Phytoplasmas (‘Candidatus Phytoplasma’) are obligate, phloem-limited, cell wall-lacking bacterial pathogens with highly reduced genomes that infect diverse plant and insect vector species. They are associated with economically important diseases worldwide, including grapevine yellows, coconut lethal yellowing, sesame phyllody, apple proliferation, potato purple top, European stone fruit yellows, sugarcane white leaf, tomato big bud, and witches’ broom of several crops, posing significant threats to global agriculture, trade, and biosecurity. Phytoplasmas induce characteristic symptoms such as yellows, witches’ broom, phyllody, virescence, little leaf, and abnormal plant development, and are primarily transmitted by phloem-feeding insects, as well as through grafting, vegetative propagation, and occasionally seeds. Advances in molecular diagnostics, including PCR, qPCR, digital PCR, LAMP, RPA, WGS and CRISPR/Cas-based assays, have greatly enabled rapid, sensitive, and quantitative detection of phytoplasmas in both plants and insects. Comparative analysis of 16S rRNA gene and whole-genome sequencing has enabled the identification and classification of more than 52 ‘Ca. Phytoplasma’ species belonging to 40 ribosomal groups and numerous subgroups. Phytoplasma effectors mainly delivered through the Sec pathway manipulate host hormonal regulation, immunity, development, and insect vector interactions to promote their own colonization and transmission. Sustainable management remains challenging and requires integrated approaches involving resistant cultivars, insect vector control, quarantine restrictions, advanced diagnostics, surveillance, and emerging biotechnological and AI based tools for effective disease detection and mitigation.
Crop losses caused by plant pathogens continue to undermine food security, since infection lowers harvestable yield, downgrades produce quality, adds to the cost of production and pushes growers towards heavier pesticide use. Fungicides and bactericides still underpin most control programmes, yet years of repeated spraying have selected resistant pathogen strains, left residues on produce, harmed organisms that were never the intended target and given uneven protection as field conditions change. Nanotechnology offers complementary tools for plant pathology. Nanomaterials can improve early pathogen detection, act as antimicrobial agents, deliver fungicides, bactericides and biological agents through controlled-release systems, and protect double-stranded RNA for spray-induced gene silencing. However, much of the available evidence still comes from in vitro assays, and field translation is limited by variation in nanoparticle composition, size, surface charge, coating chemistry, dissolution, formulation stability, application route and interactions with plant-associated microbiomes. This review critically evaluates nano-enabled disease diagnosis and management from a phytopathological perspective. Nanoparticle properties were linked to pathogen infection courts, pathogen guilds and stages of the disease cycle, while distinguishing laboratory evidence from greenhouse and field performance in this article. In addition, compatibility with integrated disease management, beneficial microbes, environmental fate, biosafety, residue concerns and regulatory endpoints was also assessed. Nano-enabled diagnostics and therapeutics tools are concluded as a viable pathway for sustainable plant disease management and agricultural resilience but it need more field validation, biosafety, and compatibility with environmental safety.
Fungal strains play a pivotal role in laboratory-based biological research, yet their long-term preservation remains a methodological challenge. This review critically evaluates the major preservation strategies applied in laboratory settings, including soil/sand storage, agar-based techniques, silica gel, sterile water, organic substrata, low and ultra-low temperature approaches, and cotton ball methods. Rather than simply listing these techniques, the article synthesizes comparative insights, highlighting how each method influences strain viability, genetic stability, and ease of application. Key findings emphasize that while low-temperature methods ensure long-term genetic fidelity, simpler approaches such as sterile water or soil/sand are more cost-effective but less reliable for extended preservation. By outlining the advantages, limitations, and practical considerations of each method, this review provides researchers with a clear framework to select preservation strategies tailored to their experimental needs and resource availability.
