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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 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 Developing future heat-resilient vegetable crops(Springer Heidelberg, 2023) Saeed, Faisal; Chaudhry, Usman Khalid; Raza, Ali; Charagh, Sidra; Bakhsh, Allah; Bohra, Abhishek; Ali, SumbulClimate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants' biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.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 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 Genomics for Abiotic Stress Resistance in Legumes(Springer International Publishing, 2023) Zia, Muhammad Abu Bakar; Ul-Allah, Sami; Sher, Ahmad; Ijaz, Muhammad; Sattar, Abdul; Yousaf, Muhammad Farhan; Chaudhry, Usman KhalidAbiotic stress is an environmental constraint that negatively influences the growth of legumes. Additionally, it is predicted that in the future, it will have devastating effects on the growth and yield of crops. Therefore, currently most of the studies are being conducted to observe the response of legume crops to ensure food for future generations. With the introduction of genomic approaches, it enabled plant scientists to screen cultivars in a more precise way by utilizing the available genomic information. It also resulted in numerous genes that play a pivotal role for stress tolerance in crops that can be positively exploited to develop tolerant cultivars. In this chapter, some of the genomic approaches have been discussed. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.Öğe Impact of Biotic and Abiotic Stresses on Onion Production: Potential Mitigation Approaches in Modern Era(Springer Nature, 2023) Chaudhry, Usman Khalid; Junaid, Muhammad Daniyal; Gökçe, Zahide Neslihan Öztürk; Gökçe, Ali FuatOnion is one of the most commonly consumed vegetable crops in the world, following tomato. Biotic and abiotic stresses are known to affect onion production, causing significant yield losses, similar to other vegetables and main crops. It is estimated that about 40% of overall losses in agricultural production is related to insects, pests, and weeds. Likewise, environmental fluctuation and climate change are threatening the production rate of onion. Strangely, in the era of omics approach to understand plants’ responses to environmental changes, there is limited literature regarding onion response to biotic and abiotic stresses. This chapter enlightens the impacts of biotic and abiotic stresses with the potential exploitation of modern plant improvement techniques. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023.Öğe Morpho-physiological response of barley to assess genotypic differences of salinity tolerance under hyper arid climate(Elsevier, 2022) Hussain, M. Iftikhar; Al-Dakheel, Abdullah J.; Chaudhry, Usman Khalid; Khan, Muhammad Imran; ALHaithloul, Haifa Abdulaziz Sakit; Alghanem, Suliman Mohammed; Alaklabi, AbdullahSalt stress is major constraint affecting agricultural productivity, land degradation and has become a serious threat for global food security. The selection and evaluation of barley genotypes that can tolerate salt stress are the main components for rehabilitation of salt-degraded marginal soils in arid and semi-arid countries, including Arabian Peninsula. A field experiment was conducted to evaluate the response of six barley genotypes (62/3 A, 76/2 A, N2-35, N2-4, Badia, Furat1) at three salinity levels (0, 7 and 14 dS m-1) to evaluate the response of genotypes based on morpho-physiological characteristics and nutrients uptake. The grain yield stability (static environmental variance (S2) and dynamic Wricke's ecovalence (W2), and harvest index (HI) was also estimated. The higher salinity treatment (14 dS m-1) resulted in devastating reduction in barley yield traits. Additionally, salt treatments (7 dS m-1, 14 dS m-1), genotypes and interaction between (genotypes * salinity levels) exhibited significant (p < 0.001) differences. The genotype N2-35 exhibited highest plant biomass, grains per spike and grains per plant, whereas the genotype 76/2 A resulted in lowest number of grains per spike and grains per plant. The highest K+ was noticed from Badia genotype, whereas the 62/3 A genotype failed to accumulate K+. The genotype, Furat1, showed substantial amount of Cl- and Na+ contents followed by Badia. Except Badia and N2-35, all other genotypes showed higher & UDelta;13C values. The Badia genotype also showed higher iWUE compared to all other genotypes. Contrarily the genotypes N2-4 and 62/3 A exhibited maximum reduction in iWUE. The delta 15N trait increased following salinity treatment. Genotypes N2-35 and N2-4 showed highest delta 15N while 62/3 A and 76/2 A exhibit lowest values for delta 15N. The study exhibited that the genotype N2-35 was tolerant to salinity stress whereas the response of Furat1 genotype suggested salt susceptible behaviour. It was concluded that salt tolerant genotype can be cultivated in saline marginal soils for food security and help in rehabilitation of marginal lands.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.Öğe Moving Beyond DNA Sequence to Improve Plant Stress Responses(Frontiers Media Sa, 2022) Saeed, Faisal; Chaudhry, Usman Khalid; Bakhsh, Allah; Raza, Ali; Saeed, Yasir; Bohra, Abhishek; Varshney, Rajeev K.Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.