Molecular Basis of Plant-Pathogen Interactions in the Agricultural Context.

Biotic stressors pose significant threats to crop yield, jeopardizing food security and resulting in losses of over USD 220 billion per year by the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements to plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have offered new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel avenues for disrupting the molecular compatibility of pathogens and for introducing durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R-gene-based plant genome-engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems.

Potential of amino acids-modified biochar in mitigating the soil Cu and Ni stresses - Targeting the tomato growth, physiology and fruit quality.

Trace heavy metals (HMs) such as copper (Cu) and nickel (Ni) are toxic to plants, especially tomato at high levels. In this study, biochar (BC) was treated with amino acids (AA) to enhance amino functional groups, which effectively alleviated the adverse effects of heavy metals (HMs) on tomato growth. Hence, this study aimed to evaluate the effect of glycine and alanine modified BC (GBC/ABC) on various tomato growth parameters, its physiology, fruit yield and Cu/Ni uptake under Cu and Ni stresses. In a pot experiment, there was 21 treatments with three replications having two rates of simple BC and glycine/alanine enriched BC (0.5% and 1% (w/w). Cu and Ni stresses were added at 150 mg kg-1 respectively. Plants were harvested after 120 days of sowing and subjected to various analysis. Under Cu and Ni stresses, tomato roots accumulated more Cu and Ni than shoots and fruits, while GBC and ABC application significantly enhanced the root and shoot dry weight irrelevant to the stress conditions. Both rates of GBC decreased the malondialdehyde and hydrogen peroxide levels in plants. The addition of 0.5% GBC with Cu enhanced the tomato fruit dry weight by 1.3 folds in comparison to the control treatment; while tomato fruit juice content also increased (50%) in the presence of 0.5% GBC with Ni as compared to control. In summary, these results demonstrated that lower rate of GBC∼0.5% proved to be the best in mitigating the Cu and Ni stress on tomato plant growth by enhancing the fruit production.

Genome-Wide Association Study for Identification of Marker-Trait Associations Conferring Resistance to Scald from Globally Collected Barley Germplasm.

Scald is one of the major economically important foliar diseases in barley, causing up to 40% yield loss in susceptible varieties. The identification of quantitative trait loci and elite alleles that confer resistance to scald is imperative in reducing the threats to barley production. In this study, genome-wide association studies were conducted using a panel of 697 barley genotypes to identify quantitative trait loci for scald resistance. Field experiments were conducted over three consecutive years. Among different models used for genome-wide association studies analysis, FarmCPU was shown to be the best-suited model. Nineteen significant marker-trait associations related to scald resistance were identified across six different chromosomes. Eleven of these marker-trait associations correspond to previously reported scald resistance genes Rrs1, Rrs4, and Rrs2, respectively. Eight novel marker-trait associations were identified in this study, with the candidate genes encoding a diverse class of proteins, including region leucine-rich repeats, AP2/ERF transcription factor, homeodomain-leucine zipper, and protein kinase family proteins. The combination of identified superior alleles significantly reduces disease severity scores. The results will be valuable for marker-assisted breeding for developing scald-resistant varieties.

Rice straw based silicon nanoparticles improve morphological and nutrient profile of rice plants under salinity stress by triggering physiological and genetic repair mechanisms.

The agricultural sector is facing numerous challenges worldwide, owing to global climate change and limited resources. Crop production is limited by numerous abiotic constraints. Among them, salinity stress as a combination of osmotic and ionic stress adversely influences the physiological and biochemical processes of the plant. Nanotechnology facilitates the production of crops either directly by eradicating the losses due to challenging environmental conditions or indirectly by improving tolerance against salinity stress. In this study, the protective role of silicon nanoparticles (SiNPs) was determined in two rice genotypes, N-22 and Super-Bas, differing in salinity tolerance. The SiNPs were confirmed through standard material characterization techniques, which showed the production of spherical-shaped crystalline SiNPs with a size in the range of 14.98-23.74 nm, respectively. Salinity stress adversely affected the morphological and physiological parameters of both varieties, with Super-Bas being more affected. Salt stress disturbed the ionic balance by minimizing the uptake of K+ and Ca2+ contents and increased the uptake of Na+ in plants. Exogenous SiNPs alleviated the toxic effects of salt stress and promoted the growth of both N-22 and Super-Bas, chlorophyll contents (16% and 13%), carotenoids (15% and 11%), total soluble protein contents (21% and 18%), and the activities of antioxidant enzymes. Expression analysis from quantitative real-time PCR showed that SiNPs relieved plants from oxidative bursts by triggering the expression of HKT genes. Overall, these findings demonstrate that SiNPs significantly alleviated salinity stress by triggering physiological and genetic repair mechanisms, offering a potential solution for food security.

