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Öğe A review of the potential involvement of small RNAs in transgenerational abiotic stress memory in plants(Springer Heidelberg, 2024) Junaid, Muhammad Daniyal; Chaudhry, Usman Khalid; Sanli, Beyazit Abdurrahman; Gokce, Ali Fuat; Ozturk, Zahide NeslihanCrop production is increasingly threatened by the escalating weather events and rising temperatures associated with global climate change. Plants have evolved adaptive mechanisms, including stress memory, to cope with abiotic stresses such as heat, drought, and salinity. Stress memory involves priming, where plants remember prior stress exposures, providing enhanced responses to subsequent stress events. Stress memory can manifest as somatic, intergenerational, or transgenerational memory, persisting for different durations. The chromatin, a central regulator of gene expression, undergoes modifications like DNA acetylation, methylation, and histone variations in response to abiotic stress. Histone modifications, such as H3K4me3 and acetylation, play crucial roles in regulating gene expression. Abiotic stresses like drought and salinity are significant challenges to crop production, leading to yield reductions. Plant responses to stress involve strategies like escape, avoidance, and tolerance, each influencing growth stages differently. Soil salinity affects plant growth by disrupting water potential, causing ion toxicity, and inhibiting nutrient uptake. Understanding plant responses to these stresses requires insights into histone-mediated modifications, chromatin remodeling, and the role of small RNAs in stress memory. Histone-mediated modifications, including acetylation and methylation, contribute to epigenetic stress memory, influencing plant adaptation to environmental stressors. Chromatin remodeling play a crucial role in abiotic stress responses, affecting the expression of stress-related genes. Small RNAs; miRNAs and siRNAs, participate in stress memory pathways by guiding DNA methylation and histone modifications. The interplay of these epigenetic mechanisms helps plants adapt to recurring stress events and enhance their resilience. In conclusion, unraveling the epigenetic mechanisms in plant responses to abiotic stresses provides valuable insights for developing resilient agricultural techniques. Understanding how plants utilize stress memory, histone modifications, chromatin remodeling, and small RNAs is crucial for designing strategies to mitigate the impact of climate change on crop production and global food security.Öğe Assessment of salt and drought stress on the biochemical and molecular functioning of onion cultivars(Springer, 2024) Chaudhry, Usman Khalid; Ozturk, Zahide Neslihan; Gokce, Ali FuatBackgroundSalt and drought stress are the main environmental constraints that limit onion growth and productivity. Turkiye is the fifth largest onion producer, whereas the stress conditions are increasing in the region, resulting in poor crop growth.Methods and ResultsA current study was conducted under greenhouse conditions according to a completely randomized design with factorial arrangements to evaluate the performance of onion cultivars. Plants were subjected to salt stress with an application of 750 mM NaCl and drought stress was applied by depriving plants of irrigation water for 20 days to measure biochemical and transcript changes. The antioxidant activities of the cultivars were quantified by using four different methods, i.e., 2,2 '-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assays, cupric reducing antioxidant capacity, 2,2-Diphenyl-1-picrylhydrazyl, and ferric reducing antioxidant power (FRAP). The damage to pigments, phenolic, osmolytes, and hydrogen peroxide (H2O2) accumulation was also evaluated. Results revealed that the cultivars Elit and Hazar had higher H2O2, maximum damage to pigments, and least accumulation of phenolics and osmolytes under both stress conditions. The cultivar Sampiyon performance was better under salt stress but exhibited a poor antioxidant defensive mechanism under drought stress conditions. The remaining cultivars suggested a resilient nature with a higher accumulation of osmolytes, antioxidants and phenolics. The change in transcript levels further strengthened the response of resilient cultivars; for instance, they showed higher transcript levels of superoxide dismutase, ascorbate oxidase and transcription factors (WRKY70, NAC29). It helped alleviate the oxidative stress in tolerant cultivars and maintained the physio-biochemical functioning of the cultivars..ConclusionThe results of the current study will fill the gap of missing literature in onion at biochemical and molecular levels. Additionally, resilient cultivars can effectively cope with abiotic stresses to ensure future food security.