Search Results (31)

The aim of this research is to investigate the potential of Raman and FT-IR spectroscopy as well as mathematical linear and non-linear models as a tool for the discrimination of different seed varieties of paprika, tomato, and lettuce species. After visual inspection of spectra, pre-processing was applied in the following combinations: (1) smoothing + linear baseline correction + unit vector normalization; (2) smoothing + linear baseline correction + unit vector normalization + full multiplicative scatter correction; (3) smoothing + baseline correction + unit vector normalization + second-order derivative. Pre-processing was followed by Principal Component Analysis (PCA), and several classification methods were applied after that: the Support Vector Machines (SVM) algorithm, Partial Least Square Discriminant Analysis (PLS-DA), and Principal Component Analysis-Quadratic Discriminant Analysis (PCA-QDA). SVM showed the best classification power in both Raman (100.00, 99.37, and 92.71% for lettuce, paprika, and tomato varieties, respectively) and FT-IR spectroscopy (99.37, 92.50, and 97.50% for lettuce, paprika, and tomato varieties, respectively). Moreover, our novel approach of merging Raman and FT-IR spectra significantly contributed to the accuracy of some models, giving results of 100.00, 100.00, and 95.00% for lettuce, tomato, and paprika varieties, respectively. Our results indicate that Raman and FT-IR spectroscopy coupled with machine learning could be a promising tool for the rapid and rational evaluation and management of genetic resources in ex situ and in situ seed collections. Full article

Soil salinity and the scarcity of freshwater resources are two of the most common environmental constraints that negatively affect plant growth and productivity worldwide. The tomato (Solanum lycopersicum Mill.) plant is moderately sensitive to salinity. The identification of salinity-responsive genes in tomato that control long-term salt tolerance could provide important guidelines for its breeding programs and genetic engineering. In this study, a holistic approach of RNA sequencing combined with measurements of physiological and agronomic traits were applied in two advanced tomato breeding lines (susceptible L46 and tolerant L56) under long-term salinity stress (9.6 dS m⁻¹). Genotype L56 showed the up-regulation of known and novel differentially expressed genes (DEGs) that aid in the salinity tolerance, which was supported by a high salt tolerance index (81%). Genotype L46 showed both similar and different gene families of DEGs. For example, 22 paralogs of CBL-interacting kinase genes were more up-regulated in L56 than in L45. In addition, L56 deployed more SALT OVERLY SENSITIVE paralogs than L45. However, both genotypes showed the up-regulation of ROS-detoxifying enzymes and ROS-scavenging proteins under salinity stress. Therefore, L56 was more effective in conveying the stress message downstream along all available regulatory pathways. The salt-tolerant genotype L56 is genetically robust, as it shows an enhanced expression of a complete network of salt-responsive genes in response to saline conditions. In contrast, the salt-susceptible genotype L46 shows some potential genetic background. Both genotypes have great potential in future breeding programs. Full article

The use of biological methods to control plant diseases has garnered attention due to their eco-friendly and economically viable nature. Trichoderma spp. are the most ubiquitous fungal saprophytes that can often grow as opportunistic symbionts, are eco-friendly, and are not reported to exert any environmental hazard. Soil-borne pathogens can significantly impact the yield of chilli and tomato crops. The study was conducted to explore the impact of various salts (NaCl, MgCl₂, CaCl₂, and KCl) and their concentrations (1%, 5%, 10%, and 15%) on the mycelial growth and sporulation of Trichoderma viride followed by its mass multiplication on diverse organic substrates like wheat seeds, wheat husks, mungbean seeds, maize seeds, rice seeds, pea seeds, sorghum seeds, banana peel, apple peel, pomegranate peel, citrus peel, tomato waste, chilli waste, spinach waste, cabbage waste, potato peel, onion peel, cucumber peel, carrot peel, used black tea leaves, used green tea leaves, poultry waste, and cow and goat dung. The study assessed the biocontrol potential of Trichoderma viride against important soil-borne pathogens in chilli (Pythium aphanidermatum, Phytophthora capsici, and Fusarium oxysporum) and tomato (Pythium aphanidermatum, Phytophthora infestans, and F. oxysporum) cropping in the pot and field experiments using saline and alkaline soils. Seed treatment with T. viride significantly enhanced the germination rates of both chilli and tomato crops, with sorghum being the most conducive substrate for mass-multiplying T. viride. The results revealed that lower salt concentrations minimally affected T. viride growth, while higher concentrations hampered both growth and sporulation. Optimal disease control and plant height were observed at a 20 mg concentration of T. viride, consequently applied in vivo using various application methods, i.e., seed treatment, root dip, irrigation, and mixed treatments (all the methods like seed treatment, root dip method, and irrigation method applied together) to manage soil-borne pathogens. Particularly, T. viride application through irrigation and mixed treatments demonstrated strong efficacy. These findings underscore the potential of T. viride application in saline and alkaline soils to manage soil-borne pathogens like Pythium, Phytophthora spp., and Fusarium spp. This study lays the foundation for the practical application of biocontrol agents, like T. viride, in Pakistani agricultural conditions. Moreover, there is a need for further exploration into the genetic mechanisms involved in disease inhibition and plant growth promotion, along with understanding the impact of T. viride on the metabolic pathways of host plants. Full article

