Genetic diversity and candidate genes for transient waterlogging tolerance in mungbean at the germination and seedling stages.

Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.

Soil, Plant, and Microorganism Interactions Drive Secondary Succession in Alpine Grassland Restoration.

Plant secondary succession has been explored extensively in restoring degraded grasslands in semiarid or dry environments. However, the dynamics of soil microbial communities and their interactions with plant succession following restoration efforts remain understudied, particularly in alpine ecosystems. This study investigates the interplay between soil properties, plant communities, and microbial populations across a chronosequence of grassland restoration on the Qinghai-Tibet Plateau in China. We examined five succession stages representing artificial grasslands of varying recovery durations from 0 to 19. We characterized soil microbial compositions using high-throughput sequencing, enzymatic activity assessments, and biomass analyses. Our findings reveal distinct plant and microbial secondary succession patterns, marked by increased soil organic carbon, total phosphorus, and NH4+-N contents. Soil microbial biomass, enzymatic activities, and microbial community diversity increased as recovery time progressed, attributed to increased plant aboveground biomass, cover, and diversity. The observed patterns in biomass and diversity dynamics of plant, bacterial, and fungal communities suggest parallel plant and fungal succession occurrences. Indicators of bacterial and fungal communities, including biomass, enzymatic activities, and community composition, exhibited sensitivity to variations in plant biomass and diversity. Fungal succession, in particular, exhibited susceptibility to changes in the soil C: N ratio. Our results underscore the significant roles of plant biomass, cover, and diversity in shaping microbial community composition attributed to vegetation-induced alterations in soil nutrients and soil microclimates. This study contributes valuable insights into the intricate relationships driving secondary succession in alpine grassland restoration.

Characterisation and agronomic evaluation of acidified food waste anaerobic digestate products.

Raw liquid anaerobic digestate was synthesised into nutrient-dense solid digestates via acidification and evaporation. Acidification retained ammonium in the digestate whilst also donating the anion to free ammonium to form an ammonium salt. Digestate was treated with the addition of sulphuric, nitric, and phosphoric acid resulting in the formation of ammonium sulphate, ammonium nitrate and ammonium phosphate, respectively then evaporated into a solid fertiliser product. FTIR, XRD and SEM-EDS collectively confirm that the addition of acids completely converted the free ammonium in the raw digestate into their respective ammonium salt counterparts. Compounds of potassium chloride, silicon dioxide, calcium carbonate, magnesium ammonium phosphate, sodium nitrate, and sodium chloride were identified in all solid digestate samples. Plant growth and grain yield was higher in urea ammonium nitrate, raw liquid digestate and acidified digestate products compared to control and unacidified solid digestate. Urea ammonium nitrate and ammonium nitrate solid digestate had the highest dry shoot, likely due to the high available nitrogen found in both fertilisers. Overall, acidification and evaporation of liquid digestate can efficiently transform it into a valuable solid fertiliser with a high nutrient density. This process not only has the potential to mitigate handling and storage constraints of low nutrient density digestate in anaerobic digestion facilities but also offers a sustainable alternative to conventional fertilisers.

Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi.

The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.

Bromine contamination and risk management in terrestrial and aquatic ecosystems.

