Browsing by Author "Tran, Lam Son Phan (TTU)"
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Item Antioxidants and bioactive compounds in licorice root extract potentially contribute to improving growth, bulb quality and yield of onion (Allium cepa)(2021) Younes, Nabil A.; Rahman, Md Mezanur; Wardany, Ahmed A.; Dawood, Mona F.A.; Mostofa, Mohammad Golam; Keya, Sanjida Sultana; Latef, Arafat Abdel Hamed Abdel; Tran, Lam Son Phan (TTU)The increasing culinary use of onion (Alium cepa) raises pressure on the current production rate, demanding sustainable approaches for increasing its productivity worldwide. Here, we aimed to investigate the beneficial effects of licorice (Glycyrrhiza glabra) root extract (LRE) in improving growth, yield, nutritional status, and antioxidant properties of two high-yielding onion cultivars, Shandaweel and Giza 20, growing under field conditions in two consecutive years. Our results revealed that pretreatments of both onion cultivars with LRE exhibited improved growth indices (plant height and number of leaves) and yield-related features (bulb length, bulb diameter, and bulb weight) in comparison with the corresponding LRE-devoid control plants. Pretreatments with LRE also improved the nutritional and antioxidant properties of bulbs of both cultivars, which was linked to improved mineral (e.g., K+ and Ca2+) acquisition, and heightened activities of enzymatic antioxidants (e.g., superoxide dismutase, catalase, ascorbate peroxidase, glutathione peroxidase, and glutathione S-transferase) and increased levels of non-enzymatic antioxidants (e.g., ascorbic acid, reduced glutathione, phenolics, and flavonoids). LRE also elevated the contents of proline, total free amino acids, total soluble carbohydrates, and water-soluble proteins in both onion bulbs. In general, both cultivars displayed positive responses to LRE pretreatments; however, the Shandaweel cultivar performed better than the Giza 20 cultivar in terms of yield and, to some extent, bulb quality. Collectively, our findings suggest that the application of LRE as biostimulant might be an effective strategy to enhance bulb quality and ultimately the productivity of onion cultivars under field conditions.Item Biochar potentially enhances maize tolerance to arsenic toxicity by improving physiological and biochemical responses to excessive arsenate(2023) Rahman, Md Mezanur (TTU); Das, Ashim Kumar; Sultana, Sharmin; Ghosh, Protik Kumar; Islam, Md Robyul; Keya, Sanjida Sultana (TTU); Ahmed, Minhaz; Nihad, Sheikh Arafat Islam; Khan, Md Arifur Rahman; Lovell, Mylea C. (TTU); Rahman, Md Abiar; Ahsan, S. M.; Anik, Touhidur Rahman (TTU); Fnu, Pallavi (TTU); Tran, Lam Son Phan (TTU); Mostofa, Mohammad GolamMetalloid pollution, including arsenic poisoning, is a serious environmental issue, plaguing plant productivity and quality of life worldwide. Biochar, a carbon-rich material, has been known to alleviate the negative effects of environmental pollutants on plants. However, the specific role of biochar in mitigating arsenic stress in maize remains relatively unexplored. Here, we elucidated the functions of biochar in improving maize growth under the elevated level of sodium arsenate (Na2AsO4, AsV). Maize plants were grown in pot-soils amended with two doses of biochar (2.5% (B1) and 5.0% (B2) biochar Kg−1 of soil) for 5 days, followed by exposure to Na2AsO4 ('B1 + AsV'and 'B2 + AsV') for 9 days. Maize plants exposed to AsV only accumulated substantial amount of arsenic in both roots and leaves, triggering severe phytotoxic effects, including stunted growth, leaf-yellowing, chlorosis, reduced photosynthesis, and nutritional imbalance, when compared with control plants. Contrariwise, biochar addition improved the phenotype and growth of AsV-stressed maize plants by reducing root-to-leaf AsV translocation (by 46.56 and 57.46% in ‘B1 + AsV’ and ‘B2 + AsV’ plants), improving gas-exchange attributes, and elevating chlorophylls and mineral levels beyond AsV-stressed plants. Biochar pretreatment also substantially counteracted AsV-induced oxidative stress by lowering reactive oxygen species accumulation, lipoxygenase activity, malondialdehyde level, and electrolyte leakage. Less oxidative stress in ‘B1 + AsV’ and ‘B2 + AsV’ plants likely supported by a strong antioxidant system powered by biochar-mediated increased activities of superoxide dismutase (by 25.12 and 46.55%), catalase (51.78 and 82.82%), and glutathione S-transferase (61.48 and 153.83%), and improved flavonoid levels (41.48 and 75.37%, respectively). Furthermore, increased levels of soluble sugars and free amino acids also correlated with improved leaf relative water content, suggesting a better osmotic acclimatization mechanism in biochar-pretreated AsV-exposed plants. Overall, our findings provided mechanistic insight into how biochar facilitates maize’s active recovery from AsV-stress, implying that biochar application may be a viable technique for mitigating negative effects of arsenic in maize, and perhaps, in other important cereal crops. Graphical Abstract: [Figure not available: see fulltext.]Item