Search Results (47)

The common bean (Phaseolus vulgaris L.), whose annual production is 26 million tons worldwide, is one of the main sources of protein and is known as one of the most important food sources. In this study, the karyotype variations and the genome size of four common bean genotypes in Turkey were investigated to determine whether the geographic variables in these regions affected the genome size and the karyotype parameters. In addition, it is known that as that the cytological and chromosomal parameters change under the influence of the climatic conditions of each region, appropriate and stable cytological methods for each plant facilitate and enable the determination of the chromosomal structure and the identification of specific chromosomes in the genotypes of the relevant region. Correct and valuable information such as this enables breeders and researchers to determine the correct shape and actual size of chromosomes. The genome size of the genotypes was measured with a flow cytometer, and chromosome analyses were performed with the squash method. For each genotype, the karyotype parameters, such as the number of somatic chromosomes, the Mean Total Chromosome Length (MTCL), the Mean Centromere Index (MCI), and the Mean Arm Ratio (MAR), were measured. The results showed that the highest and the lowest amounts of DNA per nucleus (3.28 pg and 1.49 pg) were observed in the Bitlis and Elaziğ genotypes. In addition, all genotype chromosome numbers were counted to be 2n = 2x = 22. The Mean Total Chromosome Length varied from 15.65 µm in Elaziğ to 34.24 µm in the Bitlis genotype. The Mean Chromosome Length ranged between 1.42 µm and 3.11 µm in the Elaziğ and Bitlis genotypes. The Hakkari and Van genotypes consist of eleven metacentric chromosomes, while the Bitlis and Elaziğ genotypes consist of ten metacentric chromosomes and one sub-metacentric chromosome. However, the Mean Centromere Index and Arm Ratio differed considerably among the genotypes. The highest (46.88) and the lowest (43.18) values of the Mean Centromere Index were observed in the Hakkari and Elaziğ genotypes, respectively. On the other hand, the lowest (1.15) and the highest (1.36) values of the Mean Arm Ratio were obtained in the Bitlis and Elaziğ genotypes, respectively. Eventually, intraspecies variations in genome size and chromosomal parameters were observed, and it was determined that the changes in nuclear DNA content and different chromosomal parameters among the four Phaseolus genotypes from four different regions of Turkey indicate the effect of climate change in the regions on these parameters. Such information in these areas can be used as useful information for the improvement of this plant and breeding programs. Full article

Anisodus tanguticus Maxim. (Solanaceae), a traditional endangered Tibetan herb, is endemic to the Qinghai–Tibet Plateau. Here, we report the de novo assembled chloroplast (cp) genome sequences of A. tanguticus (155,765 bp). The cp contains a pair of inverted repeated (IRa and IRb) regions of 25,881 bp that are separated by a large single copy (LSC) region (86,516 bp) and a small single copy SSC (17,487 bp) region. A total of 132 functional genes were annotated in the cp genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Moreover, 199 simple sequence repeats (SSR) and 65 repeat structures were detected. Comparative plastome analyses revealed a conserved gene order and high similarity of protein-coding sequences. The A. tanguticus cp genome exhibits contraction and expansion, which differs from Przewalskia tangutica and other related Solanaceae species. We identified 30 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which may be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Anisodus and family Solanaceae. Analysis of the Ka/Ks ratios of the Hyoscyameae tribe revealed significant positive selection exerted on the cemA, rpoC2, and clpP genes, which suggests that protein metabolism may be an important strategy for A. tanguticus and other species in Hyoscyameae in adapting to the adverse environment on the Qinghai–Tibetan Plateau. Phylogenetic analysis revealed that A. tanguticus clustered closer with Hyoscyamus niger than P. tangutica. Our results provide reliable genetic information for future exploration of the taxonomy and phylogenetic evolution of the Hyoscyameae tribe and related species. Full article

Agroforestry integrates woody perennials with arable crops, livestock, or fodder in the same piece of land, promoting the more efficient utilization of resources as compared to monocropping via the structural and functional diversification of components. This integration of trees provides various soil-related ecological services such as fertility enhancements and improvements in soil physical, biological, and chemical properties, along with food, wood, and fodder. By providing a particular habitat, refugia for epigenic organisms, microclimate heterogeneity, buffering action, soil moisture, and humidity, agroforestry can enhance biodiversity more than monocropping. Various studies confirmed the internal restoration potential of agroforestry. Agroforestry reduces runoff, intercepts rainfall, and binds soil particles together, helping in erosion control. This trade-off between various non-cash ecological services and crop production is not a serious constraint in the integration of trees on the farmland and also provides other important co-benefits for practitioners. Tree-based systems increase livelihoods, yields, and resilience in agriculture, thereby ensuring nutrition and food security. Agroforestry can be a cost-effective and climate-smart farming practice, which will help to cope with the climate-related extremities of dryland areas cultivated by smallholders through diversifying food, improving and protecting soil, and reducing wind erosion. This review highlighted the role of agroforestry in soil improvements, microclimate amelioration, and improvements in productivity through agroforestry, particularly in semi-arid and degraded areas under careful consideration of management practices. Full article