Bromine (Br) is widely distributed through the lithosphere and hydrosphere, and its chemistry in the environment is affected by natural processes and anthropogenic activities. While the chemistry of Br in the atmosphere has been comprehensively explored, there has never been an overview of the chemistry of Br in soil and aquatic systems. This review synthesizes current knowledge on the sources, geochemistry, health and environmental threats, remediation approaches, and regulatory guidelines pertaining to Br pollution in terrestrial and aquatic environments. Volcanic eruptions, geothermal streams, and seawater are the major natural sources of Br. In soils and sediments, Br undergoes natural cycling between organic and inorganic forms, with bromination reactions occurring both abiotically and through microbial activity. For organisms, Br is a non-essential element; it is passively taken up by plant roots in the form of the Br- anion. Elevated Br- levels can limit plant growth on coastal soils of arid and semi-arid environments. Br is used in the chemical industry to manufacture pesticides, flame retardants, pharmaceuticals, and other products. Anthropogenic sources of organobromine contaminants in the environment are primarily wastewater treatment, fumigants, and flame retardants. When aqueous Br- reacts with oxidants in water treatment plants, it can generate brominated disinfection by-products (DBPs), and exposure to DBPs is linked to adverse human health effects including increased cancer risk. Br- can be removed from aquatic systems using adsorbents, and amelioration of soils containing excess Br- can be achieved by leaching, adding various amendments, or phytoremediation. Developing cost-effective methods for Br- removal from wastewater would help address the problem of toxic brominated DBPs. Other anthropogenic organobromines, such as polybrominated diphenyl ether (PBDE) flame retardants, are persistent, toxic, and bioaccumulative, posing a challenge in environmental remediation. Future research directives for managing Br pollution sustainably in various environmental settings are suggested here.

A novel index for vegetation drought assessment based on plant water metabolism and balance under vegetation restoration on the Loess Plateau.

Vegetation is vital to the ecosystem, contributing to the global carbon balance, but susceptible to the impacts of climate change. Monitoring vegetation drought remains challenging due to the lack of widely accepted drought indices. This study focused on vegetation, and simulated the vegetation suitable water demand and soil available water supply (calculated by Remote-sensing-based Water Balance Assessment Tool model). The standardized Vegetation Water deficit Index (SVWDI) was established by calculating the vegetation water deficit, which reflects the response of vegetation to drought. We examined the spatiotemporal evolution of vegetation drought on the Loess Plateau and evaluated the applicability of standardized vegetation water deficit index. Our findings revealed that the standardized vegetation water deficit index demonstrated an overall upward trend across different time scales from 1991 to 2020. Drought conditions were concentrated in the first 20 years of the study period, but vegetation drought on the Loess Plateau has been alleviated in the past decade. Moreover, as the time scale extended, the trend of SVWDI generally decreased, with approximately 49.50 % (1-month scale), 46.66 % (3-month scale), 47.08 % (12-month scale), and 32.16 % (24-month scale) of the grid areas experiencing increased SVWDI. The correlation between SVWDI and tree-ring width index (TRWI) performed well under all precipitation gradients, but the Palmer drought severity index (PDSI) was only highly correlated with TRWI in regions with low precipitation. In terms of the relationship with vegetation health, SVWDI demonstrated the highest correlation with the normalized difference vegetation index (NDVI) across different time scales, followed by PDSI and standardized precipitation evapotranspiration index (SPEI). This study provides insights into the evolution of vegetation drought in response to climate change. The findings can guide initiatives such as returning farmland to forest and grassland on the Loess Plateau to aid climate change adaptation strategies.

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity.

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.

Chloroplast gene control: unlocking RNA thermometer mechanisms in photosynthetic systems.

RNA thermometers offer straightforward, protein-independent methods to regulate gene expression at the post-transcriptional level. In this context, Chung and colleagues have discovered a revolutionary RNA thermometer in the chloroplast genome of Chlamydomonas reinhardtii. This will facilitate temperature-driven control of inducible transgene expression for biotechnology applications in plant and algal systems.

The distribution, fate, and environmental impacts of food additive nanomaterials in soil and aquatic ecosystems.

