Browsing by Author "Yer E.N."

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Age-related changes of some chemical components in the leaves of oriental beech (fagus orientalis lipsky.)
(2019-12-01) Turfan N.; Ayan S.; Yer E.N.; Özel H.B.
Background and Purpose: This study presents the analysis of photosynthetic pigments, proline, total soluble protein, total amino acids, glucose, sucrose, total soluble sugars, total amount of phenolic compounds and flavonoids, malondialdehyde (MDA) and hydrogen peroxide (H2O2) concentration in the leaf samples collected from oriental beech trees, which are naturally spread in Kastamonu Province, Turkey, with differing ages, enzyme activities of ascorbate peroxidase (APX), catalase (CAT) and superoxide dismutase (SOD). Material and Methods: The research was carried out on oriental beech trees (Fagus orientalis L.) of different ages located at 1300 m high elevation in Ahlat Village of Kastamonu Province, Turkey. Oriental beech trees of different ages (≥25, ≥50, ≥100, ≥200 and ≥600 years-old) constituted the material of this study. In leaf samples taken from trees of different ages, photosynthetic pigments (chlorophyll a, chlorophyll b, total chlorophyll and carotenoid), proline, total soluble protein, total amino acid, glucose, sucrose, total soluble sugars, the amount of total phenolic compounds and flavonoids, MDA, H2O2 concentration, enzyme activities of APX, CAT and SOD, as well as the relationship between the total content of C, N and H elements and the tree ages were studied. Results: As a result of the research conducted, significant differences were determined in terms of chlorophyll, total phenolic compound, flavonoid, glucose, amounts of sucrose, nitrogenous compounds, proline, total soluble protein, MDA, H2O2 concentrations, and the activities of APX, CAT and SOD in the leaves of oriental beech trees with differing ages. The highest content of chlorophyll a was found to be in the youngest age group of ≥25 years. Total chlorophyll is low in young trees and high in middle-aged, old and very old trees. According to the results obtained, it was concluded that the MDA and H2O2 concentrations in the trees did not vary depending on the age of trees only, but also on the genotype, environmental conditions and metabolic activities. It was concluded that the fact that the total chlorophyll, phenolic compounds and sucrose content in oriental beech trees are high and that MDA content is low could have an influence on the long life of ≥600 years-old oriental beech trees. Conclusions: The activity of photosynthesis is related to leaf characteristics more than the age of trees.
ANTIOXIDANT VARIABILITY OF THE SEEDS IN CORE AND MARGINAL POPULATIONS OF TAURUS CEDAR (Cedrus libani A. Rich.)
(2018-01-01) Ayan S.; Turfan N.; Yer E.N.; Šeho M.; Özel H.B.; Ducci F.
Genetic diversity is the basis for adaptation and survival of tree species under changing environmental conditions, representing the key issue of stability and productivity of forest ecosystems. In this study, core and marginal populations of Taurus cedar (Cedrus libani A. Rich.) were investigated due to their importance in gene conservation. Assessment of genetic diversity in isolated populations is of great importance for the conservation and improvement programs. Under global climate change conditions, they may possess genotypes of future adaptive potential. The aim of this study is to determine the amount of proline to understand water deficiency stress of the population, total soluble proteins, MDA, H 2 O 2 , α-amylase, the variability of antioxidant as CAT, SOD, APX and GuPX of Taurus Cedar seeds fromfive core populations (Kahramanmaraş-Andırın/Elmadağı (AND), Adana-Pozantı/ Pozantı (POZ), Mersin-Anamur/Abanoz (ANA), Antalya-Finike/Aykırıçay (FIN) and Antalya-Kaş/Karaçay (KAS)) and one marginal provenance (Amasya-Tokat-Niksar/Çatalan (NIK)) in Turkey. According to the results, a significant difference was detected between populations. Significantly higher amounts of proline were detected for ANA (7,46 µmol/g) and POZ (7,22 µmol/g) populations, whereas the lowest amounts of proline were detected in KAS (3,98 µmol/g) population, which represent the optimal distribution of Taurus cedar. This finding indicates that POZ and ANA populations, in the transition zone from Mediterranean region to steppe territory, are more resistant to the frost, than the other populations. The highest α-amilase enzyme amount was detected in POZ population, growing in the optimum range for Taurus cedar. Significantly higher levels of H 2 O 2 were detected in NIK (11,97 µmol/g) and ANA (11,60 µmol/g). This is an indication of higher levels of oxidative stress in the seed samples of these populations. With the present research it’s verified that, enzymes such as SOD, CAT, GuPX and APX, controlling reactive oxygen species (ROS) levels in plant cells, are the elements of the antioxidant defence system functioning as protective mechanisms for plants against stress conditions. From the practical point of view, improvement in afforestation performance can be achieved on the steppe of Central Anatolia Region holding the potential afforestation areas of Turkey, through use of forest reproductive materials from POZ and ANA stands with their higher resistance against stress, and NIK as an isolated and marginal population.