Microbe-oriented nanoparticles as phytomedicines for plant health management: An emerging paradigm to achieve global food security.

Biotic and abiotic environmental stresses affect the production and quality of agricultural products worldwide. The extensive use of traditional preventive measures comprising toxic chemicals has become more problematic due to severe ecotoxicological challenges. To address this issue, engineered nanoparticles (NPs) with their distinct physical and chemical properties has gained scientific attention and can help plants to confront environmental challenges. Despite their ameliorative and beneficial effects, toxicological concerns have been raised about NPs. The recent development of biogenic NPs (bio-NPs) is getting attention in agriculture due to their diverse biocompatibility, better functional efficacy, and eco-friendly nature compared to the recalcitrant NPs, providing a promising strategy for increased crop protection against biotic and abiotic environmental stresses, with the ultimate goal of ensuring global food security. This review summarizes the recent advances in the engineering of bio-NPs with particular emphasis on the functions of bio-NPs in protecting plants from biotic and abiotic environmental stresses, delivery and entry routes of NPs to plant systems, nanotoxicity, and plant physiological/biochemical responses to nanotoxicity. Future perspectives of bio-NP-enabled strategies, remaining pitfalls, and possible solutions to combat environmental challenges via advanced nanotechnology to achieve global food security and a sustainable agricultural system are also discussed.

Bio-Functionalized Manganese Nanoparticles Suppress Fusarium Wilt in Watermelon (Citrullus lanatus L.) by Infection Disruption, Host Defense Response Potentiation, and Soil Microbial Community Modulation.

The use of nanofabricated materials is being explored for the potential in crop disease management. Chemically synthesized micronutrient nanoparticles (NPs) have been shown to reduce crop diseases; however, the potential of biogenic manganese NPs (bio-MnNPs) in disease control is unknown. Here, the potential and mechanism of bio-MnNPs in suppression of watermelon Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon) are reported. Bio-MnNPs are synthesized by cell-free cultural filtrate of a waterrmelon rhizosphere bacterial strain Bacillus megaterium NOM14, and are found spherical in shape with a size range of 27.0-65.7 nm. Application of bio-MnNPs at 100 µg mL-1 increases Mn content in watermelon roots/shoots and improves growth performance through enhancing multiple physiological processes, including antioxidative capacity. Bio-MnNPs at 100 µg mL-1 suppress Fusarium wilt through inhibiting colonization and invasive growth of Fon in watermelon roots/stems, and inhibit Fon vegetative growth, conidiation, conidial morphology, and cellular integrity. Bio-MnNPs potentiate watermelon systemic acquired resistance by triggering the salicylic acid signaling upon Fon infection, and reshape the soil microbial community by improving fungal diversity. These findings demonstrate that bio-MnNPs suppress watermelon Fusarium wilt by multiple ex planta and in planta mechanisms, and offer a promising nano-enabled strategy for the sustainable management of crop diseases.

Facile synthesis of nanomaterials as nanofertilizers: a novel way for sustainable crop production.

Nutrient fertilization plays a major role in improving crop productivity and maintaining soil fertility. In the last few decades, the productivity of current agricultural practices highly depends on the use of chemical fertilizers. Major drawback of traditional fertilizers is their low crop nutrient use efficiency and high loss into water. Nanomaterial in agriculture is a multipurpose tool for increasing growth, development, and yield of plants. Nanotechnology facilitates the amplifying of agriculture production by reducing relevant losses and improving the input efficiency. Nanotechnology has emerged as an attractive field of research and has various agriculture applications, especially the use of nano-agrochemicals to increase nutrient use efficiency and agricultural yield. Nanofertilizers are more effective as compared to chemical fertilizers due to their cost-efficient, eco-friendly, non-toxic, and more stable in nature. Overall, this chapter focuses on synthesis of nanofertilizers through physical, chemical, and biological methods. This chapter will also explore the use of nano-enabled fertilizers to enhance the nutrient use efficiency for sustainable crop production, and global food safety.