Spot blotch is an important foliar disease of wheat (Triticum aestivum L.) in the warm and humid wheat-growing regions of India, particularly in the Eastern Indo-Gangetic Plains, where favourable environmental conditions support disease development and may contribute to yield losses. Although the disease is widely prevalent, comparative information on district-wise pathogen recovery, disease severity and their association with agro-climatic conditions in Eastern Uttar Pradesh is limited. The study investigated the recovery of morphologically identified Bipolaris sorokiniana from symptomatic wheat leaves, assessed disease severity under field conditions, and examined its statistical association with selected agro-climatic factors. Field surveys were conducted during the 2018–19 and 2019–20 rabi seasons in five selected wheat-growing districts of Eastern Uttar Pradesh, with 25 farmers’ fields surveyed in each season (50 fields total). The field survey data represent historical baseline information for the surveyed period rather than current prevalence estimate. A total of 207 symptomatic leaf samples were collected, comprising 113 samples during 2018–19 and 94 samples during 2019–20. Symptomatic leaf samples were collected for pathogen isolation, identification, pathogenicity testing, and morphological and cultural characterization. The recovered cultures were morphologically identified as B. sorokiniana based on cultural and morphological characteristics; molecular confirmation was not performed. Disease severity was assessed at the dough stage using the 0–9 double-digit (DD) scale adopted by the Directorate of Wheat Research (DWR), Karnal. The Percent Disease Index (PDI) was subsequently calculated. Morphologically identified Bipolaris sorokiniana was recovered from 73.5
Cashew gummosis, caused by Botryosphaeria spp., is an important disease in West Bengal that results in reduced tree vigor and economic yield loss. An in vitro fungitoxicity test revealed that propiconazole was the most effective, recording the lowest ED₅₀ value (0.894 ppm), followed by carbendazim + mancozeb (1.063 ppm) and thiophanate methyl (1.482 ppm). In terms of toxicity index, thiophanate methyl (89.43
Tomato yellow leaf curl virus (TYLCV) is a monopartite begomovirus of the family; Geminiviridae which is responsible to cause huge economic losses in tomato production globally. Efficient inoculation systems are essential for screening resistant genotypes and studying virus pathogenicity and gene functions. However, the production of infectious clones containing two replication origins is often a laborious and time-taking process due to additional steps such as DNA dephosphorylation. In this study we developed a single-ligation approach for generating TYLCV clones which is easy, rapid and overcome the problems faced in other techniques which produce recombinant clones by direct cloning into appropriate vector. The method involves the selection of a common cloning site flanked by two unique restriction sites encompassing the viral replication origin, followed by direct ligation of the recovered viral fragments into the binary vector pGreen0029 without dephosphorylation. The efficiency of this approach was validated using TYLCV, where agroinoculation resulted in successful infection of all Nicotiana benthamiana and tomato plants. The novelty of this technique is we can get 100
The leaf rust (Puccinia triticina) occurs wherever wheat is grown in the world and is known to cause more losses than the other two rusts. Cultivating varieties with diverse resistance is the best option to manage wheat rusts. However, rust resistance of wheat varieties becomes ineffective frequently due to the emergence of new pathotypes. Therefore, to know the cause of susceptibility of wheat varieties, avoid rust epidemics, regular surveys and analyses of samples are conducted to identify new pathotypes in the initial stages. Analyses of 2035 samples during 2014–2018 from different parts of India revealed the occurrence of three new virulences of Puccinia triticina. A leaf rust sample of wheat from Karnataka yielded a new pathotype, 179 (24R44; CHTLL), with virulence to Lr3, Lr13, and Lr26. Another sample from Madhya Pradesh harboured a pathotype belonging to the 162 group, which showed virulence to Lr2c, Lr2a, Lr3, Lr13, Lr14a, Lr17, Lr18, and Lr26. This pathotype is designated as 162-4 (29R39; KHTPM). Third new pathotype 77 − 12 (1R31; TGPNB) having virulence to Lr1, Lr2c, Lr2a, Lr3, Lr14a, and Lr20, was identified in a sample from north-eastern India. These variants pose a threat to wheat cultivation as rust resistance of many Indian wheat varieties is based on Lr13, Lr26, Lr1, and Lr3. Eleven genes; Lr9, Lr24, Lr25, Lr28, Lr32, Lr39, Lr45, Lr47, Lr53, Lr61, and Lr62 confer resistance to all the pathotypes of P. triticina in India, including these three. The distinguishing features of the new virulences, their avirulence/ virulence formulae, molecular differences, and resistance sources are listed in this publication. The 70 leaf rust resistant accessions, and 11 Lr genes identified in this study, would be useful for resistance breeding and deployment. To identify additional leaf rust resistant sources, these pathotypes will be used for the continued screening of the pipeline wheat material and other sources.