Brassinosteroid Signaling Pathways: Insights into Plant Responses under Abiotic Stress(2023) Khan, Tanveer Alam; Kappachery, Sajeesh; Karumannil, Sameera; AlHosani, Mohamed; Almansoori, Nemah; Almansoori, Hamda; Yusuf, Mohammad; Tran, Lam Son Phan (TTU); Gururani, Mayank AnandWith the growing global population, abiotic factors have emerged as a formidable threat to agricultural food production. If left unaddressed, these stress factors might reduce food yields by up to 25% by 2050. Plants utilize natural mechanisms, such as reactive oxygen species scavenging, to mitigate the adverse impacts of abiotic stressors. Diverse plants exhibit unique adaptations to abiotic stresses, which are regulated by phytohormones at various levels. Brassinosteroids (BRs) play a crucial role in controlling essential physiological processes in plants, including seed germination, xylem differentiation, and reproduction. The BR cascade serves as the mechanism through which plants respond to environmental stimuli, including drought and extreme temperatures. Despite two decades of research, the complex signaling of BRs under different stress conditions is still being elucidated. Manipulating BR signaling, biosynthesis, or perception holds promise for enhancing crop resilience. This review explores the role of BRs in signaling cascades and summarizes their substantial contribution to plants’ ability to withstand abiotic stresses.Item Carrageenans as biostimulants and bio-elicitors: plant growth and defense responses(2024) Hossain, Md Motaher; Sultana, Farjana; Khan, Sabia; Nayeema, Jannatun; Mostafa, Mahabuba; Ferdus, Humayra; Tran, Lam Son Phan (TTU); Mostofa, Mohammad GolamIn the context of climate change, the need to ensure food security and safety has taken center stage. Chemical fertilizers and pesticides are traditionally used to achieve higher plant productivity and improved plant protection from biotic stresses. However, the widespread use of fertilizers and pesticides has led to significant risks to human health and the environment, which are further compounded by the emissions of greenhouse gases during fertilizer and pesticide production and application, contributing to global warming and climate change. The naturally occurring sulfated linear polysaccharides obtained from edible red seaweeds (Rhodophyta), carrageenans, could offer climate-friendly substitutes for these inputs due to their bi-functional activities. Carrageenans and their derivatives, known as oligo-carrageenans, facilitate plant growth through a multitude of metabolic courses, including chlorophyll metabolism, carbon fixation, photosynthesis, protein synthesis, secondary metabolite generation, and detoxification of reactive oxygen species. In parallel, these compounds suppress pathogens by their direct antimicrobial activities and/or improve plant resilience against pathogens by modulating biochemical changes via salicylate (SA) and/or jasmonate (JA) and ethylene (ET) signaling pathways, resulting in increased production of secondary metabolites, defense-related proteins, and antioxidants. The present review summarizes the usage of carrageenans for increasing plant development and defense responses to pathogenic challenges under climate change. In addition, the current state of knowledge regarding molecular mechanisms and metabolic alterations in plants during carrageenan-stimulated plant growth and plant disease defense responses has been discussed. This evaluation will highlight the potential use of these new biostimulants in increasing agricultural productivity under climate change.Item Comparative genomics of the medicinal plants Lonicera macranthoides and L. japonica provides insight into genus genome evolution and hederagenin-based saponin biosynthesis(2023) Yin, Xiaojian; Xiang, Yaping; Huang, Feng Qing; Chen, Yahui; Ding, Hengwu; Du, Jinfa; Chen, Xiaojie; Wang, Xiaoxiao; Wei, Xinru; Cai, Yuan Yuan; Gao, Wen; Guo, Dongshu; Alolga, Raphael N.; Kan, Xianzhao; Zhang, Baolong; Alejo-Jacuinde, Gerardo (TTU); Li, Ping; Tran, Lam Son Phan (TTU); Herrera-Estrella, Luis (TTU); Lu, Xu; Qi, Lian WenLonicera macranthoides (LM) and L. japonica (LJ) are medicinal plants widely used in treating viral diseases, such as COVID-19. Although the two species are morphologically similar, their secondary metabolite profiles are significantly different. Here, metabolomics analysis showed that LM contained ~86.01 mg/g hederagenin-based saponins, 2000-fold higher than LJ. To gain molecular insights into its secondary metabolite production, a chromosome-level genome of LM was constructed, comprising 9 pseudo-chromosomes with 40 097 protein-encoding genes. Genome evolution analysis showed that LM and LJ were diverged 1.30–2.27 million years ago (MYA). The two plant species experienced a common whole-genome duplication event that occurred ∼53.9–55.2 MYA before speciation. Genes involved in hederagenin-based saponin biosynthesis were arranged in clusters on the chromosomes of LM and they were more highly expressed in LM than in LJ. Among them, oleanolic acid synthase (OAS) and UDP-glycosyltransferase 73 (UGT73) families were much more highly expressed in LM than in LJ. Specifically, LmOAS1 was identified to effectively catalyse the C-28 oxidation of β-Amyrin to form oleanolic acid, the precursor of hederagenin-based saponin. LmUGT73P1 was identified to catalyse cauloside A to produce α-hederin. We further identified the key amino acid residues of LmOAS1 and LmUGT73P1 for their enzymatic activities. Additionally, comparing with collinear genes in LJ, LmOAS1 and LmUGT73P1 had an interesting phenomenon of ‘neighbourhood replication’ in LM genome. Collectively, the genomic resource and candidate genes reported here set the foundation to fully reveal the genome evolution of the Lonicera genus and hederagenin-based saponin biosynthetic pathway.Item Comparative transcriptome analysis of respiration-related genes in nodules of phosphate-deficient soybean (Glycine max cv. Williams 82)(2024) Sulieman, Saad; Van Ha, Chien (TTU); Le, Dung Tien; Abdelrahman, Mostafa (TTU); Tran, Cuong Duy; Watanabe, Yasuko; Tanaka, Maho; Ulhassan, Zaid; Sheteiwy, Mohamed S.; Gangurde, Sunil S.; Mochida, Keiichi; Seki, Motoaki; Tran, Lam Son Phan (TTU)A transcriptome analysis was used to compare the nodule transcriptomes of the model soybean ‘Williams 82’ inoculated with two Bradyrhizobium diazoefficiens strains (USDA110 vs. CB1809) under phosphate (Pi) deficiency. The entire dataset revealed a core set of low-Pi-responsive genes and recognized enormous differential transcriptional changes between the Pi-deprived USDA110-nodules and CB1809-nodules. The lower symbiotic efficiency of the Pi-starved USDA110 nodules was ascribed to the downregulation of an F1-ATPase gene engaged in oxidative phosphorylation, more likely contributing to diminished ATP production. To cope with energy shortage caused by Pi stress, the Pi-deprived USDA110-nodules preferentially upregulated the expression of a large number of genes encoding enzymes implicated in specialized energy-demanding pathways, such as the mitochondrial respiratory chain (i.e., cytochrome c oxidase), alcoholic fermentation (i.e., pyruvate decarboxylase and alcohol dehydrogenase) and glycolysis (e.g., hexokinase, phosphofructokinase, glyceraldehyde‐3‐phosphate dehydrogenase and pyruvate kinase). These respiratory adjustments were likely associated with higher metabolic cost and redox imbalance, thereby, negatively affecting nodule symbiosis under Pi deprivation. In contrast, the Pi-starved CB1809-nodules reduced the metabolic cost by regulating a lower number of genes and increasing the expression of genes encoding proteins implicated in non-phosphorylating bypasses (e.g., flavoprotein alpha and flavoprotein:ubiqionone oxidoreductase), which could promote the carbohydrate utilization efficiency and energy metabolism. Notably, the upregulation of a transcript encoding a malate dehydrogenase could boost the CB1809-nodules under Pi stress. The dynamic shifts in energy metabolism in the Pi-deprived USDA110-nodules and CB1809-nodules could be transformative to upgrade the mechanistic/conceptual understandings of soybean adaptation to Pi deficiency at the transcriptional level.Item Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication(2022) Tian, Lei; Chang, Jingjing; Shi, Shaohua; Ji, Li; Zhang, Jianfeng; Sun, Yu; Li, Xiaojie; Li, Xiujun; Xie, Hongwei; Cai, Yaohui; Chen, Dazhou; Wang, Jilin; van Veen, Johannes A.; Kuramae, Eiko E.; Tran, Lam Son Phan (TTU); Tian, ChunjieMicrobial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.Item Cytokinin and MAX2 signaling pathways act antagonistically in drought adaptation of Arabidopsis thaliana(2024) Nguyen, Kien Huu; Li, Zihan; Wang, Chengliang; Van Ha, Chien (TTU); Tran, Cuong Duy; Abdelrahman, Mostafa (TTU); Pham, Xuan Hoi; Trung, Khuat Huu; Khanh, Tran Dang; Chu, Ha Duc; Mostofa, Mohammad Golam; Watanabe, Yasuko; Wang, Yaping; Miao, Yuchen; Mochida, Keiichi; Pal, Sikander; Li, Weiqiang; Tran, Lam Son Phan (TTU)Understanding the mechanisms, especially those associated with phytohormones, of plant drought adaptation is crucial for sustaining agricultural production in the era of climate change. Arabidopsis histidine kinases (AHKs), an integral part of the cytokinin signaling pathway, and more axillary growth 2 (MAX2), a key component of the strigolactone and karrikin signaling pathways are reported to act as negative and positive regulators, respectively, in plant adaption to drought. However, the potential interaction between these singaling pathways in plant drought adaptation is not fully understood. To address this query, we assessed drought tolerance levels and associated phenotypic and physiological traits of the max2 single mutant, ahk2 ahk3 double mutant, ahk2 ahk3 max2 triple mutant, and wild-type (WT) Arabidopsis thaliana plants. Our findings revealed a distinct hierarchy in drought tolerance among these genotypes, as indicated by the differences in plant growth and stress survival rates. Specifically, the max2 mutant displayed the lowest drought tolerance level, followed by WT, ahk2 ahk3 max2, and ahk2 ahk3 plants. Additionally, the observed changes in leaf