Öğe Role of macronutrients in cotton production(Springer Singapore, 2020) Ahmed, Niaz; Ali, Muhammad Arif; Danish, Subhan; Chaudhry, Usman Khalid; Hussain, Sajjad; Hassan, Waseem; Ahmad, FiazSound nutrition plays a key role in enhancing cotton yield. As cotton undergoes vegetative and reproductive growth at the same time, its nutritional requirements are dissimilar, compared to other field crops. Cotton is grown as an annual crop with an indeterminate growth pattern. The vegetative branching provides a potential fruiting place except under abiotic and biotic stresses. Moreover, cotton has a deep root system with low density of roots in the surface layer of soils where availability of nutrients is high. The rooting system makes cotton crop more dependent on the subsoil for nutrition. A continuous supply of nutrients is required to sustain morphogenesis. The rate of both nutrients absorption and dry matter production increases progressively during the seedling, vegetative, and fruiting periods and peaks near the end of the bloom period. Nitrogen, phosphorus, and potassium are required in large quantities and are limited in many soils. The deficiencies of macro-and micronutrients decrease plant growth and development, and consequently seed cotton yield is reduced. The deficiency of phosphorous (P), calcium (Ca), potassium (K), boron (B), magnesium (Mg), and zinc (Zn) affects fruit production in cotton than vegetative growth, while the deficiencies of nitrogen (N), sulfur (S), molybdenum (Mo), and manganese (Mn) affect equally vegetative and reproductive growth of cotton. A bevy of literature concerning the role of macronutrients in growth and development is presented in the following paragraphs. © Springer Nature Singapore Pte Ltd. 2020. All rights reserved.Öğe Salinity tolerance in cotton(Springer Singapore, 2020) Ahmed, Niaz; Chaudhry, Usman Khalid; Ali, Muhammad Arif; Ahmad, Fiaz; Sarfraz, Muhammad; Hussain, SajjadCotton is the chief crop and main pillar of textile industry. Its fiber and seed have significant economic importance. However, salinity interferes with the normal growth functioning and results in halted growth and declined yield of fiber and seed. Salinity effects are more obvious at early growth stages of cotton, limiting final yield. Salt decreases boll formation per plant which ultimately gives decreased fiber yield and poor lint quality. Salinity is a global issue increasing every year due to uncontrolled measures and improper land management. Application of saline irrigation water is adding increments to already existing salts and deteriorating the productive soil. Arid regions are totally dependent upon rain for growth of cotton. Salt problem is more in arid regions due least availability of moisture and water for flushing salts from cotton root zone. Moreover, higher temperature favors excessive evaporation under arid conditions and leaving salt on the upper surface of soil. Salts at the surface soil impede cotton seed germination. In this chapter, we discussed formation of saline soils and their sources which deter cotton growth. Physiological changes, oxidative stress caused due to salinity, role of molecular transporters involved in detoxification and specific gene expression is also illuminated. © Springer Nature Singapore Pte Ltd. 2020. All rights reserved.Öğe Salinity Tolerance in Rice(wiley, 2022) Chaudhry, Usman Khalid; Ahmed, Niaz; Junaid, Muhammad Daniyal; Ali, Muhammad Arif; Saboor, Abdul; Danish, Subhan; Hussain, SajjadRice is the main staple food crop across the globe. Among abiotic stresses, salinity stress is increasing at an alarming rate. It inhibits rice growth and yield as rice is a sensitive crop to salinity. It influences various physiological functioning of the rice, which results in retarded growth and ultimately gives poor yield. In this chapter, we highlighted influence of physiological changes and effect on rice grain in response to salinity stress and their adaptation strategies. Moreover, currently numerous studies have explored the molecular response/changes in rice to cope with salinity stress. In this regard, we explained the abscisic acid and signaling under salinity stress along with the functions of transcription factors. Final part of this chapter covers the importance of modern breeding techniques to screen and develop salt tolerant cultivars within a short period of time as compared to conventional breeding approaches. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2022.Öğe Unraveling Sorghum Allelopathy in Agriculture: Concepts and Implications(Mdpi, 2021) Iftikhar Hussain, M.; Danish, Subhan; Sanchez-Moreiras, Adela M.; Vicente, Oscar; Jabran, Khawar; Chaudhry, Usman Khalid; Branca, FerdinandoAllelopathy is an ecological phenomenon that involves the production and release of biomolecules from different crops, cultivated plants, and bacteria or fungi into the soil rhizosphere and impacts other organisms in the vicinity. Sorghum possesses vital allelopathic characteristics due to which it produces and releases different biomolecules from its root hairs, stems, and grains. Several studies have reported that sorghum acts as an allelopathic crop, decreasing the growth and eco-physiological attributes of surrounding plants and weeds growing simultaneously or subsequently in the field. Sorghum allelopathy has been exploited in the context of green manure, crop rotations, cover crops, and intercropping or mulching, whereas plant aqueous extracts or powder might be an alternate method of weed control. A diverse group of allelochemicals, including benzoic acid, p-hydroxybenzoic acid, vanillic acid, ferulic acid, chlorogenic acid, m-coumaric acid, p-coumaric acid, gallic acid, caffeic acid, p-hydroxibenzaldehyde, dhurrin, sorgoleone, m-hydroxybenzoic acid and protocatechuic acid, have been isolated and identified from different plant tissues of sorghum and root exudates. These allelochemicals, especially sorgoleone, have been investigated in terms of their mode(s) of action, specific activity and selectivity, release in the rhizosphere and uptake and translocation in sensitive species. The present review describes the importance of sorghum allelopathy as an ecological tool in managing weeds, highlighting the most recent advances in the allelochemicals present in sorghum, their modes of action, and their fate in the ecosystem. Further research should focus on the evaluation and selection of sorghum cultivars with high allelopathic potential, so that sorghum allelopathy can be better utilized for weed control and yield enhancement.