Öğe Classical Genetics on Gene Mapping(Springer International Publishing Ag, 2018) Gokce, Ali FuatWhile onion (Allium cepa L.) plants have significantly different morphologies in height, leaves, scape, and inflorescence, their bulbs differ in pungency, color, size, firmness, shape, tightness of bulb scales and neck. As in other vegetables, resistance to diseases, better quality, high yield, and uniformity are the major breeding achievements in onion. However, being a biennial plant with alternative seed-to-bulb and bulb-to-seed generations, the genetic progression of any desired trait in onion is relatively slow. This chapter reviews general breeding objectives, genetics and morphological markers found in seed, seedling, leaf, scape, bulb scale, and flower, genetics of some biotic and abiotic stresses, and cautions for marker-assisted selection to develop maintainer lines.Öğe Comparative transcriptomics of drought stress response of taproot meristem region of contrasting purple carrot breeding lines supported by physio-biochemical parameters(Springer Heidelberg, 2022) Gokce, Zahide Neslihan Ozturk; Gokce, Ali Fuat; Junaid, Muhammad Daniyal; Chaudhry, Usman KhalidCarrot is one of the nutritious vegetable crops sensitive to drought stress resulting in loss of quality and yield. There are a lot of studies on detailed molecular mechanisms of drought stress response of main crops; however, very little information available on vegetables, including carrots. Hence, in this study, we investigated root transcriptome profiles from the meristematic region of two contrasting purple carrot (B7262A, drought tolerant; P1129, drought sensitive) lines under varying stress levels (85% and 70%) by using RNA-Seq technique. The morpho-physiological and biochemical response of B7262A line exhibited tolerance behavior to both DS (85% and 70%). RNA-Seq analysis revealed that 15,839 genes were expressed commonly in both carrot lines. The carrot line B7262A showed regulation of 514 genes in response to 85% DS, whereas P1129 showed differential regulation of 622 genes under 70% DS. The B7262A carrot line showed higher upregulation of transcripts that suggested its resilient behavior contrary to P1129 line. Furthermore, validation of transcript gene by qRT-PCR also confirmed the RNA-Seq analysis resulting in elevated expression levels of MYB48 transcription factor, MAPK mitogen-activated protein kinase ANP1, GER geraniol 8-hydroxylase, ABA ABA-induced in somatic embryo 3, FBOX putative F-box protein, FRO ferric reduction oxidase, and PDR probable disease resistance protein. Current study provided unprecedented insights of purple carrot lines that can be potentially exploited for the screening and development of resilient carrot.Öğe Determination of Resistance Levels of Some Onion Cultivars or Inbreed Lines with Fusarium Testing at Seedling Stage(2022) Karabulut, Ebrar; Gokce, Ali FuatThis study was carried out to determine the resistance levels of some onion genotypes in Yalova onion gene pool by Fusarium testing during seedling stage. The isolate used in the study was Fusarium oxysporum f. sp. cepae, which causes damping off during the seedling stage and later basal rot in onion bulbs. The variance analysis for the onion seedling test and the mean differences against control were analyzed by using General Linear Model of the Tukey test. The germination rate of control seeds varied between 72% to 98%, while the germination rate of inoculated seeds varied between 39% to 93%. Texas Early Grano 502 showed the highest level of resistance with a survival rate of 83.8%, and resistance levels of 19Y07 and 19Y142 genotypes were higher than other genotypes. Resistance levels of 19Y51, 19Y15 and 19Y73 genotypes were lower than other genotypes. Akgün 12 showed moderate resistance with a survival rate of 59.6%. Determining the resistance levels of these onion genotypes during the seedling stage may be a preliminary step towards further studies.Öğe Drought and salt stress effects on biochemical changes and gene expression of photosystem II and catalase genes in selected onion cultivars(Springer, 2021) Chaudhry, Usman Khalid; Gokce, Zahide Neslihan Ozturk; Gokce, Ali FuatOnion is the main condiment vegetable crop that is grown and consumed due to its rich nutraceutical properties. Globally, drought and salt stress are the major hurdles for onion growth and pose greater threat to the future crop growth. Numerous studies reported the response of vegetable crops with the acclimatization to fluctuating environmental conditions but data for onion appears to be limited on biochemical and gene expression changes. In this study, we investigated the response of seven onion cultivars from Turkey for biochemical and gene expression responses to drought and salt stresses under greenhouse conditions. There