Cucurbitaceous vegetables, such as cucumber, bottle gourd, and squash, are widely cultivated in India, including the temperate Jammu and Kashmir, during the summer. However, these crops are susceptible to various viral pathogens. A survey conducted across major cucurbit-producing districts in the Kashmir valley (Srinagar, Budgam, Baramulla, and Pulwama) revealed viral incidence ranging from 46.66
Climate change has altered the epidemiology of plant pathogens, leading to the emergence of minor pathogens as major threats to crop production and necessitating sustainable disease management strategies. In the present study, crosslinked biopolymer-based seed coating formulations integrating Trichoderma spp. and compatible fungicides were developed and evaluated for the management of seed- and soil-borne diseases in major oilseed crops. Initial in vitro screening identified Trichoderma harzianum Th4d as the most effective antagonist against Fusarium oxysporum f. sp. ricini, Sclerotium rolfsii, and Macrophomina phaseolina (sesame), while T. asperellum TaDOR-7316 exhibited superior antagonistic activity against M. phaseolina infecting soybean. Compatibility studies identified thiram, cymoxanil + mancozeb, and mancozeb as suitable fungicides for integration with the selected bioagents. Subsequently, crop-specific seed coating formulations incorporating crosslinked biopolymers (CP-1 and CP-2), Trichoderma isolates, and compatible fungicides were evaluated under greenhouse and field conditions. Among the treatments, the CP-2-based formulation combined with compatible Trichoderma and fungicide (T5) consistently provided superior disease control, reducing disease incidence to 12.3
Cashew shoot dieback caused by Diaporthe sp. is a major year-round constraint limiting productivity in cashew orchards. A field study was conducted during 2018–2020 to evaluate the effect of pruning and fungicide application on disease management in orchard and yield, supported by in vitro fungicide sensitivity assays. The pathogen showed high sensitivity to Carbendazim + Mancozeb (ED₅₀: 0.264 ppm), Thiophanate methyl (0.839 ppm), and Propiconazole (1.309 ppm). Field results revealed that pruning combined with fungicide application significantly reduced disease severity and increased nut yield. Pruning of diseased shoot decreased the disease severity (26.14
The physiological, morphological, and host reaction responses of eighteen green gram cultivars were evaluated to determine their relative susceptibility to the root-knot nematode infection. Inoculation with 2000 J2 of Meloidogyne incognita/kg soil incited extensive galling on the roots and induced stunting of plant growth, leaf yellowing, reduced flowering and podding, and lower grain yield losses. The root galling among the cultivars, varied greatly with 32—152 galls/root system, being highest in cv. K-851 and lowest in cv. ML-5. The M. incognita infection significantly reduced the plant growth (22—28
Banana is an important commercial fruit crop grown in the tropical and subtropical regions of the world. India is the world’s largest producer and exporter of banana, accounting for 25.56
In the face of increasing environmental concerns, demand for chemical-free natural and organic farming produce is rising across the globe. Organic farming is fast emerging as sustainable and environment-friendly alternative to conventional crop production. The use of Biocontrol Agents (BCAs) and Botanicals has emerged as a major component of Integrated Disease Management (IDM). BCAs provide an environmentally safe approach by reducing reliance on synthetic pesticides while enhancing crop resilience and soil health. This review critically explains the current and evolving role of BCAs and botanicals in modern crop protection system. This also explores how BCAs can be effectively integrated with organic and natural farming system for habitat manipulation to suppress pathogenic populations and improve overall soil fertility and biodiversity. The mechanism of actions of BCAs along with recent technological advances in formulation and delivery systems have also been discussed. Key challenges, such as inconsistent field performance, regulatory barriers, shelf life of formulations, delivery system and adoption constraints, were analysed highlighting successful applications. Policy frameworks and research priorities have also been outlined to facilitate broader adoption and integration of BCAs into sustainable agricultural systems. BCAs are transformative tools capable of creating resilient, disease-suppressive cropping systems that align with the goals of sustainable and environmentally responsible agriculture.
