and has molecular weights ranging from 35.11 kDa to 77.67 kDa. The theoretical isoelectric points range from 6.03 (Pvul-PIF-3.3) to 8.30 (Pvul-PIF-3.2). Pvul-PIF proteins were shown to be clustered in three main groups with Arabidopsis thaliana, Populus trichocarpa, Solanum lycopersicum, Zea mays, Arachis hypogaea L., Oryza sativa, Vitis vinifera, Glycine max, and Phaseolus vulgaris species as a result of the phylogenetic study. Segmental duplication was detected between Pvul-PIF-3.2, Pvul-PIF-3.3 and Pvul-PIF-3.1 genes, Pvul-PIF-4.1 and Pvul-PIF-4.2 genes and Pvul-PIF-3.3 and Pvul-PIF-3.1 genes. When the expression patterns of the Pvul-PIF genes were examined, it was observed that they had different levels of expression under salt and drought stress and that they may be involved in specific biological and molecular processes in response to different abiotic and biotic stresses. The results of this research, which were established for the first time in response to salt and drought stress in P. vulgaris of the PIF gene family, will be a valuable source of knowledge and additional information in the fields of plant biotechnology, agricultural biotechnology, and molecular biology.
Genome-Wide Analysis and Functional Identification of Kcs Gene Family Under Drought and Salt Stresses in Phaseolus Vulgaris L
(2023) Aydın, Murat; Ilhan, Emre; Yildirim, Ertan; Kasapoğlu, Ayşe Gül; Turan, Murat; Yılmaz, Ceren; Muslu, Selman
Β-ketoacyl-CoA synthase (KCS) is an important enzyme that catalyzes the biosynthesis of very-long-chain fatty acids (VLCFAs). In this study, the genome-wide analysis and functional characterization of the KCS gene family members in common bean (Phaseolus vulgaris L.) plants were conducted, and the response of the identified gene family to abiotic stresses was evaluated. In this study, 19 KCS genes were identified and characterized in the P. vulgaris genome. The molecular weights of these KCS proteins ranged from 49.14 kDa to 60.57 kDa, their amino acid lengths varied from 437 to 534, and their pI values ranged from 8.81 to 9.47, indicating a basic nature. Segmental and tandem duplications were observed in the Pvul-KCS gene family. Phylogenetic analysis revealed that Pvul-KCS proteins clustered into three main groups with Arabidopsis thaliana and Glycine max species. Comparative mapping analysis was also conducted with A. thaliana and G. max. Expression profile comparisons indicated that these genes had different expression levels in common bean varieties and played a role in the plant’s response to biotic and abiotic stresses. This study provides important insights into the biological functions of KCS genes in Phaseolus vulgaris and offers valuable information for improving drought and salt stress tolerance in common beans.
Genome-Wide Analysis of Glutathione S-Transferase Gene Family in P. Vulgaris Under Drought and Salinity Stress
(Springer, 2024) Muslu, Selman; Kasapoglu, Ayse Gul; Gunes, Ebru; Aygoren, Ahmed Sidar; Yigider, Esma; Ilhan, Emre; Aydin, Murat
The enzymes known as glutathione S-transferases (GST), which are present in many evolved organisms, are essential for the defense against reactive oxygen species. GSTs have a role in the development of defenses against biotic and abiotic challenges, especially defending plants from various stresses such as drought, salinity, and heavy metal. This study uses a genome-wide investigation of the GST gene family in Phaseolus vulgaris to pinpoint several distinctive traits. 55 Pv-GST proteins have been identified in P. vulgaris. The molecular weights of these proteins range from 15.02 kDa to 47.99 kDa; the range of amino acid numbers 132 to 420 and the range of theoretical isoelectric points 5.03 to 9.61 were identified. Pv-GST genes are estimated to have at least 2 and a maximum of 10 exons, with an average of 4 exons. Phylogenetic analysis was performed with GST proteins from Arabidopsis thaliana, Glycine max, and Phaseolus vulgaris species, and subfamilies of these GSTs were identified. Using RNAseq data, the expression profiles of Pv-GST genes in leaf tissue of common bean during drought and salinity stress were identified. Using the obtained sequence data, primers for qRT-PCR were designed. Changes in the expression profiles of GST genes caused by salt and drought stress and melatonin treatments in two different common bean cultivars were determined by qRT-PCR experiments. Under drought and salt stress, the expression levels of GSTs decreased, while melatonin treatment with few exceptions increased these expression levels. As a result of this study, it was observed that Pv-GST genes may play a role in the growth and development of bean and may be involved in the response to abiotic stresses. Moreover, the results of this study will provide a basis for functional gene research and the expression profiles and qRT-PCR results under different stress conditions in common bean will provide a valuable contribution to the understanding of the functions of the GST gene family.