is limited data available on NCBI for onion genes; therefore, degenerate PCR approach was used to amplify the catalase (CAT) and photosystem (PSII) genes of onion to observe correlation between their activity with transcript levels. Results of biochemical attributes indicated that the cultivars Perama, Inci, and Seyhan performed better compared to other cultivars with the exposure to salt and drought stress. Additionally, these cultivars also accumulated higher transcript level of CAT gene and showed least decrease in the degradation of PSII mRNA. Overall, results revealed that the cultivars Perama, Inci, and Seyhan were tolerant, whereas the cultivars Elit and Hazar were grouped as sensitive to salt and drought stress conditions. Results of this study can be used for screening of tolerant and susceptible cultivars. Moreover, the tolerant cultivars Perama, Inci, and Seyhan can be used for future abiotic stress breeding programs.Öğe Drought stress effects on morphophysiological and quality characteristics of commercial carrot cultivars(Tubitak Scientific & Technological Research Council Turkey, 2023) Junaid, Muhammad Daniyal; Ozturk, Zahide Neslihan; Gokce, Ali FuatThe effects of drought stress on plant growth and development are getting more pronounced due to increasing influence of climate change on environmental stresses. Current study was devised to explore the drought effects on eight commercial carrot cultivars, having different root colors as a base for further studies to understand the response of carrot. Drought stress for 10 days was applied to carrot plants at taproot formation stage in semicontrolled greenhouse. The results revealed that orange and yellow colored carrot cultivars exhibited the least decline in physiological functioning (relative water contents and dry matter) that assisted in maintaining higher yield and quality attributes in contrast to purple and black carrot cultivars. However, anthocyanin contents in nonpurple cultivars Tendersweet and Solar Yellow showed 72% decrease, whereas in purple carrot cultivars 3-fold increase was observed in Eregli Black and Cosmic Purple. Beta-carotene contents showed 59% decrease in cultivar Eregli Black under drought; however, it was increased in cultivars Solar Yellow and Coral Orange by 17% and 3%, respectively. Sugar accumulation exhibited variable response of carrot cultivars; minimal sucrose contents in cultivars Cosmic Purple, Solar Yellow and Tendersweet were detected after they were subjected to drought. Overall, the results showed that cultivars Atomic Red and Coral Orange performed well under water scarce condition. We believe this study may help the researchers to move forward in understanding the drought effects for the selection of promising cultivars to be used in development of tolerant varieties with breeding strategies.Öğe Effects of Salinity and Drought Stresses on the Physio-Morphological Attributes of Onion Cultivars at Bulbification Stage(Friends Science Publ, 2020) Chaudhry, Usman Khalid; Gokce, Zahide Neslihan Ozturk; Gokce, Ali FuatOnion (Allium cepa L.) has huge importance due to its health benefits. Salinity and drought stress appear to be the major threats towards the productivity of crops and vegetables across the globe. Although in literature several studies summarize responses of agricultural crops to abiotic stresses but data for onion appears to be limited. In this greenhouse study, seven onion cultivars were compared for their morphological and physiological responses to salinity stress (SS) and drought stress (DS). Salinity stress was applied to SS group through irrigating with water containing increasing doses of NaCl (100, 125, 150, 175 and 200 mM) in 3-day intervals, whereas water was suspended for 20 days to DS group for drought stress application. Salinity and drought stress decreased photosynthetic rate, lower leaf number, leaf length and bulb yield. SS interfered with root length and diameter, whereas thicker and elongated root length was noticed in response to DS. The cultivars 'Elit', 'Hazar' and 'Sampiyon' exhibited the reduction in photosynthetic rate. Maximum damage to chlorophyll contents was observed in cultivars 'Elit', 'Hazar' and 'Sampiyon' under SS and DS conditions. The cultivar 'Perama' manifested the highest bulb weight under SS and DS condition. The cultivars 'Perama' and 'Seyhan' were referred to as tolerant based on their overall performance under SS and DS, supported by the results of principal component analysis (PCA), however, the cultivars 'Elit', 'Hazar', and 'Sampiyon' performed poorly, so grouped as sensitive cultivars. Results of this study can be helpful in screening of tolerant and susceptible onion cultivars which will be useful for future breeding programs. (C) 2020 Friends Science PublishersÖğe Evaluation of