relative water content, leaf surface temperature, and cuticle formation were coherently aligned with the observed hierarchy of drought tolerance levels. Under drought conditions, the max2 mutant exhibited higher oxidative stress and membrane damage, as evidenced by increased levels of reactive oxygen species (ROS), malondialdehyde, and electrolyte leakage. In contrast, the ahk2 ahk3 and ahk2 ahk3 max2 mutants showed low and intermediate levels, respectively, for these parameters. The max2 mutant displayed reduced sensitivity, whereas ahk2 ahk3 and ahk2 ahk3 max2 mutants demonstrated high and intermediate sensitivities, respectively, to exogenous abscisic acid (ABA) treatments. Additionally, the expression analysis of several genes associated with the investigated drought tolerance-related traits showed a positive correlation between the transcript levels and corresponding trait(s) in both mutant and WT plants under drought conditions. Our results collectively indicate the presence of an antagonistic interaction between AHK and MAX2 signaling pathways in plant drought adaptation, impacting ABA responsiveness, leaf water retention, cuticle development, and ROS homestasis. The findings of this study provide a valuable foundation for developing agricultural methods to improve plant drought resilience.Item Driving factor analysis of ecosystem service balance for watershed management in the Lancang river valley, Southwest China(2021) Liu, Shiliang; Sun, Yongxiu; Wu, Xue; Li, Weiqiang; Liu, Yixuan; Tran, Lam Son Phan (TTU)Revealing the spatio-temporal change of the supply, demand and balance of ecosystem services (ESs) associated with human activities and land-use changes is of great significance for watershed ecosystem management. Taking the Lancang river valley as a case, we explicitly studied the ES spatial characteristics, using the land use/land cover (LULC) matrix model, Optimized Hot Spot Analysis and landscape pattern analysis. Furthermore, we screened out the dominant explanatory variables that had significant influence on the ES supply, demand and balance by means of the Geographical Weighted Regression (GWR) method at pixel scale. The results showed that the ES demand intensity varied little throughout the watershed, while the downstream ES supply capacity and balance values were greater than upstream ones. Meanwhile, the hotspots of ES supply and demand were mainly distributed in the south part with coldspots in the north part. Human activity factors integrating landscape pattern variables were verified to have a negative impact on the ES balance in general. Among them, the Largest Patch Index (LPI) had a negative influence on the majority of pixels, while the Gross Domestic Product (GDP), cultivated land ratio and Area Weighted Average Patch Fractal Dimension (AWAPFD) had positive effects on a few pixels. This study will provide scientific support for regional ecosystem service trade-off and regulation at multiple scales.Item Effect of Reproductive Stage-Waterlogging on the Growth and Yield of Upland Cotton (Gossypium hirsutum)(2023) Somaddar, Uzzal; Mia, Shamim; Khalil, Md Ibrahim; Sarker, Uttam Kumer; Uddin, Md Romij; Kaysar, Md Salahuddin; Chaki, Apurbo Kumar; Robin, Arif Hasan Khan; Hashem, Abeer; Abd_Allah, Elsayed Fathi; Ha, Chien Van (TTU); Gupta, Aarti (TTU); Park, Jong In; Tran, Lam Son Phan (TTU); Saha, GopalThe reproductive stage of cotton (Gossypium sp.) is highly sensitive to waterlogging. The identification of potential elite upland cotton (Gossypium hirsutum) cultivar(s) having higher waterlogging tolerance is crucial to expanding cotton cultivation in the low-lying areas. The present study was designed to investigate the effect of waterlogging on the reproductive development of four elite upland cotton cultivars, namely, Rupali-1, CB-12, CB-13, and DM-3, against four waterlogging durations (e.g., 0, 3, 6, and 9-day). Waterlogging stress significantly impacted morpho-physiological, biochemical, and yield attributes of cotton. Two cotton cultivars, e.g., CB-12 and Rupali-1, showed the lowest reduction in plant height (6 and 9%, respectively) and boll weight (8 and 5%, respectively) at the highest waterlogging duration of 9 days. Physiological and biochemical data revealed that higher leaf chlorophyll, proline, and relative water contents, and lower malondialdehyde contents, particularly in CB-12 and Rupali-1, were positively correlated with yield. Notably, CB-12 and Rupali-1 had higher seed cotton weight (90.34 and 83.10 g, respectively), lint weight (40.12 and 39.32 g, respectively), and seed weight (49.47 and 43.78 g, respectively) per plant than CB-13 and DM-3 in response to the highest duration of waterlogging of 9 days. Moreover, extensive multivariate analyses like Spearman correlation and the principle component analysis revealed that CB-12 and Rupali-1 had greater coefficients in yield and physiological attributes at 9-day waterlogging, whereas CB-13 and DM-3 were sensitive cultivars in response to the same levels of waterlogging. Thus, CB-12 and Rupali-1 might be well adapted to the low-lying waterlogging-prone