Determination of deadwood volume & the affecting factors in Trojan fir forests
(2017-01-01) Topacoǧlu O.; Kara F.; Yer E.N.; Savci M.
Deadwood is one of the important components of forest ecosystems since it is considered as an indicator of resource availability and biodiversity, an important carbon stock, and habitat for insect and fungal species. Removal of dead trees from forests may result in the elimination of many species, and also reduce the number and density of species. Trojan fir (Abies nordmanniana subsp. equi-trojani) is known to be rich in species composition; however, our knowledge on the amount and type of deadwood (i.e. standing or lying) in these forests is limited. Thus, in this study, deadwood quantity and type in Trojan fir forests were determined. In addition, less is known about the factors that influence the amount of deadwood volume; therefore, the effects of stand type, elevation (m), aspect, quadratic mean diameter (QMD) (cm), basal area (BA) (m2 ha-1) and stand volume (m3 ha-1) on deadwood volume were also observed. Stand type, QMD and BA significantly affected the volume of deadwood in Trojan fir forests while stand volume, elevation and aspect had no influence on the deadwood volume. In comparison to the values in the literature, the amount of deadwood observed seems to be acceptable across all stand types. Given the initial results from this study, it can be recommended that large scale deadwood assessments are needed in Turkey, and it can be combined with the current inventory system.
Drought-Responsive Hsp70 Gene Analysis in Populus at Genome-Wide Level
(2016-04-01) Yer E.N.; Baloglu M.C.; Ziplar U.T.; Ayan S.; Unver T.
The heat shock protein 70 (Hsp70) family members are known as molecular chaperones. They play a crucial role in protecting plant cells and tissues from thermal or abiotic stress through protein folding and in assembly, stabilization, activation, and degradation processes. Although many studies have been performed to identify molecular functions of individual family members, there is a limited study on genome-wide identification and characterizations of Hsps in the Populus model tree genus. We have identified 34 poplar Hsp70 genes, which were phylogenetically clustered into three major groups. Gene structure and motif composition are relatively conserved in each group. Mainly tandem and infrequently segmental duplications have a significant role in poplar Hsp70 gene expansion. The in silico microRNA (miRNA) and target transcript analyses identified that a total of 19 PtHsp70 genes were targeted by 27 plant miRNAs. PtHSP70-14 and PtHSP70-33 are the most targeted by miR390 and miR414 family members, respectively. For determination of drought response to Hsp70 genes, publicly available RNA-seq data were analyzed. Poplar Hsp70s are differentially expressed upon exposure to different drought stress conditions. Expression analysis of PtHsp70 genes was also examined under drought stress in drought-sensitive and drought-resistant Populus clones with quantitative real-time PCR (qRT-PCR). PtHsp70-16 and PtHsp70-26 genes might provide adaptation to drought stress for both clones. Because of high expression responses to drought in only resistant Populus clone, PtHsp70-25 and PtHsp70-33 genes might be used for determination of drought-tolerant clones for molecular breeding studies. This research provides a fundamental clue for contribution of PtHsp70s to drought tolerance in poplar.
Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes
(2017-01-01) Celik Altunoglu Y.; Baloglu M.C.; Baloglu P.; Yer E.N.; Kara S.
Late embryogenesis abundant (LEA) proteins are large and diverse group of polypeptides which were first identified during seed dehydration and then in vegetative plant tissues during different stress responses. Now, gene family members of LEA proteins have been detected in various organisms. However, there is no report for this protein family in watermelon and melon until this study. A total of 73 LEA genes from watermelon (ClLEA) and 61 LEA genes from melon (CmLEA) were identified in this comprehensive study. They were classified into four and three distinct clusters in watermelon and melon, respectively. There was a correlation between gene structure and motif composition among each LEA groups. Segmental duplication played an important role for LEA gene expansion in watermelon. Maximum gene ontology of LEA genes was observed with poplar LEA genes. For evaluation of tissue specific expression patterns of ClLEA and CmLEA genes, publicly available RNA-seq data were analyzed. The expression analysis of selected LEA genes in root and leaf tissues of drought-stressed watermelon and melon were examined using qRT-PCR. Among them, ClLEA-12-17-46 genes were quickly induced after drought application. Therefore, they might be considered as early response genes for water limitation conditions in watermelon. In addition, CmLEA-42-43 genes were found to be up-regulated in both tissues of melon under drought stress. Our results can open up new frontiers about understanding of functions of these important family members under normal developmental stages and stress conditions by bioinformatics and transcriptomic approaches.