biochemical and molecular response of onion breeding lines to drought and salt stresses(Elsevier, 2023) Gokce, Ali Fuat; Gokce, Zahide Neslihan Oztuerk; Junaid, Muhammad Daniyal; Chaudhry, Usman KhalidOnion is the most important crop in the Alliaceae family which is diversely used all over the world. Turkiye is the 5th largest onion producer with the production of 2.24 million tons, but onion production is under threat due to climatic changes especially in the Anatolia region. Therefore, in the present study, six onion breeding lines were investigated to quantify the biochemical and gene expressional changes under drought and salt stresses. Plants were divided into control, salt stress, and drought stress to apply stress treatment under semi-controlled greenhouse conditions. Current study showed that salt stress restricted the uptake of minerals from the soil. Study also revealed that under both stresses the chlorophyll a and b contents were stable in K41, U47 and U49 breeding lines. Moreover, gene expression for stress related genes showed that K41 and U47 breeding lines showed tolerance to drought and salt stress by adequately regulating their SOD, CAT, AOX, WRKY70 and NAC29 gene expressions, moreover highest antioxidant enzymatic activity was also observed in these breeding lines under drought and salt stress. The H2O2 concentration was highest in the sensitive breeding lines suggesting the sensitivity to both stresses. PCA analysis revealed that breeding lines K41, U47 and U49 showed tolerance to both stresses. These results can further used to understand onion stress tolerance mechanism and it may enable onion breeders for the development of abiotic stress resilient onion cultivars.Öğe Exploitation of tolerance to drought stress in carrot (Daucus carota L.): an overview(Springernature, 2023) Junaid, Muhammad Daniyal; Ozturk, Zahide Neslihan; Gokce, Ali FuatDrought stress is a significant environmental factor that adversely affects the growth and development of carrot (Daucus carota L.), resulting in reduced crop yields and quality. Drought stress induces a range of physiological and biochemical changes in carrots, including reduced germination, hindered cell elongation, wilting, and disrupted photosynthetic efficiency, ultimately leading to stunted growth and decreased root development. Recent research has focused on understanding the molecular mechanisms underlying carrot's response to drought stress, identifying key genes and transcription factors involved in drought tolerance. Transcriptomic and proteomic analyses have provided insights into the regulatory networks and signaling pathways involved in drought stress adaptation. Among biochemical processes, water scarcity alters carrot antioxidant levels, osmolytes, and hormones. This review provides an overview of the effects of drought stress on carrots and highlights recent advances in drought stress-related studies on this crop. Some recent advances in understanding the effects of drought stress on carrots and developing strategies for drought stress mitigation are crucial for ensuring sustainable carrot production in the face of changing climate conditions. However, understanding the mechanisms underlying the plant's response to drought stress is essential for developing strategies to improve its tolerance to water scarcity and ensure food security in regions affected by drought.Öğe Investigation of drought induced biochemical and gene expression changes in carrot cultivars(Springer, 2023) Junaid, Muhammad Daniyal; Gokce, Zahide Neslihan Ozturk; Gokce, Ali FuatBackground Carrot is the most important vegetable in Apiaceae family, and it is consumed globally due to its high nutritional quality. Drought stress is major environmental constraint for vegetables especially carrot. Limited data is available regarding the mechanisms conferring drought tolerance in carrot. Methods and Results Eight commercial carrot cultivars were used in this study and subjected to drought stress under semi-controlled greenhouse conditions. Biochemical, antioxidant enzymatic activity and changes in transcript level of drought related genes was estimated, the gene expression analysis was done by using qRT-PCR in comparison with reference gene expression Actin (Act1). Results revealed that cultivars Coral Orange, Tendersweet and Solar Yellow were tolerant to drought stress, which was supported by their higher transcript levels of catalase gene (CAT), superoxide dismutase genes (Cu/ZN-SOD, Cu/Zn-SDC) in these cultivars. The downregulation of PDH1 gene (Proline dehydrogenase 1) was also observed that was associated with upregulation of proline accumulation in carrot plants. Moreover, results also suggested that PRT genes (Proline transporter genes) played a key role in drought tolerance in carrot cultivars. Conclusion Among the cultivars studied, Coral Orange showed overall tolerance to drought stress conditions, whereas cultivars Cosmic Purple and Eregli Black were sensitive based on their biochemical and gene expression levels. According to our knowledge, this is the first comparative study on drought tolerance in several carrot cultivars. It will provide a background for carrot breeding to understand biochemical and molecular responses of carrot plant to drought stress and mechanisms behind it.