Enterobacter xiangfangensis is a novel, multidrug-resistant pathogen belonging to the Enterobacter genus and has the ability to acquire resistance to multiple antibiotic classes. However, there is currently no registered E. xiangfangensis drug on the market that has been shown to be effective. Hence, there is an urgent need to identify novel therapeutic targets and effective treatments for E. xiangfangensis. In the current study, a bacterial pan genome analysis and subtractive proteomics approach was employed to the core proteomes of six strains of E. xiangfangensis using several bioinformatic tools, software, and servers. However, 2611 nonredundant proteins were predicted from the 21,720 core proteins of core proteome. Out of 2611 nonredundant proteins, 372 were obtained from Geptop2.0 as essential proteins. After the subtractive proteomics and subcellular localization analysis, only 133 proteins were found in cytoplasm. All cytoplasmic proteins were examined using BLASTp against the virulence factor database, which classifies 20 therapeutic targets as virulent. Out of these 20, 3 cytoplasmic proteins: ferric iron uptake transcriptional regulator (FUR), UDP-2,3diacylglucosamine diphosphatase (UDP), and lipid-A-disaccharide synthase (lpxB) were chosen as potential drug targets. These drug targets are important for bacterial survival, virulence, and growth and could be used as therapeutic targets. More than 2500 plant chemicals were used to molecularly dock these proteins. Furthermore, the lowest-binding energetic docked compounds were found. The top five hit compounds, Adenine, Mollugin, Xanthohumol C, Sakuranetin, and Toosendanin demonstrated optimum binding against all three target proteins. Furthermore, molecular dynamics simulations and MM/GBSA analyses validated the stability of ligand–protein complexes and revealed that these compounds could serve as potential E. xiangfangensis replication inhibitors. Consequently, this study marks a significant step forward in the creation of new and powerful drugs against E. xiangfangensis. Future studies should validate these targets experimentally to prove their function in E. xiangfangensis survival and virulence. Full article

The genera Triticum and Aegilops have been considered as the main gene pool of wheat due to their features, such as tolerance of all types of abiotic and biotic stresses. This study was conducted to evaluate the cytogenetic analyses in 115 native and wild populations from eleven Aegilops species using their nuclear DNA quantification. Mean 2C nuclear DNA contents of different ploidy levels in the wild wheat of Turkey and Iran were measured using the flow cytometry technique. The obtained results showed that the mean nuclear DNA content in diploid species varied from 10.09 pg/2C (Ae. umbellulata) to 10.95 pg/2C (Ae. speltoides var. ligustica) in Turkey. In Iranian diploids, the mean nuclear DNA content varied from 10.20 pg/2C (Ae. taushii) to 11.56 pg/2C (Ae. speltoides var. ligustica). This index in the tetraploid species of Turkey varied from 18.09 pg/2C (Ae. cylindrica) to 21.65 pg/2C (Ae. triaristata), and in Iranian species, it was from 18.61 pg/2C (Ae. cylindrica) to 21.75 pg/2C (Ae. columnaris). On the other hand, in the hexaploid species of Turkey, this index varied from 31.59 pg/2C (Ae. crassa) to 31.81 pg/2C (Ae. cylindrica); in the Iranian species, it varied from 32.58 pg/2C (Ae. cylindrica) to 33.97 pg/2C (Ae. crassa). There was a significant difference in the DNA content of Turkey and Iran diploid as well as tetraploid species; however, in hexaploid species, the difference was not significant. It was concluded that the variation in intraspecific genome size was very low in diploid and tetraploid populations; this means that the low variation is not dependent on geographic and climatic parameters. On the other hand, the interspecific variation is significant at the diploid and tetraploid populations. It is generally very difficult to distinguish Aegilops species from each other in natural conditions; meanwhile, in this study, all species could be, easily, quickly and unambiguously, distinguished and separated using the FCM technique. Full article