areas for high and sustained yield.Item Effects of microbial biostimulants (Trichoderma album and Bacillus megaterium) on growth, quality attributes, and yield of onion under field conditions(2023) Younes, Nabil A.; Anik, Touhidur Rahman (TTU); Rahman, Md Mezanur (TTU); Wardany, Ahmed A.; Dawood, Mona F.A.; Tran, Lam Son Phan (TTU); Abdel Latef, A. A.H.; Mostofa, Mohammad GolamMicrobial biostimulants (MBs) promote plant growth and stress tolerance in a sustainable manner. However, precise field trials of MBs are required in natural setting with a range of crop varieties to harness the benefits of biostimulants on crop yield improvement. This study investigated the effects of two MBs, Trichoderma album and Bacillus megaterium, on an onion cultivar's growth, nutritional qualities, antioxidant properties, and yield potentials under field conditions for two successive years. Before transplantation, onion bulbs were gelatin-coated with 2.0 and 4.0 g L−1 of each of the MB. Results revealed that MBs-pretreated onion plants exhibited better growth indices, photosynthetic pigment contents, and yield-attributing features like bulb weight than control plants. Nutraceutical analysis demonstrated that T. album-pretreated (by 2.0 g L−1) onion cultivar enhanced the level of K+ (by 105.79%), Ca2+ (by 37.77%), proline (by 34.21%), and total free amino acids (by 144.58%) in bulb tissues over the control plants. Intriguingly, the pretreatment with both T. album and B. megaterium (by 2.0 g L−1) increased the levels of total soluble carbohydrates (by 19.10 and 84.02%), as well as antioxidant properties, including increased activities of superoxide dismutase (by 58.52 and 31.34%), catalase (by 164.71 and 232%), ascorbate peroxidase (by 175.35 and 212.69%), and glutathione-S-transferase (by 31.99 and 9.34%) and improved the contents of ascorbic acid (by 19.1 and 44.05%), glutathione (by 6.22 and 33.82%), and total flavonoids (by 171.98 and 56.24%, respectively) in the bulb tissues than control plants. Although both MBs promoted the growth and nutraceutical qualities of onion bulbs, T. album pretreatment showed better effects than that of B. megaterium in the field settings. Based on the morphophysiological attributes and biochemical properties, a low dose (2.0 g L−1) was more effective than a high dose (4.0 g L−1) of T. album in promoting onion growth. Overall, the current research findings imply that T. album might be a potential MB in improving growth and quality attributes, and hence the productivity of onion cultivars under field circumstances.Item Ethanol Positively Modulates Photosynthetic Traits, Antioxidant Defense and Osmoprotectant Levels to Enhance Drought Acclimatization in Soybean(2022) Rahman, Md Mezanur (TTU); Mostofa, Mohammad Golam (TTU); Das, Ashim Kumar; Anik, Touhidur Rahman; Keya, Sanjida Sultana (TTU); Ahsan, S. M.; Khan, Md Arifur Rahman; Ahmed, Minhaz; Rahman, Md Abiar; Hossain, Md Motaher; Tran, Lam Son Phan (TTU)Drought is a major environmental threat to agricultural productivity and food security across the world. Therefore, addressing the detrimental effects of drought on vital crops like soybean has a significant impact on sustainable food production. Priming plants with organic compounds is now being considered as a promising technique for alleviating the negative effects of drought on plants. In the current study, we evaluated the protective functions of ethanol in enhancing soybean drought tolerance by examining the phenotype, growth attributes, and several physiological and biochemical mechanisms. Our results showed that foliar application of ethanol (20 mM) to drought-stressed soybean plants increased biomass, leaf area per trifoliate, gas exchange features, water-use-efficiency, photosynthetic pigment contents, and leaf relative water content, all of which contributed to the improved growth performance of soybean under drought circumstances. Drought stress, on the other hand, caused significant accumulation of reactive oxygen species (ROS), such as superoxide and hydrogen peroxide, and malondialdehyde, as well as an increase of electrolyte leakage in the leaves, underpinning the evidence of oxidative stress and membrane damage in soybean plants. By comparison, exogenous ethanol reduced the ROS-induced oxidative burden by boosting the activities of antioxidant enzymes, including peroxidase, catalase, glutathione S-transferase, and ascorbate peroxidase, and the content of total flavonoids in soybean leaves exposed to drought stress. Additionally, ethanol supplementation increased the contents of total soluble sugars and free amino acids in the leaves of drought-exposed plants, implying that ethanol likely employed these compounds for osmotic adjustment in soybean under water-shortage conditions. Together, our findings shed light on the ethanol-mediated protective mechanisms by which soybean plants coordinated different morphophysiological and biochemical responses in order to increase their drought tolerance.Item Ethanol Treatment Enhances Physiological and Biochemical Responses to Mitigate Saline Toxicity in