Öğe Molecular Characterization of Turkish Onion Germplasm Using SSR Markers(CZECH ACADEMY AGRICULTURAL SCIENCES, 2016) Hanci, Fatih; Gokce, Ali FuatIn this study, molecular markers were used for the first time to study the genetic diversity of Turkish onion (Allium cepa L.) accessions. We used 83 turkish landraces, 3 breeding lines and 10 commercial varieties, in total 96 accessions, to study the genetic diversity. Bulked samples of 10 seeds were used to generate a representative profile of the accessions. Variability was evaluated at 46 microsatellite loci. We identified 308 alleles with these markers, out of which 303 were polymorphic. A dendrogram based on the UPGMA analysis grouped the 96 accessions into five main clusters. Dice's similarity coefficient ranged from 0.407 to 0.767 with an average of 0.587. The results showed that 44 out of the 46 SSR markers were convenient and polymorphic enough to distinguish all the studied accessions.Öğe MORPHOLOGIC AND CYTOPLASMIC ASSESSMENTS OF BULB ONION(Serbian Genetics Soc, 2021) Cebeci, Esra; Padem, Huseyin; Gokce, Ali FuatCebeci E., H. Padem, A. F. Gokce (2021). Morphologic and cytoplasmic assessments of bulb onion (Allium cepa L.) landraces. -Genetika, Vol 53, No.1,167-180. Today climate change threatens to reduce crop yield and harming the food security. Local landraces have adaptation skills to shifting climatic conditions. Using of this local source in plant breeding programs becoming an alternative strategy. In this study, 97 landraces were collected to initiate the bulb onion breeding program eligible for the current trends. Collected materials were morphologically characterized using 21 descriptors, derived from UPOV (International Union for the Protection of New Varieties of Plants). Clustering which was conducted by the NTSYS (Numerical Taxonomy and Multivariate Analysis System) program using UPGMA (Unweighted Pair Group Method of Arithmetic Averages) method, showed that the genetic similarity rate of the landraces was calculated between 0.06-0.96. Hybrid onion breeding program depends on the cytoplasmic-genic male sterility (CMS) system. Thus, the PCR-markers were applied to identify the cytoplasm types of the landraces. Among landraces N-cytoplasm was found in 78 accessions and S-cytoplasm was found in 19 accessions. At the end of the study, a qualified gene pool has been established consisted of characterized onion genotypes which will might be used in further breeding studies.Öğe Morphological, physiological, and biochemical responses of onion (Allium cepa L.) breeding lines to single and combined salt and drought stresses(Springer, 2022) Gokce, Zahide Neslihan Ozturk; Gokce, Ali Fuat; Junaid, Muhammad Daniyal; Chaudhry, Usman KhalidAbiotic stresses deteriorate plant growth resulting in devastating yield losses. Salt stress solely cause ionic toxicity and disturbed homeostasis, whereas combined salt and drought stress has more pronounced effects on plants. This study aimed to screen 32 Turkish onion breeding lines and commercial cultivars based on their morpho-physiological and biochemical responses after exposure to drought, salt, and salt + drought stresses at the bulbification stage under greenhouse conditions. Physiological characteristics, such as gaseous exchange traits, chlorophyll index, leaf temperature, and morphological traits including the number of leaves, length, and diameter of leaf were measured during stress treatment, and yield response of the onions was quantified by measuring bulb length, bulb diameter, and bulb weight after harvest. Proline and malondialdehyde accumulation was estimated for the biochemical effect of stress on onion genotypes. All genotypes responded differentially to the applied single and combined stresses. Overall results revealed that in the breeding lines K25, U6, U17 and commercial cultivar K58, the bulb weight (41.71-47.93 g) was significantly (p <= 0.05) lower, therefore they were grouped as sensitive across all stresses; whereas in the breeding lines K41, U47, U49 and commercial cultivar K52, the bulb weight (96.75-106.31 g) was significantly (p <= 0.05) higher among all the tested breeding lines and commercial cultivars and therefore found to be the most stable upon stress. These resilient genotypes can be used as breeding material for future abiotic stress studies.