Genome-Wide Analysis of Mir172-Mediated Response to Heavy Metal Stress in Chickpea (Cicer Arietinum L.): Physiological, Biochemical, and Molecular Insights
(BMC, 2024) Ucar, Sumeyra; Yaprak, Esra; Yigider, Esma; Kasapoglu, Ayse Gul; Oner, Burak Muhammed; Ilhan, Emre; Aydin, Murat
BackgroundChickpea (Cicer arietinum L.), a critical diploid legume in the Fabaceae family, is a rich source of protein, vitamins, and minerals. However, heavy metal toxicity severely affects its growth, yield, and quality. MicroRNAs (miRNAs) play a crucial role in regulating plant responses to both abiotic and biotic stress, including heavy metal exposure, by suppressing the expression of target genes. Plants respond to heavy metal stress through miRNA-mediated regulatory mechanisms at multiple physiological, biochemical, and molecular levels. Although the Fabaceae family is well represented in miRNA studies, chickpeas have been notably underrepresented. This study aimed to investigate the effects of heavy metal-induced stress, particularly from 100 mu M concentrations of cadmium (Cd), chromium (Cr), nickel (Ni), lead (Pb), and 30 mu M arsenic (As), on two chickpea varieties: ILC 482 (sensitive) and Azkan (tolerant). The assessment focused on physiological, biochemical, and molecular parameters. Furthermore, a systematic characterization of the miR172 gene family in the chickpea genome was conducted to better understand the plant's molecular response to heavy metal stress.ResultsVariance analysis indicated significant effects of genotype (G), treatment (T), and genotype-by-treatment (GxT) interactions on plant growth, physiological, and biochemical parameters. Heavy metal stress negatively impacted plant growth in chickpea genotypes ILC 482 and Azkan. A reduction in chlorophyll content and relative leaf water content was observed, along with increased cell membrane damage. In ILC 482, the highest hydrogen peroxide (H2O2) levels in shoot tissue were recorded under As, Cd, and Ni treatments, while in Azkan, peak levels were observed with Pb treatment. Malondialdehyde (MDA) levels in root tissue were highest in ILC 482 under Cd and Ni exposure and in Azkan under As, Cr, and Cd treatments. Antioxidant enzyme activities, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX), were significantly elevated under heavy metal stress in both genotypes. Gene expression analysis revealed upregulation of essential antioxidant enzyme genes, such as SOD, CAT, and APX, with APX showing notable increases in both shoot and root tissues compared to the control. Additionally, seven miR172 genes (miR172a, miR172b, miR172c, miR172d, miR172e, miR172f, and miR172g) were identified in the chickpea genome, distributed across five chromosomes. All genes exhibited conserved hairpin structures essential for miRNA functionality. Phylogenetic analysis grouped these miR172 genes into three clades, suggesting strong evolutionary conservation with other plant species. The expression analysis of miR172 and its target genes under heavy metal stress showed varied expression patterns, indicating their role in enhancing heavy metal tolerance in chickpea.ConclusionsHeavy metal stress significantly impaired plant growth and physiological and biochemical parameters in chickpea genotypes, except for cell membrane damage. The findings underscore the critical role of miR172 and its target genes in modulating chickpea's response to heavy metal stress. These insights provide a foundational understanding for developing stress-tolerant chickpea varieties through miRNA-based genetic engineering approaches.
Genome-Wide Analysis of Phaseolus Vulgaris C2c2-Yabby Transcription Factors Under Salt Stress Conditions
(Springer Heidelberg, 2017) Inal, Behcet; Buyuk, Ilker; Ilhan, Emre; Aras, Sumer
The aim of this study was to identify and characterize the C2C2-YABBY family of genes by a genome-wide scale in common bean. Various in silico approaches were used for the study and the results were confirmed through common molecular biology techniques. Quantitative real-time PCR (qPCR) analysis was performed for identified putative PvulYABBY genes in leaf and root tissues of two common bean cultivars, namely Yakutiye and Zulbiye under salt stress condition. Eight candidate PvulYABBY proteins were discovered and the length of these proteins ranged from 173 to 256 amino acids. The isoelectric points (pIs) of YABBY proteins were between 5.18 and 9.34 and ranged from acidic to alkaline, and the molecular weight of PvulYABBYs were between 18978.4 and 28916.8 Da. Three segmentally duplicated gene couples among the identified eight PvulYABBY genes were detected. These segmentally duplicated gene couples were PvulYABBY-1/PvulYABBY-3, PvulYABBY-5/PvulYABBY-7 and PvulYABBY-6/PvulYABBY-8. The predicted number of exons among the PvulYABBY genes varied from 6 to 8 exons. Additionally, all genes found included introns within ORFs. PvulYABBY-2, -4, -5 and -7 genes were targeted by miRNAs of five plant species and a total of five miRNA families (miR5660, miR1157, miR5769, miR5286 and miR8120) were detected. According to RNA-seq analysis, all genes were up- or down-regulated except for PvulYABBY-1 and PvulYABBY-6 after salt stress treatment in leaf and root tissues of common bean. According to the qPCR analysis, six out of eight genes were expressed in the leaves but only four out of eight genes were expressed in the roots and these genes exhibited tissue-and cultivar-specific expression patterns.