Soybean(2022) Das, Ashim Kumar; Anik, Touhidur Rahman; Rahman, Md Mezanur (TTU); Keya, Sanjida Sultana (TTU); Islam, Md Robyul; Rahman, Md Abiar; Sultana, Sharmin; Ghosh, Protik Kumar; Khan, Sabia; Ahamed, Tofayel; Ghosh, Totan Kumar; Tran, Lam Son Phan (TTU); Mostofa, Mohammad Golam (TTU)Soil salinity, a major environmental concern, significantly reduces plant growth and production all around the world. Finding solutions to reduce the salinity impacts on plants is critical for global food security. In recent years, the priming of plants with organic chemicals has shown to be a viable approach for the alleviation of salinity effects in plants. The current study examined the effects of exogenous ethanol in triggering salinity acclimatization responses in soybean by investigating growth responses, and numerous physiological and biochemical features. Foliar ethanol application to saline water-treated soybean plants resulted in an enhancement of biomass, leaf area, photosynthetic pigment contents, net photosynthetic rate, shoot relative water content, water use efficiency, and K+ and Mg2+ contents, leading to improved growth performance under salinity. Salt stress significantly enhanced the contents of reactive oxygen species (ROS), malondialdehyde, and electrolyte leakage in the leaves, suggesting salt-induced oxidative stress and membrane damage in soybean plants. In contrast, ethanol treatment of salt-treated soybean plants boosted ROS-detoxification mechanisms by enhancing the activities of antioxidant enzymes, including peroxidase, ascorbate peroxidase, catalase, and glutathione S-transferase. Ethanol application also augmented the levels of proline and total free amino acids in salt-exposed plants, implying a role of ethanol in maintaining osmotic adjustment in response to salt stress. Notably, exogenous ethanol decreased Na+ uptake while increasing K+ and Mg2+ uptake and their partitioning to leaves and roots in salt-stressed plants. Overall, our findings reveal the protective roles of ethanol against salinity in soybean and suggest that the use of this cost-effective and easily accessible ethanol in salinity mitigation could be an effective approach to increase soybean production in salt-affected areas.Item Exploring the Phenotypic and Genetic Variabilities in Yield and Yield-Related Traits of the Diallel-Crossed F5 Population of Aus Rice(2023) Khan, Md Arifur Rahman (TTU); Mahmud, Apple; Ghosh, Uttam Kumar; Hossain, Md Saddam; Siddiqui, Md Nurealam; Islam, A. K.M.Aminul; Anik, Touhidur Rahman (TTU); Rahman, Md Mezanur (TTU); Sharma, Anket (TTU); Abdelrahman, Mostafa (TTU); Ha, Chien Van (TTU); Mostofa, Mohammad Golam; Tran, Lam Son Phan (TTU)Rice (Oryza sativa) is a major crop and a main food for a major part of the global population. Rice species have derived from divergent agro-climatic regions, and thus, the local germplasm has a large genetic diversity. This study investigated the relationship between phenotypic and genetic variabilities of yield and yield-associated traits in Aus rice to identify short-duration, high-yielding genotypes. Targeting this issue, a field experiment was carried out to evaluate the performance of 51 Aus rice genotypes, including 50 accessions in F5 generation and one short-duration check variety BINAdhan-19. The genotypes exhibited a large and significant variation in yield and its associated traits, as evidenced by a wide range of their coefficient of variance. The investigated traits, including days to maturity (DM), plant height (PH), panicle length (PL) and 1000-grain weight (TW) exhibited a greater genotypic coefficient of variation than the environmental coefficient of variation. In addition, the high broad-sense heritability of DM, PH, PL and TW traits suggests that the genetic factors significantly influence the observed variations in these traits among the F5 Aus rice accessions. This study also revealed that the grain yield per hill (GY) displayed a significant positive correlation with PL, number of filled grains per panicle (FG) and TW at both genotype and phenotype levels. According to the hierarchical and K-means cluster analyses, the accessions BU-R-ACC-02, BU-R-ACC-08 and R2-36-3-1-1 have shorter DM and relatively higher GY than other Aus rice accessions. These three accessions could be employed in the ongoing and future breeding programs for the improvement of short-duration and high-yielding rice cultivars.Item Genome-wide characterization of the glutathione S-transferase gene family in Phaseolus vulgaris reveals insight into the roles of their members in responses to multiple abiotic stresses(2024) Anik, Touhidur Rahman (TTU); Chu, Ha Duc; Ahmed, Md Shahabuddin; Van Ha, Chien (TTU); Gangurde, Sunil S.; Khan, Md Arifur Rahman (TTU); Le, Thao Duc; Le, Dung Tien; Abdelrahman, Mostafa (TTU); Tran, Lam Son Phan (TTU)Glutathione S-transferases (GSTs) are a class of multifunctional enzymatic antioxidants that play a significant role in several aspects of plant physiology, including growth, development, and cellular protection from biotic and abiotic stressors. A total of 59 GST genes were