Nanomaterials in the food industry are used as food additives, and the main function of these food additives is to improve food qualities including texture, flavor, color, consistency, preservation, and nutrient bioavailability. This review aims to provide an overview of the distribution, fate, and environmental and health impacts of food additive nanomaterials in soil and aquatic ecosystems. Some of the major nanomaterials in food additives include titanium dioxide, silver, gold, silicon dioxide, iron oxide, and zinc oxide. Ingestion of food products containing food additive nanomaterials via dietary intake is considered to be one of the major pathways of human exposure to nanomaterials. Food additive nanomaterials reach the terrestrial and aquatic environments directly through the disposal of food wastes in landfills and the application of food waste-derived soil amendments. A significant amount of ingested food additive nanomaterials (> 90 %) is excreted, and these nanomaterials are not efficiently removed in the wastewater system, thereby reaching the environment indirectly through the disposal of recycled water and sewage sludge in agricultural land. Food additive nanomaterials undergo various transformation and reaction processes, such as adsorption, aggregation-sedimentation, desorption, degradation, dissolution, and bio-mediated reactions in the environment. These processes significantly impact the transport and bioavailability of nanomaterials as well as their behaviour and fate in the environment. These nanomaterials are toxic to soil and aquatic organisms, and reach the food chain through plant uptake and animal transfer. The environmental and health risks of food additive nanomaterials can be overcome by eliminating their emission through recycled water and sewage sludge.

Tuning active sites on biochars for remediation of mercury-contaminated soil: A comprehensive review.

Mercury (Hg) contamination is acknowledged as a global issue and has generated concerns globally due to its toxicity and persistence. Tunable surface-active sites (SASs) are one of the key features of efficient BCs for Hg remediation, and detailed documentation of their interactions with metal ions in soil medium is essential to support the applications of functionalized BC for Hg remediation. Although a specific active site exhibits identical behavior during the adsorption process, a systematic documentation of their syntheses and interactions with various metal ions in soil medium is crucial to promote the applications of functionalized biochars in Hg remediation. Hence, we summarized the BC's impact on Hg mobility in soils and discussed the potential mechanisms and role of various SASs of BC for Hg remediation, including oxygen-, nitrogen-, sulfur-, and X (chlorine, bromine, iodine)- functional groups (FGs), surface area, pores and pH. The review also categorized synthesis routes to introduce oxygen, nitrogen, and sulfur to BC surfaces to enhance their Hg adsorptive properties. Last but not the least, the direct mechanisms (e.g., Hg- BC binding) and indirect mechanisms (i.e., BC has a significant impact on the cycling of sulfur and thus the Hg-soil binding) that can be used to explain the adverse effects of BC on plants and microorganisms, as well as other related consequences and risk reduction strategies were highlighted. The future perspective will focus on functional BC for multiple heavy metal remediation and other potential applications; hence, future work should focus on designing intelligent/artificial BC for multiple purposes.

Fulvic acid modified ZnO nanoparticles improve nanoparticle stability, mung bean growth, grain zinc content, and soil biodiversity.

Zinc oxide nanoparticles (ZnO NPs) have emerged as a novel solution to combat Zn deficiency in agriculture. However, challenges persist regarding their Zn utilization efficiency and environmental impact. Fulvic acid (FA), as a relatively mature modified material, is a promising candidate to enhance the environmental stability of ZnO NPs. This study investigates modifying ZnO NPs with FA to improve their stability and increase Zn content in mung bean fruit and explores their effect on plants and the soil ecosystem. We combined FA and ZnO NPs (FZ-50) at mass ratios of 1: 5, 1: 2, and 4: 5, denoted as 20 % FZ, 50 % FZ, and 80 % FZ, respectively. Initial germination tests revealed that the 50 % FZ treatment improved sprout growth and Zn content and minimized agglomeration the most. A subsequent pot experiment compared FZ-50 with ZnO, ZnO NPs, and F + Z (1: 1 FA: ZnO NPs). Notably, the FZ-50 treatment (50 % FZ applied to the soil) demonstrated superior results, exhibiting a 30.25 % increase in yield, 121 % improvement in root nodule quality, and 56.38 % increase in Zn content, with no significant changes in enzyme activities (catalase and peroxidase). Furthermore, FZ-50 increased soil available Zn content and promoted soil microorganism diversity, outperforming ZnO and ZnO NPs. This study underscores the potential of FA as a relatively mature material for modifying ZnO NPs to increase grain Zn content, presenting a novel approach to addressing Zn deficiency in agriculture.

Diversifying crop rotation increases food production, reduces net greenhouse gas emissions and improves soil health.