Pollen is becoming an increasingly important subject for molecular researchers in genetic engineering, plant breeding, and environmental monitoring. To broaden the scope of these studies, it is essential to develop accessible methods for scientists who are not specialized in palynology. The article presents a simplified technical procedure for preparing pollen grains for scanning electron microscopy (SEM). The protocol is convenient for any molecular laboratory due to its small set of reagents, ease of execution, low cost, does not require special equipment, and takes only one hour to complete. The high penetrating ability of formaldehyde and the final delicate dehydration using hexamethyldisilazane (HMDS) instead of critical point drying allow for sufficient preservation of the architecture of the aperture, which is considered a gateway for the passage of biomolecules. The method was successfully applied to pollen grains of representatives of dicotyledons (beetroot, petunia, radish, tomato and tobacco) and monocotyledons (lily, onion, corn, rye and wheat). Species studied included insect-pollinated (entomophilous) and wind-pollinated (anemophilous) species. A comparative analysis of the sizes of fresh living pollen grains under a light microscope and those prepared for SEM showed some shrinkage. Quantitative analysis of the degree of pollen grain shrinkage showed that this process depends on the initial shape of dry pollen grains, and the number and structure of apertures. The results support the theoretical model of the folding/unfolding pathways of pollen grains. Full article

Food security remains a critical global challenge, increasingly threatened by the adverse effects of climate change on agricultural productivity and food supply chains. Ensuring the stability, availability, and accessibility of food resources necessitates innovative strategies to assess and mitigate climate-related risks. This study presents a comprehensive analysis of the impact of climate change on global food systems, focusing on the risk assessment and optimization of food supply chains from the perspective of importers. Deploying the Analytical Hierarchy Process (AHP), this study evaluates climate change risks associated with seven different suppliers for three key crops, considering a range of factors, including surface temperature, arable land, water stress, and adaptation policies. Utilizing these assessments, a multi-objective optimization model is developed and solved using MATLAB (R2018a)’s Genetic Algorithm, aiming to identify optimal suppliers to meet Qatar’s food demand, with consideration of the economic, environmental, and risk factors. The findings underscore the importance of a comprehensive approach in managing food supply chains and offer insights to enhance the resilience and sustainability of global food systems amid climate uncertainties. This study contributes to the literature by applying AHP and multi-objective optimization in climate risk management within food systems, providing valuable perspectives for policymakers and stakeholders in the agricultural sector. Furthermore, the multi-objective optimization model analyzed three crop networks, yielding total costs of USD 16 million, USD 6 million, and USD 10 million for tomatoes, onions, and cucumbers, respectively, with associated CO₂eq emissions and risk percentages. The findings reveal concentrated global vegetable markets, with major importers accounting for over 60% of imports, though the leading importers differ across crops, highlighting regional demand and production disparities, potentially impacting food security and supply chain resilience. Full article