Interest in conservation measures, including reduced tillage, zero tillage, and crop residue retention, is growing in major rice growing areas of the world; particularly in the Indo-Gangetic plains. Of late, research interest is increasing in India for a specialised method of cultivation known as natural farming, which aims at maintain the functional biodiversity of the farm with little or no use of external inputs. With the increasing water crisis at a global level, it became imperative to develop technologies that can reduce the water use, particularly in water-guzzling low land paddy, by developing alternate cultivation methods; direct seeded rice is one such technology. A two-year field experiment was carried out at two locations during 2019–2020 and 2020–2021 to find out the impact of different cultivation and varieties on the productivity and profitability of the rice–wheat cropping system. The experiments were conducted in split plot design, replicated thrice, with cultivation practices in the main plot and varieties of both wheat and rice in the sub plot. The results so obtained reveal that conventional tillage significantly out yielded other methods of cultivation in both the crops at both the locations, while significantly lower grain yield in both crops was observed from natural farming. Adoption of reduced tillage, zero tillage and natural farming reduced the grain yield of wheat by 4.6%, 10.9%, and 59.4% over conventional tillage, while the corresponding decline in grain yield of rice was 10.8%, 16.1%, and 34.0% with reduced tillage, zero tillage, and natural farming, respectively. Among the varieties tested, HPW 368 and Him Palam Lal Dhan 1 (HPR 2795) produced significantly higher grain yield of wheat and rice, respectively, at both the locations during both years. Conventional tillage among cultivation practices and HPW 368 and Him Palam Lal Dhan 1 (HPR 2795) among wheat and rice varieties also proved to be better in terms of various economic indicators, including gross return, net return, and ratio benefit cost ratio (B:C ratio). Full article

A plant’s response to osmotic stress is a complex phenomenon that causes many abnormal symptoms due to limitations in growth and development or even the loss of yield. The current research aimed to analyze the agronomical, physiological, and biochemical mechanisms accompanying the acquisition of salt resistance in the Vigna radiata L. variety ‘Ramzan’ using seed osmo- and thermopriming in the presence of PEG-4000 and 4 °C under induced salinity stresses of 100 and 150 mM NaCl. Seeds were collected from CCRI, Nowshera, and sowing was undertaken in triplicate at the Department of Botany, Peshawar University, during the 2018–2019 growing season. Rhizospheric soil pH (6.0), E.C (2.41 ds/m), field capacity, and moisture content level were estimated in the present study. We observed from the estimated results that the agronomic characteristics, i.e., shoot fresh weight and shoot dry weight in T9 (4oC + 150 mM NaCl), root fresh weight and root dry weight in T4 (PEG + 100 mM NaCl), shoot moisture content in T5 (PEG + 100 mM NaCl), and root moisture content in T6 (PEG + 150 mM NaCl) were the highest, followed by the lowest in T1 (both shoot and root fresh weights) and T2 (shoot and root dry weights). Similarly, the shoot moisture content was the maximum in T5 and the minimum in T6, and root moisture was the highest in T6. We observed from the estimated results that agronomical parameters including dry masses (T4, T6, T4), leaf area index, germination index, leaf area, total biomass, seed vigor index under treatment T9, and relative water content and water use efficiency during T5 and T6 were the highest. Plant physiological traits such as proline, SOD enhanced by T1, carotenoids in treatment T2, and chlorophyll and protein levels were the highest under treatment T4, whereas sugar and POD were highest under treatments T7 and T8. The principal component analysis enclosed 63.75% of the total variation among all biological components. These estimated results confirmed the positive resistance by Vigna radiata during osmopriming (PEG) and thermopriming (4 °C) on most of the features with great tolerance under a low-saline treatment such as T4 (PEG), T5 (PEG + 100 mM NaCl), T7 (4 °C), and T8 (4 °C + 100 mM NaCl), while it was susceptible in the case of T6 (PEG + 150 mM NaCl) and T9 (4 °C + 150 mM NaCl) to high salt application. We found that the constraining impact of several priming techniques improved low salinity, which was regarded as economically inexpensive and initiated numerous metabolic processes in plants, hence decreasing germination time. The current study will have major applications for combatting the salinity problem induced by climate change in Pakistan. Full article