Global food production faces challenges in balancing the need for increased yields with environmental sustainability. This study presents a six-year field experiment in the North China Plain, demonstrating the benefits of diversifying traditional cereal monoculture (wheat-maize) with cash crops (sweet potato) and legumes (peanut and soybean). The diversified rotations increase equivalent yield by up to 38%, reduce N2O emissions by 39%, and improve the system's greenhouse gas balance by 88%. Furthermore, including legumes in crop rotations stimulates soil microbial activities, increases soil organic carbon stocks by 8%, and enhances soil health (indexed with the selected soil physiochemical and biological properties) by 45%. The large-scale adoption of diversified cropping systems in the North China Plain could increase cereal production by 32% when wheat-maize follows alternative crops in rotation and farmer income by 20% while benefiting the environment. This study provides an example of sustainable food production practices, emphasizing the significance of crop diversification for long-term agricultural resilience and soil health.

Plant hormones and secondary metabolites under environmental stresses: Enlightening defense molecules.

The climatic changes have great threats to sustainable agriculture and require efforts to ensure global food and nutritional security. In this regard, the plant strategic responses, including the induction of plant hormones/plant growth regulators (PGRs), play a substantial role in boosting plant immunity against environmental stress-induced adversities. In addition, secondary metabolites (SMs) have emerged as potential 'stress alleviators' that help plants to adapt against environmental stressors imposing detrimental impacts on plant health and survival. The introduction of SMs in plant biology has shed light on their beneficial effects in mitigating environmental crises. This review explores SMs-mediated plant defense responses and highlights the crosstalk between PGRs and SMs under diverse environmental stressors. In addition, genetic engineering approaches are discussed as a potential revenue to enhance plant hormone-mediated SM production in response to environmental cues. Thus, the present review aims to emphasize the significance of SMs implications with PGRs association and genetic approachability, which could aid in shaping the future strategies that favor agro-ecosystem compatibility under unpredictable environmental conditions.

A mechanistic approach to arsenic adsorption and immobilization in aqueous solution, groundwater, and contaminated paddy soil using pine-cone magnetic biochar.

Arsenic (As) poisoning in groundwater and rice paddy soil has increased globally, impacting human health and food security. There is an urgent need to deal with As-contaminated groundwater and soil. Biochar can be a useful remedy for toxic contaminants. This study explains the synthesis of pinecone-magnetic biochar (PC-MBC) by engineering the pinecone-pristine biochar with iron salts (FeCl3.6H2O and FeSO4.7H2O) to investigate its effects on As(V) adsorption and immobilization in water and soil, respectively. The results indicated that PC-MBC can remediate As(V)-contaminated water, with an adsorption capacity of 12.14 mg g-1 in water. Isotherm and kinetic modeling showed that the adsorption mechanism involved multilayer, monolayer, and diffusional processes, with chemisorption operating as the primary interface between As(V) and biochar. Post-adsorption analysis of PC-MBC, using FTIR and XRD, further revealed chemical fixing and outer-sphere complexation between As(V) and Fe, O, NH, and OH as the main reasons for As(V) adsorption onto PC-MBC. Recycling of PC-MBC also had excellent adsorption even after several regeneration cycles. Similarly, PC-MBC successfully immobilized As in paddy soil. Single and sequential extraction results showed the transformation of mobile forms of As to a more stable form, confirmed by non-destructive analysis using SEM, EDX, and elemental dot mapping. Thus, Fe-modified pine-cone biochar could be a suitable and cheap adsorbent for As-contaminated water and soil.

Protein biomarkers for root length and root dry mass on chromosomes 4A and 7A in wheat.