The comprehensive evaluation of crop germplasm serves to scientifically and objectively assess the quality of different genetic accessions against certain standards. Here, we propose an optimized approach to enhance the result’s stability when assessing salt tolerance in crop germplasm. This protocol was applied to a case study involving 249 tomato genotypes, systematically refining the processes involved in constructing an evaluation index system, data preprocessing, statistical method selection, and weight calculation. The optimization process reduced the system variance of salt tolerance evaluation results and achieved an 85.42% concordance with a classical approach, across a tomato population covering 241 genotypes, suggesting the improved stability and high accuracy of the optimized protocol. Moreover, an 83.82% consistency rate between pre- and post-optimization results also suggested the high accuracy of the optimized protocol. The enhanced stability was further confirmed by a secondary validation on a subpopulation (covering 39 genotypes), which demonstrated a consistency rate of 83.87% between the two populations. The study identified 8.43% of the evaluated germplasm as salt-tolerant accessions, providing valuable parental materials for breeding programs. The findings underscore the potential of our protocol for the precise identification of stress-resistant germplasm, contributing to the development of stress-tolerant crop varieties. Full article

Salinity is a major stress factor that compromises vegetable production in semi-arid climates such as the Mediterranean. The accumulation of salts in the soil can be attributed to limited water availability, which can be exacerbated by changes in rainfall patterns and rising temperatures. These factors can alter soil moisture levels and evaporation rates, ultimately leading to an increase in soil salinity, and, concomitantly, the extent to which crop yield is affected by salinity stress is considered cultivar-dependent. In contrast to tomato hybrids, tomato landraces often exhibit greater genetic diversity and resilience to environmental stresses, constituting valuable resources for breeding programs seeking to introduce new tolerance mechanisms. Therefore, in the present study, we investigated the effects of mild salinity stress on the growth, yield, and nutritional status of sixteen Mediterranean tomato landraces of all size types that had been pre-selected as salinity tolerant in previous screening trials. The experiment was carried out in the greenhouse facilities of the Laboratory of Vegetable Production at the Agricultural University of Athens. To induce salinity stress, plants were grown hydroponically and irrigated with a nutrient solution containing NaCl at a concentration that could maintain the NaCl level in the root zone at 30 mM, while the non-salt-treated plants were irrigated with a nutrient solution containing 0.5 mM NaCl. Various plant growth parameters, including dry matter content and fruit yield (measured by the number and weight of fruits per plant), were evaluated to assess the impact of salinity stress. In addition, the nutritional status of the plants was assessed by determining the concentrations of macro- and micronutrients in the leaves, roots, and fruit of the plants. The key results of this study reveal that cherry-type tomato landraces exhibit the highest tolerance to salinity stress, as the landraces ‘Cherry-INRAE (1)’, ‘Cherry-INRAE (3)’, and ‘Cherry-INRAE (4)’ did not experience a decrease in yield when exposed to salinity stress. However, larger landraces such as ‘de Ramellet’ also exhibit mechanisms conferring tolerance to salinity, as their yield was not compromised by the stress applied. The identified tolerant and resistant varieties could potentially be used in breeding programs to develop new varieties and hybrids that are better adapted to salinity-affected environments. The identification and utilization of tomato varieties that are adapted to salinity stress is an important strategy for promoting agriculture sustainability, particularly in semi-arid regions where salinity stress is a major challenge. Full article

Melon is a recalcitrant plant for stable genetic transformation. Various protocols have been tried to improve melon transformation efficiency; however, it remains significantly low compared to other plants such as tomato. In this study, the primary focus was on the optimization of key parameters during the inoculation and co-culture steps of the genetic transformation protocol. Our results showed that immersing the explants in the inoculation medium for 20 min significantly enhanced transformation efficiency. During the co-culture step, the use of filer paper, 10 mM 2-(N-morpholino)-ethanesulfonic acid (MES), and a temperature of 24 °C significantly enhanced the melon transformation efficiency. Furthermore, the impact of different ethylene inhibitors and absorbers on the transformation efficiency of various melon varieties was explored. Our findings revealed that the use of these compounds led to a significant improvement in the transformation efficiency of the tested melon varieties. Subsequently, using our improved protocol and reporter-gene construct, diploid transgenic melons successfully generated. The efficiency of plant genetic transformation ranged from 3.73 to 4.83%. Expanding the scope of our investigation, the optimized protocol was applied to generate stable gene-edited melon lines using the Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated cytosine base editor and obtained melon lines with editions (C-to-T and C-to-G) in the eukaryotic translation initiation factor 4E, CmeIF4E gene. In conclusion, the optimized melon transformation protocol, along with the utilization of the CRISPR/Cas9-mediated cytosine base editor, provides a reliable framework for functional gene engineering in melon. These advancements hold significant promise for furthering genetic research and facilitating crop improvement in this economically important plant species. Full article