Identification and expression analysis of LEA gene family members in cucumber genome
(2016-11-01) Celik Altunoglu Y.; Baloglu P.; Yer E.N.; Pekol S.; Baloglu M.C.
LEA (late embryogenesis abundant) proteins are firstly discovered in seeds and then identified in vegetative tissues of different plant species. They are mainly regulated under abiotic stress conditions. Although genome wide studies of different gene family members have been performed in cucumber, there is no such a study for LEA genes. We have identified 79 LEA genes in the cucumber genome. Based on phylogenetic analysis, CsLEA genes could be classified into seven groups in which structural motifs are relatively conserved. Tandem duplications play an important role in cucumber genome for LEA gene expansion. Orthologous and chromosomal relationships of CsLEA genes were observed based on comparative mapping analysis with other species. The in silico micro-RNA (miRNA) target analyses indicated that 37 CsLEA genes were targeted by different miRNAs, especially mir854 and mir414 are the most abundant identified ones. Public available RNA-seq data were analyzed for expression analysis of CsLEA genes in different tissues of cucumber. According to genome-wide expression analysis, nine CsLEA genes showed higher expression profiles in all tissues. The expression profiles of ten CsLEA genes in the root and leaf tissues of drought-stressed cucumber were examined using qRT-PCR. Among them, CsLEA-54 induced after stress application in leaf and root tissues and might provide adaptation to drought stress for cucumber. CsLEA-09, CsLEA-32 and CsLEA-57 genes responded to drought after 3 h later and might be considered as early response genes to water limitation. This research could help us to improve understanding of contribution of CsLEAs to drought tolerance in cucumber.
Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones
(2018-12-15) Yer E.N.; Baloglu M.C.; Ayan S.
Heat shock proteins (Hsps) play a key role for regulation of the changes during different stress conditions including salinity, drought, heavy metal and extreme temperature. Molecular based studies on the response mechanisms of forest trees to abiotic stresses started in 2006 when Populus trichocarpa genome sequence was completed as a model tree species. In recent years, bioinformatic analyzes have been carried out to determine functional gene regions of tree species. In this study, sHsp, Hsp40, Hsp60, Hsp90 and Hsp100 gene family members were identified in poplar genome. Some bioinformatics analyses were conducted, such as: identification of DNA/protein sequences, chromosomal localization, gene structure, calculation of genomic duplications, determination of phylogenetic groups, examination of protected motif regions, identification of gene ontology categories, modeling of protein 3D structure, determination of miRNA targeting genes, examination of sHsp, Hsp40, Hsp60, Hsp90 and Hsp100 gene family members in transcriptome data during salinity stress. As a result of bioinformatic analyzes made on P. trichocarpa genome; 60, 145, 49, 34, 12 and 90 genes belonging to members of sHsp, Hsp40, Hsp60, Hsp70, Hsp90 and Hsp100 protein families were firstly defined within the scope of this study. A total of 390 genes belonging to all Hsps gene families were characterized using different bioinformatics tools. In addition, salinity stress was applied to Populus tremula L. (Samsun) naturally grown in Turkey, Hybrid poplar species I-214 (Populus euramericana Dode. Guinier) and Black Poplar species (Populus nigra L.), Geyve and N.03.368.A clones. The expression levels of the selected Hsps genes were determined by the qRT-PCR method. After salt stress application in various poplar clones, expression levels of genes including PtsHsp-11, PtsHsp-21, PtsHsp-36, PtHsp40-113, PtHsp40-117, PtHsp60-31, PtHsp60-33, PtHsp60-38, PtHsp60-49, PtHsp70-09, PtHsp70-12, 33, PtHsp90-09, PtHsp90-12, PtHsp100-21, and PtHsp100-75 were increased. The role of the Hsps genes during salt stress has been revealed. Together with detailed bioinformatics analyses, gene expression analysis greatly contributes to understand functions of these gene family members. This research serves as a blueprint for future studies and offers a significant clue for the further study of the functions of this important gene family. Moreover, determined genes in this study can also be used for cloning studies in agricultural practices.