Biofertilizer microorganisms accompanying pathogenic attributes: a potential threat.

Application of biofertilizers containing living or dormant plant growth promoting bacterial cells is considered to be an ecofriendly alternative of chemical fertilizers for improved crop production. Biofertilizers opened myriad doors towards sustainable agriculture as they effectively reduce heavy use of chemical fertilizers and pesticides by keeping soils profuse in micro and macronutrients, regulating plant hormones and restraining infections caused by the pests present in soil without inflicting environmental damage. Generally, pathogenicity and biosafety testing of potential plant growth promoting bacteria (PGPB) are not performed, and the bacteria are reported to be beneficial solely on testing plant growth promoting characteristics. Unfortunately, some rhizosphere and endophytic PGPB are reported to be involved in various diseases. Such PGPB can also spread virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Therefore, deployment of such microbial populations in open fields could lead to disastrous side effects on human health and environment. Careless declaration of bacteria as PGPB is more pronounced in research publications. Here, we present a comprehensive report of declared PGPB which are reported to be pathogenic in other studies. This review also suggests the employment of some additional safety assessment protocols before reporting a bacteria as beneficial and product development.

Green molybdenum nanoparticles-mediated bio-stimulation of Bacillus sp. strain ZH16 improved the wheat growth by managing in planta nutrients supply, ionic homeostasis and arsenic accumulation.

The present work mechanistically addressed the problem of arsenic (As) contamination in agricultural soils by using locally isolated Bacillus sp. strain ZH16 and biogenic molybdenum nanoparticles (MoNPs) simultaneously for the first time. The interactions of MoNPs with strain ZH16 and ZH16-inoculated wheat plants were examined under As non-spiked and spiked conditions. The biogenic MoNPs showed efficient biocompatibility with strain ZH16 by promoting indole-3-acetic acid synthesis, phosphate solubilization and ACC deaminase activity without and with As stress. The results from greenhouse experiment revealed that co-application of biogenic MoNPs and bacterial strain ZH16 significantly promoted the morphological parameters, nutrients content and ionic balance of wheat plants under normal and As spiked conditions. Furthermore, combining the bacterial strain ZH16 with biogenic MoNPs dramatically reduced As translocation in plants (30.3%) as compared to ZH16-inoculated wheat plants. Conclusively, our results elucidate the importance of synergistic application of plant growth promoting rhizobacteria (PGPR) and biogenic MoNPs to counteract global food safety issues in a sustainable manner. The biogenic NPs could serve as stabilizing agent for PGPR by facilitating their colonization in plant holobiont regardless of environmental conditions. These novel advancements will provide new insights into nano-oriented PGPR research in the agricultural sector.

Genome-Wide Identification, Genomic Organization, and Characterization of Potassium Transport-Related Genes in Cajanus cajan and Their Role in Abiotic Stress.

Potassium is the most important and abundant inorganic cation in plants and it can comprise up to 10% of a plant's dry weight. Plants possess complex systems of transporters and channels for the transport of K+ from soil to numerous parts of plants. Cajanus cajan is cultivated in different regions of the world as an economical source of carbohydrates, fiber, proteins, and fodder for animals. In the current study, 39 K+ transport genes were identified in C. cajan, including 25 K+ transporters (17 carrier-like K+ transporters (KUP/HAK/KTs), 2 high-affinity potassium transporters (HKTs), and 6 K+ efflux transporters (KEAs) and 14 K+ channels (9 shakers and 5 tandem-pore K+ channels (TPKs). Chromosomal mapping indicated that these genes were randomly distributed among 10 chromosomes. A comparative phylogenetic analysis including protein sequences from Glycine max, Arabidopsis thaliana, Oryza sativa, Medicago truncatula Cicer arietinum, and C. cajan suggested vital conservation of K+ transport genes. Gene structure analysis showed that the intron/exon organization of K+ transporter and channel genes is highly conserved in a family-specific manner. In the promoter region, many cis-regulatory elements were identified related to abiotic stress, suggesting their role in abiotic stress response. Abiotic stresses (salt, heat, and drought) adversely affect chlorophyll, carotenoids contents, and total soluble proteins. Furthermore, the activities of catalase, superoxide, and peroxidase were altered in C. cajan leaves under applied stresses. Expression analysis (RNA-seq data and quantitative real-time PCR) revealed that several K+ transport genes were expressed in abiotic stress-responsive manners. The present study provides an in-depth understanding of K+ transport system genes in C. cajan and serves as a basis for further characterization of these genes.