Drought is a major abiotic stressor that causes yield losses and limits the growing area for most crops. Soybeans are an important legume crop that is sensitive to water-deficit conditions and suffers heavy yield losses from drought stress. To improve drought-tolerant soybean cultivars through breeding, it is necessary to understand the mechanisms of drought tolerance in soybeans. In this study, we applied several transcriptome datasets obtained from soybean plants under drought stress in comparison to those grown under normal conditions to identify novel drought-responsive genes and their underlying molecular mechanisms. We found 2168 significant up/downregulated differentially expressed genes (DEGs) and 8 core modules using gene co-expression analysis to predict their biological roles in drought tolerance. Gene Ontology and KEGG analyses revealed key biological processes and metabolic pathways involved in drought tolerance, such as photosynthesis, glyceraldehyde-3-phosphate dehydrogenase and cytokinin dehydrogenase activity, and regulation of systemic acquired resistance. Genome-wide analysis of plants’ cis-acting regulatory elements (CREs) and transcription factors (TFs) was performed for all of the identified DEG promoters in soybeans. Furthermore, the PPI network analysis revealed significant hub genes and the main transcription factors regulating the expression of drought-responsive genes in each module. Among the four modules associated with responses to drought stress, the results indicated that GLYMA_04G209700, GLYMA_02G204700, GLYMA_06G030500, GLYMA_01G215400, and GLYMA_09G225400 have high degrees of interconnection and, thus, could be considered as potential candidates for improving drought tolerance in soybeans. Taken together, these findings could lead to a better understanding of the mechanisms underlying drought responses in soybeans, which may useful for engineering drought tolerance in plants. Full article

The medicinal herb coriander (Coriandrum sativum L.), with a high linalool (LIN) content, is widely recognized for its therapeutic benefits. As a novel report, the goals of this study were to determine how methyl jasmonate (MeJA) affects total phenolic content (TPC), LIN content, flavonoid content (TFC), and changes in gene expression involved in the linalool biosynthesis pathway (CsγTRPS and CsLINS). Our findings showed that, in comparison to the control samples, MeJA treatment substantially enhanced the TPC, LIN, and TFC content in both ecotypes. Additionally, for both Iranian coriander ecotypes, treatment-induced increases in CsγTRPS and CsLINS expression were connected to LIN accumulation in all treatments. A 24 h treatment with 150 µM MeJA substantially increased the LIN content in the Mashhad and Zanjan ecotypes, which was between 1.48 and 1.69 times greater than that in untreated plants, according to gas chromatography–mass spectrometry (GC-MS) analysis. Our findings demonstrated that MeJA significantly affects the accumulation of LIN, TPC, and TFC in Iranian C. sativum treated with MeJA, which is likely the consequence of gene activation from the monoterpene biosynthesis pathway. Our discoveries have improved the understanding of the molecular mechanisms behind LIN synthesis in coriander plants. Full article

Nanotechnology has emerged as a new tool to combat phytopathogens in agricultural crops. Cucurbit chlorotic yellows virus (CCYV) mainly infects Solanaceae crops and causes significant crop losses. Nanomaterials (NMs) may have efficacy against plant viruses, but the mechanisms underlying complex nanomaterials-plant-virus interactions remain elusive. We challenged Nicotiana benthamiana plants with GFP-tagged CCYV and observed morphological, physiological, and molecular changes in response to 21-d foliar exposure to nanoscale Fe and Zn and C₆₀ fullerenes at 100 mg/L concentration for 21 days. We observed that in response to C₆₀ (100 mg/L) treatment, plants displayed a normal phenotype while the viral infection was not seen until 5 days post-inoculation. On the contrary, Fe and Zn were unable to suppress viral progression. The mRNA transcriptional analysis for GFP and viral coat protein revealed that the transcripts of both genes were 5-fold reduced in response to C₆₀ treatment. Evaluation of the chloroplast ultrastructure showed that NMs treatment maintained the normal chloroplast structure in the plants as compared to untreated plants. C₆₀ upregulated the defense-related phytohormones (abscisic acid and salicylic acid) by 42–43%. Our results demonstrate the protective function of carbon-based NMs, with suppression of CCYV symptoms via inhibition of viral replication and systemic movement. Full article

More than 70% of our planet is covered by extremely cold environments, nourishing a broad diversity of microbial life. Temperature is the most significant parameter that plays a key role in the distribution of microorganisms on our planet. Psychrophilic microorganisms are the most prominent inhabitants of the cold ecosystems, and they possess potential cold-active enzymes with diverse uses in the research and commercial sectors. Psychrophiles are modified to nurture, replicate, and retain their active metabolic activities in low temperatures. Their enzymes possess characteristics of maximal activity at low to adequate temperatures; this feature makes them more appealing and attractive in biotechnology. The high enzymatic activity of psychrozymes at low temperatures implies an important feature for energy saving. These enzymes have proven more advantageous than their mesophilic and thermophilic counterparts. Therefore, it is very important to explore the efficiency and utility of different psychrozymes in food processing, pharmaceuticals, brewing, bioremediation, and molecular biology. In this review, we focused on the properties of cold-active enzymes and their diverse uses in different industries and research areas. This review will provide insight into the areas and characteristics to be improved in cold-active enzymes so that potential and desired enzymes can be made available for commercial purposes. Full article