Evaluating microbial-based alternatives to conventional fungicides and biofertilizers enables us to gain a deeper understanding of the biocontrol and plant growth-promoting activities. Two genetically distinct Bacillus halotolerans strains (Cal.l.30, Cal.f.4) were evaluated for the levels of their compatibility. They were applied individually or in combination under in vitro and greenhouse conditions, using seed bio-priming and soil drenching as inoculum delivery systems, for their plant growth-promoting effect. Our data indicate that application of Cal.l.30 and Cal.f.4 as single strains and as a mixture significantly enhanced growth parameters of Arabidopsis and tomato plants. We investigated whether seed and an additional soil treatment with these strains could induce the expression of defense-related genes in leaves of young tomato seedling plants. These treatments mediated a long lasting, bacterial-mediated, systemic-induced resistance as evidenced by the high levels of expression of RP3, ACO1 and ERF1 genes in the leaves of young tomato seedlings. Furthermore, we presented data showing that seed and soil treatment with B. halotolerans strains resulted in an effective inhibition of Botrytis cinerea attack and development on tomato leaves. Our findings highlighted the potential of B. halotolerans strains as they combine both direct antifungal activity against plant pathogens and the ability to prime plant innate immunity and enhance plant growth. Full article

Syntenic cell wall QTLs (SQTLs) can identify genetic determinants of biomass traits in understudied species based on results from model crops. However, their effective use in plant breeding requires SQTLs to display intraspecific allelic variability and to predict causative loci in other populations/species than the ones used for SQTLs identification. In this study, genome assemblies from different accessions of Arabidopsis, rapeseed, tomato, rice, Brachypodium and maize were used to evaluate the intraspecific variability of SQTLs. In parallel, a genome-wide association study (GWAS) on cell wall quality traits was performed in miscanthus to verify the colocalization between GWAS loci and miscanthus SQTLs. Finally, an analogous approach was applied on a set of switchgrass cell wall QTLs retrieved from the literature. These analyses revealed large SQTLs intraspecific genetic variability, ranging from presence–absence gene variation to SNPs/INDELs and changes in coded proteins. Cell wall genes displaying gene dosage regulation, such as PAL and CAD, displayed presence–absence variation in Brachypodium and rapeseed, while protein INDELs were detected for the Brachypodium homologs of the rice brittle culm-like 8 locus, which may likely impact cell wall quality. Furthermore, SQTLs significantly colocalized with the miscanthus and switchgrass QTLs, with relevant cell wall genes being retained in colocalizing regions. Overall, SQTLs are useful tools to screen germplasm for relevant genes and alleles to improve biomass quality and can increase the efficiency of plant breeding in understudied biomass crops. Full article

In this study, we investigated how increasing temperature affects tomato fruit physicochemical traits and looked for genetic variability to help maintain fruit quality in the context of climate change. High temperature (HT: +3 °C) was applied at four fruit developmental stages, from anthesis and 15, 30 or 45 days after anthesis until ripening to three genotypes, a commercial cultivar (Money Maker, “MM”) and two genotypes likely more tolerant to HT (Campeche 40 “C40”, a landrace from a warm, humid region, and a hybrid Chapingo F1, “F1”, resulting from crossbreeding landraces tolerant to high temperature). Increasing average diurnal temperature (from 27.0 to 29.9) reduced fruit firmness and size and affected fruit composition according to genotype. Sugar and acid contents were highly impacted in MM and C40 fruits, especially when HT was applied during the rapid fruit growth period. The application of HT at different fruit developmental stages revealed that HT could enhance acid accumulation and degradation (rate and/or duration), resulting in different effects on fruit acidity between genotypes. The F1 genotype appeared to be more adapted to HT, producing larger fruits with higher sugar, lower acid and increased vitamin C and calcium content. These results provide interesting directions for breeding programs that want to maintain future tomato fruit yields and quality. Full article

Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats—CRISPR/Cas—is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs. Full article

The tomato is one of the most important vegetables in the world. The demand for tomatoes is high in virtually any country, owing to their gastronomic versatility and nutritional and aromatic value. Drought, salinity, and inadequate temperature can be major factors in diminishing yield, affecting physiological and biochemical processes and altering various metabolic pathways, from the aggregation of low molecular–weight substances to the transcription of specific genes. Various biotechnological tools can be used to alter the tomato genes so that this species can more rapidly or better adapt to abiotic stress. These approaches range from the introgression of genes coding for specific enzymes for mitigating a prevailing stress to genetic modifications that alter specific metabolic pathways to help tomato perceive environmental cues and/or withstand adverse conditions. In recent years, environmental and social concerns and the high complexity of the plant response may increase the attention of applied plant biotechnology toward biomimetic strategies, generally defined as all the approaches that seek to develop more sustainable and acceptable strategies by imitating nature’s time-tested solutions. In this review, we provide an overview of some of the genetic sequences and molecules that were the objects of biotechnological intervention in tomato as examples of approaches to achieve tolerance to abiotic factors, improving existing nature-based mechanisms and solutions (biomimetic biotechnological approaches (BBA)). Finally, we discuss implications and perspectives within the GMO debate, proposing that crops modified with BBA should receive less stringent regulation. Full article

The ability of certain human pathogens to adapt to plants without losing their virulence toward people is a major concern today. Thus, the aim of the present work was the investigation of the presence of cross-over pathogenic bacteria in infected tomato and pepper plants. The objects of the study were 21 samples from seven different parts of the plants and three from tomato rhizosphere. In total, 26 strains were isolated, identified by MALDI-TOF, and phenotypically characterized. The PCR amplification of the rpoB gene was applied as an approach for the rapid detection of cross-over pathogens in plant samples. A great bacterial diversity was revealed from tomato samples as nine species were identified (Leclercia adecarboxylata, Pseudesherichia vulneris, Enterobacter cancerogenus, Enterobacter cloacae, Enterobacter bugandensis, Acinetobacter calcoaceticus, Pantoea agglomerans, Pantoea ananatis, and Pectobacterium carotovorum). Polymicrobial contaminations were observed in samples T2 (tomato flower) and T10 (tomato fruit). Five species were identified from pepper samples (P. agglomerans, L. adecarboxylata, Pseudomonas sp., Pseudomonas putida, and Enterococcus sp.). Antibiotic resistance patterns were assigned in accordance with EFSA recommendations. All isolates showed varying resistance to the tested antibiotics. The genetic basis for the phenotypic antibiotic resistance was not revealed. No genes for the virulence factors were found among the population. To our knowledge, this is the first overall investigation of tomato and pepper cross-over pathogenic bacterial populations in Bulgaria. Full article

Tomato (Solanum lycopersicum) is one of the most important vegetable crops worldwide; however, environmental stressors severely restrict tomato growth and yield. Therefore, it is of great interest to discover novel regulators to improve tomato growth and environmental stress adaptions. Here, we applied a comprehensive bioinformatics approach to identify putative tomato C-TERMINALLY ENCODED PEPTIDE (CEP) genes and to explore their potential physiological function in tomato root development and abiotic stress responses. A total of 17 tomato CEP genes were identified and grouped into two subgroups based on the similarity of CEP motifs. The public RNA-Seq data revealed that tomato CEP genes displayed a diverse expression pattern in tomato tissues. Additionally, CEP genes expression was differentially regulated by nitrate or ammonium status in roots and shoots, respectively. The differences in expression levels of CEP genes induced by nitrogen indicate a potential involvement of CEPs in tomato nitrogen acquisition. The synthetic CEP peptides promoted tomato primary root growth, which requires nitric oxide (NO) and calcium signaling. Furthermore, we also revealed that CEP peptides improved tomato root resistance to salinity. Overall, our work will contribute to provide novel genetic breeding strategies for tomato cultivation under adverse environments. Full article