found in Phaseolus vulgaris genome, which were categorized into 11 distinct classes according to their evolutionary connection and the existence of conserved structural domains and motifs. Gene duplication analysis revealed that the evolution of the members of the GST gene family in P. vulgaris was driven by both segmental and tandem duplication events. Analysis of the expression profiles of identified PvGST genes using the available transcriptome data demonstrated notable expression patterns and organ specificity of many genes throughout several developmental stages and under drought or salinity. Subsequent RT-qPCR analysis of several drought-responsive or salinity-responsive candidate genes showed that PvGSTF4 was up-regulated solely by drought, PvGSTU11 was up-regulated only by salinity, and PvGSTU3, PvGSTU12, PvGSTU13, PvGSTU14, PvGSTU16, PvGSTT1, and PvGSTZ2 were up-regulated by both salt and drought. The up-regulated PvGSTs under drought and/or salinity might enable P. vulgaris to adapt to stressful environments. These candidate genes could be explored in genetic engineering programs for development of stress-tolerant P. vulgaris varieties.Item Identification of bZIP Transcription Factors That Regulate the Development of Leaf Epidermal Cells in Arabidopsis thaliana by Single-Cell RNA Sequencing(2024) Wu, Rui; Liu, Zhixin; Sun, Susu; Qin, Aizhi; Liu, Hao; Zhou, Yaping; Li, Weiqiang; Liu, Yumeng; Hu, Mengke; Yang, Jincheng; Rochaix, Jean David; An, Guoyong; Herrera-Estrella, Luis (TTU); Tran, Lam Son Phan (TTU); Sun, XuwuEpidermal cells are the main avenue for signal and material exchange between plants and the environment. Leaf epidermal cells primarily include pavement cells, guard cells, and trichome cells. The development and distribution of different epidermal cells are tightly regulated by a complex transcriptional regulatory network mediated by phytohormones, including jasmonic acid, and transcription factors. How the fate of leaf epidermal cells is determined, however, is still largely unknown due to the diversity of cell types and the complexity of their regulation. Here, we characterized the transcriptional profiles of epidermal cells in 3-day-old true leaves of Arabidopsis thaliana using single-cell RNA sequencing. We identified two genes encoding BASIC LEUCINE-ZIPPER (bZIP) transcription factors, namely bZIP25 and bZIP53, which are highly expressed in pavement cells and early-stage meristemoid cells. Densities of pavement cells and trichome cells were found to increase and decrease, respectively, in bzip25 and bzip53 mutants, compared with wild-type plants. This trend was more pronounced in the presence of jasmonic acid, suggesting that these transcription factors regulate the development of trichome cells and pavement cells in response to jasmonic acid.Item Medicago sativa and Medicago truncatula Show Contrasting Root Metabolic Responses to Drought(2021) Echeverria, Andres; Larrainzar, Estíbaliz; Li, Weiqiang; Watanabe, Yasuko; Sato, Muneo; Tran, Cuong Duy; Moler, Jose A.; Hirai, Masami Yokota; Sawada, Yuji; Tran, Lam Son Phan (TTU); Gonzalez, Esther M.Drought is an environmental stressor that affects crop yield worldwide. Understanding plant physiological responses to stress conditions is needed to secure food in future climate conditions. In this study, we applied a combination of plant physiology and metabolomic techniques to understand plant responses to progressive water deficit focusing on the root system. We chose two legume plants with contrasting tolerance to drought, the widely cultivated alfalfa Medicago sativa (Ms) and the model legume Medicago truncatula (Mt) for comparative analysis. Ms taproot (tapR) and Mt fibrous root (fibR) biomass increased during drought, while a progressive decline in water content was observed in both species. Metabolomic analysis allowed the identification of key metabolites in the different tissues tested. Under drought, carbohydrates, abscisic acid, and proline predominantly accumulated in leaves and tapRs, whereas flavonoids increased in fibRs in both species. Raffinose-family related metabolites accumulated during drought. Along with an accumulation of root sucrose in plants subjected to drought, both species showed a decrease in sucrose synthase (SUS) activity related to a reduction in the transcript level of SUS1, the main SUS gene. This study highlights the relevance of root carbon metabolism during drought conditions and provides evidence on the specific accumulation of metabolites throughout the root system.Item Positive roles of the Ca2+ sensors GbCML45 and GbCML50 in improving cotton Verticillium wilt resistance(2024) Yi, Feifei; Li, Yuzhe; Song, Aosong; Shi, Xinying; Hu, Shanci; Wu, Shuang; Shao, Lili; Chu, Zongyan; Xu, Kun; Li, Liangliang; Tran, Lam Son Phan (TTU); Li, Weiqiang; Cai, YingfanAs a universal second messenger, cytosolic calcium (Ca2+) functions in multifaceted intracellular processes, including growth, development and responses to biotic/abiotic stresses in plant. The plant-specific Ca2+ sensors, calmodulin and calmodulin-like (CML) proteins, function