Improving the wheat (Triticum aestivum L.) root system is important for enhancing grain yield and climate resilience. Total root length (RL) and root dry mass (RM) significantly contribute to water and nutrient acquisition directly impacting grain yield and stress tolerance. This study used label-free quantitative proteomics to identify proteins associated with RL and RM in wheat near-isogenic lines (NILs). NIL pair 6 had 113 and NIL pair 9 had 30 differentially abundant proteins (DAPs). Three of identified DAPs located within the targeted genomic regions (GRs) of NIL pairs 6 (qDT.4A.1) and 9 (QHtscc.ksu-7A), showed consistent gene expressions at the protein and mRNA transcription (qRT-PCR) levels for asparagine synthetase (TraesCS4A02G109900), signal recognition particle 19 kDa protein (TraesCS7A02G333600) and 3,4-dihydroxy-2-butanone 4-phosphate synthase (TraesCS7A02G415600). This study discovered, for the first time, the involvement of these proteins as candidate biomarkers for increased RL and RM in wheat. However, further functional validation is required to ascertain their practical applicability in wheat root breeding. SIGNIFICANCE OF THE STUDY: Climate change has impacted global demand for wheat (Triticum aestivum L.). Root traits such as total root length (RL) and root dry mass (RM) are crucial for water and nutrient uptake and tolerance to abiotic stresses such as drought, salinity, and nutrient imbalance in wheat. Improving RL and RM could significantly enhance wheat grain yield and climate resilience. However, breeding for these traits has been limited by lack of appropriate root phenotyping methods, advanced genotypes, and the complex nature of the wheat genome. In this study, we used a semi-hydroponic root phenotyping system to collect accurate root data, near-isogenic lines (NILs; isolines with similar genetic backgrounds but contrasting target genomic regions (GRs)) and label-free quantitative proteomics to explore the molecular mechanisms underlying high RL and RM in wheat. We identified differentially abundant proteins (DAPs) and their molecular pathways in NIL pairs 6 (GR: qDT.4A.1) and 9 (GR: QHtscc.ksu-7A), providing a foundation for further molecular investigations. Furthermore, we identified three DAPs within the target GRs of the NIL pairs with differential expression at the transcript level, as confirmed by qRT-PCR analysis which could serve as candidate protein biomarkers for RL and RM improvement.

Biochar modulating soil biological health: A review.

Biochar can be used for multifunctional applications including the improvement of soil health and carbon storage, remediation of contaminated soil and water resources, mitigation of greenhouse gas emissions and odorous compounds, and feed supplementation to improve animal health. A healthy soil preserves microbial biodiversity that is effective in supressing plant pathogens and pests, recycling nutrients for plant growth, promoting positive symbiotic associations with plant roots, improving soil structure to supply water and nutrients, and ultimately enhancing soil productivity and plant growth. As a soil amendment, biochar assures soil biological health through different processes. First, biochar supports habitats for microorganisms due to its porous nature and by promoting the formation of stable soil micro-aggregates. Biochar also serves as a carbon and nutrient source. Biochar alters soil physical and chemical properties, creating optimum soil conditions for microbial diversity. Biochar can also immobilize soil pollutants and reduce their bioavailability that would otherwise inhibit microbial growth. However, depending on the pyrolysis settings and feedstock resources, biochar can be comprised of contaminants including polycyclic aromatic hydrocarbons and potentially toxic elements that can inhibit microbial activity, thereby impacting soil health.

Enhancing climate change resilience in agricultural crops.

Climate change threatens global food and nutritional security through negative effects on crop growth and agricultural productivity. Many countries have adopted ambitious climate change mitigation and adaptation targets that will exacerbate the problem, as they require significant changes in current agri-food systems. In this review, we provide a roadmap for improved crop production that encompasses the effective transfer of current knowledge into plant breeding and crop management strategies that will underpin sustainable agriculture intensification and climate resilience. We identify the main problem areas and highlight outstanding questions and potential solutions that can be applied to mitigate the impacts of climate change on crop growth and productivity. Although translation of scientific advances into crop production lags far behind current scientific knowledge and technology, we consider that a holistic approach, combining disciplines in collaborative efforts, can drive better connections between research, policy, and the needs of society.

Uncovering the transcriptional responses of tobacco (Nicotiana tabacum L.) roots to Ralstonia solanacearum infection: a comparative study of resistant and susceptible cultivars.