Agriculture has a lot of responsibility as the rise in the world’s population demands more food requirements. However, more than one type of biotic and abiotic stress continually impacts agricultural productivity. Drought stress is a major abiotic stress that significantly affects agricultural productivity every year as the plants undergo several morphological, biochemical, and physiological modifications, such as repressed root and shoot growth, reduced photosynthesis and transpiration rate, excessive production of reactive oxygen species (ROS), osmotic adjustments, and modified leaf senescence regulating and stress signaling pathways. Such modifications may permanently damage the plants; therefore, mitigation strategies must be developed. The use of drought resistant crop cultivars is more expensive and labor-intensive with few advantages. However, exploiting plant growth promoting rhizobacteria (PGPR) is a proven alternative with numerous direct and indirect advantages. The PGPR confers induced systemic tolerance (IST) mechanisms in plants in response to drought stress via multiple mechanisms, including the alteration of root architecture, maintenance of high relative water content, improvement of photosynthesis rate, production of phytohormones, exopolysaccharides, ACC deaminase, carotenoids and volatiles, induction of antioxidant defense system, and alteration in stress-responsive gene expression. The commercial application of PGPR as bioinoculants or biostimulants will remain contingent on more robust strain selection and performance under unfavorable environmental conditions. This review highlights the possible mechanisms of PGPR by activating the plant adaptive defense systems for enhancing drought tolerance and improving overall growth and yield. Full article

The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique. Full article

Nanomaterials with unique and diverse physico-chemical properties are used in plant science since they improve plant growth and development and offer protection against biotic and abiotic stressors. Previous studies have explored the effects of such nanomaterials on different plant mechanisms, but information about the effects of nanomaterials on induced DNA methylation, genomic instability and LTR retrotransposon polymorphism in wheat is lacking. Therefore, the present study highlights the key role of nanoparticles in DNA methylation and polymorphism in wheat by investigating the effects of ZnO, CuO and γ-Fe₃O₄ nanoparticles (NPs) on mature embryo cultures of wheat (Triticum aestivum L.). Nanoparticles were supplemented with Murashige and Skoog (MS) basal medium at normal (1X), double (2X) and triple (3X) concentrations. The findings revealed different responses to the polymorphism rate depending on the nanoparticle type and concentration. Genomic template stability (GTS) values were used to compare the changes encountered in iPBS profiles. ZnO, CuO and γ-Fe₃O₄ NPs increased the polymorphism rate and cytosine methylation compared to the positive control while reducing GTS values. Moreover, non-γ-Fe₃O₄ NPs treatments and 2X ZnO and CuO NP treatments yielded higher polymorphism percentages in both MspI- and HpaII-digested CRED-iPBS assays and were thus classified as hypermethylation when the average polymorphism percentage for MspI digestion was considered. On the other hand, the 3X concentrations of all nanoparticles decreased HpaII and MspI polymorphism percentages and were thus classified as hypomethylation. The findings revealed that MS medium supplemented with nanoparticles had epigenetic and genotoxic effects. Full article

In the present study, we estimated genetic diversity and population structure in 186 accessions of Triticum and Aegilops species using 24 simple sequence repeat markers (SSR). Furthermore, an association analysis was performed for antioxidant activities, including guaiacol peroxidase (GPX), ascorbate peroxidase (APX), peroxidase (POX), catalase (CAT), and dry matter (DM) under two control and drought stress conditions. Our findings showed that drought treatment significantly decreased DM, whereas activities of all antioxidant enzymes were increased compared to the control conditions. The results of correlation analysis indicated that, under drought stress conditions, all biochemical traits had a positive and significant association with each other and with dry matter. In the molecular section, the results of the analysis of molecular variance (AMOVA) indicated that the molecular variation within species is more than within them. The dendrogram obtained by cluster analysis showed that grouping the investigated accessions was in accordance with their genomic constitutions. The results of association analysis revealed 8 and 9 significant marker–trait associations (MTA) under control and drought stress conditions, respectively. Among identified MTAs, two associations were simultaneously found in both growing conditions. Moreover, several SSR markers were associated with multiple traits across both conditions. In conclusion, our results could provide worthwhile information regarding marker-assisted selection for the activity of antioxidant enzymes in future breeding programs. Full article