Current trends and future prospective in nanoremediation of heavy metals contaminated soils: A way forward towards sustainable agriculture.

Heavy metals (HMs) contamination in agricultural soils is a major concern for global food safety and human health. Although, various in-situ and ex-situ remediation methods have been used for the treatment of HMs contaminated soils, however, they also have many drawbacks viz., capital investment, toxicity, and environmental health hazards. Consequently, there is an urgent need to develop a novel method to ameliorate the toxicity of HMs in agricultural soils. In recent years, nanoparticles (NPs) have gained significant attention due to their potential applications in the environment and agriculture fields. Nanoremediation employs NPs that effectively reduce the contents of toxic HMs in the soil-plant system. Several studies have reported that the application of NPs in HMs-polluted soils, which reduced plant-available HMs concentration soils. However, the long-term efficiency of NPs immobilization is still unclear. Here, we provide details about the toxicity of HMs to environmental systems and potential applications NPs to alleviate the accumulation of HMs in agricultural soils. Finally, we present the mechanistic route of HMs-toxicity alleviation in plants by NPs application as well as their long-term efficiency and future prospects.

Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants.

Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.

Pathogenic Specialization in Uromyces viciae-fabae in Australia and Rust Resistance in Faba Bean.

The pathogen Uromyces viciae-fabae causes rust (a fungal disease) on faba bean (Vicia faba). This disease limits faba bean production in Africa, Asia, Europe, and Australia. The development of resistant cultivars to U. viciae-fabae is the optimal solution for sustainable disease management. However, unknown virulence in Australian U. viciae-fabae populations has confounded resistance breeding. This study examined differences in virulence among Australian U. viciae-fabae isolates collected from various locations and established a differential set of faba bean genotypes. Ten rust isolates were collected from the major faba bean growing regions in Australia and single spore cultures produced. These cultures were subsequently used for assessing virulence on 40 diverse faba bean genotypes. Based on the host-pathogen interactions, 12 putative host genotypes were identified as a differential set. A nomenclature system was subsequently developed using the binary pathotype naming system. Based upon host-pathogen interactions, nine virulence patterns were detected, and the isolates were named using the new nomenclature. We report characterization and naming of U. viciae-fabae pathotypes using differential genotypes in Australia. This differential set will help identify and track the evolution of new virulence in pathogen population and will assist pyramiding of rust resistance genes.

Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses.

Potassium (K+) is one of the most important cations that plays a significant role in plants and constitutes up to 10% of plants' dry weight. Plants exhibit complex systems of transporters and channels for the distribution of K+ from soil to numerous parts of plants. In this study, we have identified 39 genes encoding putative K+ transport-related genes in Vigna radiata. Chromosomal mapping of these genes indicated an uneven distribution across eight out of 11 chromosomes. Comparative phylogenetic analysis of different plant species, i.e., V. radiata, Glycine max, Cicer arietinum, Oryza sativa, and Arabidopsis thaliana, showed their strong conservation in different plant species. Evolutionary analysis of these genes suggests that gene duplication is a major route of expansion for this family in V. radiata. Comprehensive promoter analysis identified several abiotic stresses related to cis-elements in the promoter regions of these genes, suggesting their role in abiotic stress tolerance. Our additional analyses indicated that abiotic stresses adversely affected the chlorophyll concentration, carotenoids, catalase, total soluble protein concentration, and the activities of superoxide and peroxidase in V. radiata. It also disturbs the ionic balance by decreasing the uptake of K+ content and increasing the uptake of Na+. Expression analysis from high-throughput sequencing data and quantitative real-time PCR experiments revealed that several K+ transport genes were expressed in different tissues (seed, flower, and pod) and in abiotic stress-responsive manners. A highly significant variation of expression was observed for VrHKT (1.1 and 1.2), VrKAT (1 and 2) VrAKT1.1, VrAKT2, VrSKOR, VrKEA5, VrTPK3, and VrKUP/HAK/KT (4, 5, and 8.1) in response to drought, heat or salinity stress. It reflected their potential roles in plant growth, development, or stress adaptations. The present study gives an in-depth understanding of K+ transport system genes in V. radiata and will serve as a basis for a functional analysis of these genes.