as members of the second-messenger system to transfer Ca2+ signal into downstream responses. However, the functions of CMLs in the responses of cotton (Gossypium spp.) after Verticillium dahliae infection, which causes the serious vascular disease Verticillium wilt, remain elusive. Here, we discovered that the expression level of GbCML45 was promoted after V. dahliae infection in roots of cotton, suggesting its potential role in Verticillium wilt resistance. We found that knockdown of GbCML45 in cotton plants decreased resistance while overexpression of GbCML45 in Arabidopsis thaliana plants enhanced resistance to V. dahliae infection. Furthermore, there was physiological interaction between GbCML45 and its close homologue GbCML50 by using yeast two-hybrid and bimolecular fluorescence assays, and both proteins enhanced cotton resistance to V. dahliae infection in a Ca2+-dependent way in a knockdown study. Detailed investigations indicated that several defence-related pathways, including salicylic acid, ethylene, reactive oxygen species and nitric oxide signalling pathways, as well as accumulations of lignin and callose, are responsible for GbCML45- and GbCML50-modulated V. dahliae resistance in cotton. These results collectively indicated that GbCML45 and GbCML50 act as positive regulators to improve cotton Verticillium wilt resistance, providing potential targets for exploitation of improved Verticillium wilt-tolerant cotton cultivars by genetic engineering and molecular breeding.Item Quantifying Carbon Sequestration Service Flow Associated with Human Activities Based on Network Model on the Qinghai-Tibetan Plateau(2022) Wang, Qingbo; Liu, Shiliang; Wang, Fangfang; Liu, Hua; Liu, Yixuan; Yu, Lu; Sun, Jian; Tran, Lam Son Phan (TTU); Dong, YuhongThe flow of ecosystem services between regions as a result of the mismatch of supply and demand has increasingly become a new research focus. Clarifying the spatial regularity of ecosystem service flow is of great significance for realizing regional sustainable development and improving human well-being. This study applied a network model to map the interregional carbon flow based on the supply and demand of carbon sequestration service, and the driving effect of various driving factors was further analyzed. The results showed that the demand for carbon sequestration service on the Qinghai-Tibet Plateau increased steadily from 2000 to 2019, resulting in an increasingly significant difference between supply and demand with more than 20 million tons. In the carbon sequestration service flow network, the number of defined deficit nodes increased to 22 in 2010, but decreased to 21 in 2019. The interrupted edges continued to increase to 16, and the network density dropped to 0.022. The carbon sequestration service flow network on the northeastern parts of the Qinghai-Tibet Plateau was severely damaged. With the high-quality development of animal husbandry, the impact of grazing intensity on the difference between the supply and demand of carbon sequestration service has been weakened. When urbanization reached a certain level, the driving effects of urbanization and agricultural activities increased significantly. The study provided a reference for the use of network models to analyze ecosystem service flow, and provided a theoretical basis and data support for local ecological management decisions.Item Sclerotinia sclerotiorum (Lib.) de Bary: Insights into the Pathogenomic Features of a Global Pathogen(2023) Hossain, Md Motaher; Sultana, Farjana; Li, Weiqiang; Tran, Lam Son Phan (TTU); Mostofa, Mohammad GolamSclerotinia sclerotiorum (Lib.) de Bary is a broad host-range fungus that infects an inclusive array of plant species and afflicts significant yield losses globally. Despite being a notorious pathogen, it has an uncomplicated life cycle consisting of either basal infection from myceliogenically germinated sclerotia or aerial infection from ascospores of carpogenically germinated sclerotia. This fungus is unique among necrotrophic pathogens in that it inevitably colonizes aging tissues to initiate an infection, where a saprophytic stage follows the pathogenic phase. The release of cell wall-degrading enzymes, oxalic acid, and effector proteins are considered critical virulence factors necessary for the effective pathogenesis of S. sclerotiorum. Nevertheless, the molecular basis of S. sclerotiorum pathogenesis is still imprecise and remains a topic of continuing research. Previous comprehensive sequencing of the S. sclerotiorum genome has revealed new insights into its genome organization and provided a deeper comprehension of the sophisticated processes involved in its growth, development, and virulence. This review focuses on the genetic and genomic aspects of fungal biology and molecular pathogenicity to summarize current knowledge of the processes utilized by S. sclerotiorum to parasitize its hosts. Understanding the molecular mechanisms regulating the infection process of S. sclerotiorum will contribute to devising strategies for preventing infections caused by this destructive pathogen.