BACKGROUND: Tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum is the most serious soil-borne disease of tobacco that significantly reduces crop yield. However, the limited availability of resistance in tobacco hinders breeding efforts for this disease. RESULTS: In this study, we conducted hydroponic experiments for the root expression profiles of D101 (resistant) and Honghuadajinyuan (susceptible) cultivars in response to BW infection at 0 h, 6 h, 1 d, 3 d, and 7d to explore the defense mechanisms of BW resistance in tobacco. As a result, 20,711 and 16,663 (total: 23,568) differentially expressed genes (DEGs) were identified in the resistant and susceptible cultivars, respectively. In brief, at 6 h, 1 d, 3 d, and 7 d, the resistant cultivar showed upregulation of 1553, 1124, 2583, and 7512 genes, while the susceptible cultivar showed downregulation of 1213, 1295, 813, and 7735 genes. Similarly, across these time points, the resistant cultivar had downregulation of 1034, 749, 1686, and 11,086 genes, whereas the susceptible cultivar had upregulation of 1953, 1790, 2334, and 6380 genes. The resistant cultivar had more up-regulated genes at 3 d and 7 d than the susceptible cultivar, indicating that the resistant cultivar has a more robust defense response against the pathogen. The GO and KEGG enrichment analysis showed that these genes are involved in responses to oxidative stress, plant-pathogen interactions, cell walls, glutathione and phenylalanine metabolism, and plant hormone signal transduction. Among the DEGs, 239 potential candidate genes were detected, including 49 phenylpropane/flavonoids pathway-associated, 45 glutathione metabolic pathway-associated, 47 WRKY, 48 ERFs, eight ARFs, 26 pathogenesis-related genes (PRs), and 14 short-chain dehydrogenase/reductase genes. In addition, two highly expressed novel genes (MSTRG.61386-R1B-17 and MSTRG.61568) encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins were identified in both cultivars at 7 d. CONCLUSIONS: This study revealed significant enrichment of DEGs in GO and KEGG terms linked to glutathione, flavonoids, and phenylpropane pathways, indicating the potential role of glutathione and flavonoids in early BW resistance in tobacco roots. These findings offer fundamental insight for further exploration of the genetic architecture and molecular mechanisms of BW resistance in tobacco and solanaceous plants at the molecular level.

Progress in gene editing tools, implications and success in plants: a review.

Genetic modifications are made through diverse mutagenesis techniques for crop improvement programs. Among these mutagenesis tools, the traditional methods involve chemical and radiation-induced mutagenesis, resulting in off-target and unintended mutations in the genome. However, recent advances have introduced site-directed nucleases (SDNs) for gene editing, significantly reducing off-target changes in the genome compared to induced mutagenesis and naturally occurring mutations in breeding populations. SDNs have revolutionized genetic engineering, enabling precise gene editing in recent decades. One widely used method, homology-directed repair (HDR), has been effective for accurate base substitution and gene alterations in some plant species. However, its application has been limited due to the inefficiency of HDR in plant cells and the prevalence of the error-prone repair pathway known as non-homologous end joining (NHEJ). The discovery of CRISPR-Cas has been a game-changer in this field. This system induces mutations by creating double-strand breaks (DSBs) in the genome and repairing them through associated repair pathways like NHEJ. As a result, the CRISPR-Cas system has been extensively used to transform plants for gene function analysis and to enhance desirable traits. Researchers have made significant progress in genetic engineering in recent years, particularly in understanding the CRISPR-Cas mechanism. This has led to various CRISPR-Cas variants, including CRISPR-Cas13, CRISPR interference, CRISPR activation, base editors, primes editors, and CRASPASE, a new CRISPR-Cas system for genetic engineering that cleaves proteins. Moreover, gene editing technologies like the prime editor and base editor approaches offer excellent opportunities for plant genome engineering. These cutting-edge tools have opened up new avenues for rapidly manipulating plant genomes. This review article provides a comprehensive overview of the current state of plant genetic engineering, focusing on recently developed tools for gene alteration and their potential applications in plant research.