Genome-Wide Identification and Comparative Analysis of MYB Transcription Factor Family in Musa acuminata and Musa balbisiana.

MYB transcription factors (TFs) make up one of the most important TF families in plants. These proteins play crucial roles in processes related to development, metabolism, and stimulus-response; however, very few studies have been reported for the characterization of MYB TFs from banana. The current study identified 305 and 251 MYB genes from Musa acuminata and Musa balbisiana, respectively. Comprehensive details of MYBs are reported in terms of gene structure, protein domain, chromosomal localization, phylogeny, and expression patterns. Based on the exon-intron arrangement, these genes were classified into 12 gene models. Phylogenetic analysis of MYBs involving both species of banana, Oryza sativa, and Arabidopsis thaliana distributed these genes into 27 subfamilies. This highlighted not only the conservation, but also the gain/loss of MYBs in banana. Such genes are important candidates for future functional investigations. The MYB genes in both species exhibited a random distribution on chromosomes with variable densities. Estimation of gene duplication events revealed that segmental duplications represented the major factor behind MYB gene family expansion in banana. Expression profiles of MYB genes were also explored for their potential involvement in acetylene response or development. Collectively, the current comprehensive analysis of MYB genes in both species of banana will facilitate future functional studies.

A genome-wide comparative analysis of bZIP transcription factors in G. arboreum and G. raimondii (Diploid ancestors of present-day cotton).

Basic leucine zipper motif (bZIP) transcription factors (TFs) are involved in plant growth regulation, development, and environmental stress responses. These genes have been well characterized in model plants. In current study, a genome-wide analysis of bZIP genes was performed in Gossypium raimondii and Gossypium arboreum taking Arabidopsis thaliana as a reference genome. In total, 85 members of G. raimondii and 87 members of G. arboreum were identified and designated as GrbZIPs and GabZIPs respectively. Phylogenetic analysis clustered bZIP genes into 11 subgroups (A, B, C, D, F, G, H, I, S and X). Gene structure analysis to find the intro-exon structures revealed 1-14 exons in both species. The maximum number of introns were present in subgroup G and D while genes in subgroup S were intron-less except GrbZIP78, which is a unique characteristic as compared to other groups. Results of motif analysis predicted that all three species share a common bZIP motif. A detailed comparison of bZIPs gene distribution on chromosomes has shown a diverse arrangement of genes in both cotton species. Moreover, the functional similarity with orthologs was also predicted. The findings of this study revealed close similarity in gene structure of both cotton species and diversity in gene distribution on chromosomes. This study supports the divergence of both species from the common ancestor and later diversity in gene distribution on chromosomes due to evolutionary changes. Additionally, this work will facilitate the functional characterization of bZIP genes in cotton. Outcomes of this study represent foundation research on the bZIP TFs family in cotton and as a reference for other crops.

Genome-wide identification and expression analysis of two component system genes in Cicer arietinum.

The two-component system (TCS) plays an important role in signal transduction pathways, cytokinin signaling and stress resistance of prokaryotes and eukaryotes. It is comprised of three types of proteins in plants; histidine kinases (HKs), histidine phosphotransfer proteins (HPs) and response regulators (RRs). Chickpea (Cicer arietinum L.) is one of the most important legume crops worldwide with special economic value in semi-arid tropics. Availability of complete genome sequence of chickpea presents a valuable resource for comparative analysis among angiosperms. In current study, Arabidopsis thaliana and Oryza sativa were used as reference plant species for comparative genomics analysis with C. arietinum. A genome-wide computational survey enabled us to identify putative members of TCS protein family including 18HKs, 26 RRs (7 type-A, 7 type-B, 2 type C and 10 pseudo) and 7 HPs (5 true and 2pseudo) genes in chickpea. The predicted TCS genes displayed family specific intron/exon organization and were randomly distributed across all the eight chromosomes. Comparative phylogenetic and evolutionary analysis suggested a variable conservation of TCS genes in relation to mono/dicot model plants and segmental duplication was the principal route of expansion for this family in chickpea. The promoter regions of TCS genes exhibited several abiotic stress-related cis-elements indicating their involvement in abiotic stress response. The expression analysis of TCS genes demonstrated stress (drought, heat, osmotic and salt) specific differential expression. Current study provides insight into TCS genes in C. arietinum, which will be helpful for further functional analysis of these genes in response to different abiotic stresses.