Capsicum annuum is an economically important spice and vegetable crop valued for its pungency, flavour, nutritional and medicinal properties. Chilli productivity is increasingly compromised by a complex spectrum of plant pathogens, particularly by begomoviruses (family Geminiviridae). In the present study, chilli plants exhibiting typical symptoms, including upward or downward leaf curling, leaf puckering and stunted growth, were collected from the field. Viral infection was initially detected using PCR with begomovirus-specific primers, followed by rolling circle amplification (RCA) for whole-genome amplification. Sequence analysis confirmed the presence of a begomovirus along with its associated betasatellite. Full-genome characterization revealed that the isolate PQ876122 shared 89.87
Capsicum (Capsicum annuum L.) is an economically important vegetable crop belonging to the family Solanaceae. During March 2023, severe leaf spot symptoms were observed on Capsicum cv. California Wonder at the BHU Horticulture Farm, Varanasi, Uttar Pradesh, India. Symptoms appeared as brown-to-black necrotic spots that later coalesced, causing extensive blighting and leaf death. The associated pathogen was isolated and identified using morphological and molecular approaches. The fungal isolate exhibited dark olive green colored mycelium with abundant sporulation on Potato Dextrose Agar medium. Microscopic observations revealed brown septate conidiophores and 2–4 septate conidia with hair-like appendages measuring 20–50 × 10–20 μm. Based on morphological and molecular analyses of the rDNA-ITS and GAPDH regions, the associated pathogen was identified as Curvularia tuberculata. Koch’s postulates were proved confirming Curvularia tuberculata as the causal organism of leaf spot disease in Capsicum.
The impact of cultural (mulching, sowing time, and seed priming) and nutrient management practices (drip fertigation) were investigated on the incidence of Alternaria leaf blight (ALB), and stem rot (SR) in peanut for two consecutive cultural seasons. Sowing time was identified as the most critical factor governing disease development. The study revealed that early sowing substantially suppressed ALB incidence (17.0
Downy mildew caused by Pseudoperonospora cubensis (Berk. Curt.) Rostow is a major constraint to cucumber production due to rapid disease development and unstable resistance. Host plant resistance represents the most effective and sustainable management strategy. This study investigated disease resistance responses in selected Indian slicing cucumber genotypes, viz., IC527431, IC572024, IC527400, IC613488 and Gol Kheera 1, identified as potential sources of resistance to downy mildew, along with Swarna Agethi as a susceptible check and uninoculated control plants. At 16 dpi, Swarna Agethi (71.72
Planting material plays an important role in the production of fruit crops. Inadequate availability of quality planting material is one of the important deterring factors in development of a sound fruit industry. Keeping this in mind we produce a citrus graft-transmissible pathogens CGTPs free planting material for the north east India, where the citrus production is reducing due to decline cause by CGTPs. Khasi mandarin (KM) (Citrus reticulata) is a vital fruit crop in Northeast India, contributing significantly to regional livelihoods. However, its production is severely threatened by citrus graft-transmissible pathogens (CGTPs), including Citrus tristeza virus (CTV), Indian citrus ringspot virus (ICRSV), Citrus yellow mosaic virus (CYMV), and Huanglongbing (HLB) bacteria. This study conducted a comprehensive survey across Assam, Manipur, and Meghalaya to assess CGTP incidence using ELISA (CTV) and PCR-based detection. Among the 77 KM samples analyzed, 67.5
In July 2023, fruit rot symptoms were observed on pear (Pyrus communis) fruits in an orchard in Darjeeling, India. Initial symptoms included white to grayish mycelia at the pedicel end, which rapidly led to complete fruit rot. Fungal isolates cultured on PDA produced white, fluffy colonies with conidial features consistent with Lasiodiplodia theobromae. Molecular identification using ITS1/ITS4, NL1/NL4 and EF1688/F11251 primers confirmed the pathogen, with ITS (OR528818), LSU (PP825371) and TEF lα (PX872900) sequences showing 100
