Sugarcane smut, caused by the biotrophic fungus Sporisorium scitamineum (Syd.), leads to substantial yield loss in sugarcane-growing regions worldwide. To elucidate the molecular mechanisms governing fungal development and pathogenicity, a comprehensive comparative transcriptome analysis was conducted across distinct developmental stages of high-virulent (Ss97009) and low-virulent (SsV89101) isolates, under both in vitro culture conditions (haploid and dikaryotic mycelial stages) and during host interactions at 2 days post inoculation (dpi; primary hyphae formation), 5 dpi (intercellular colonization) and 60 dpi (sporogenesis/teliospore formation). The analysis identified key virulence factors involved in the formation of infective dikaryotic mycelia, which are essential for host colonization. Key metabolic pathways, including amino acid and nucleotide metabolism, glycolysis, and glycerol–lipid metabolism, were consistently up-regulated during this dimorphic transition in both isolates. During interaction with the host, the high-virulent isolate exhibited a markedly higher number of up-regulated genes at the whip-emergence stage, compared with its axenic dikaryotic mycelial stage, whereas early infection stages exhibited widespread down-regulation of genes in both isolates. During the later biotrophic phase, genes encoding effector proteins, cell wall–degrading enzymes (CWDEs), transcription factors (TFs), and membrane transporters were predominantly up-regulated in the high-virulent isolate, suggesting their potential roles in disease development. Notably, virulence-associated effectors, including EFF1, MIG1, PEP1, STP, and TIN showed elevated expression during whip formation in the high-virulent isolate, reinforcing their association with pathogenicity. Collectively, these findings provide valuable insights into the stage-specific regulatory networks governing smut fungus development and its interaction with sugarcane, advancing our molecular understanding of smut disease biology.

Plants exhibit complex molecular, physiological, and morphological responses to stress, which may be specific to the phenological phase of the crop. Knowledge of signalling cascades leading to the molecular and functional regulation of sugarcane in response to high-temperature stress is essential for the development of climate-resilient sugarcane varieties with stable expression of cane yield and quality under stress. In the present study, a comparative proteomic analysis was carried out with the commercial sugarcane variety Co 99004, which was established as tolerant to high-temperature stress based on evaluation of growth and physiological parameters. Proteins such as Poly[ADP-ribose] polymerase 2-B, REF/SRPP-like protein cpx, Putative F-box/kelch-repeat protein, Putative cyclin-dependent kinase F-2, Probable F-box protein, Thioredoxin O2, Dirigent protein, MYB family transcription factor, stress-response A/B barrel domain, and Protein TIFY 11d were identified as high-temperature stress-responsive in the heat-tolerant variety Co 99004. These proteins showing differential expression patterns or function under high-temperature stress were revealed to be essential for plant survival, with diverse roles such as protection of intercellular proteins from denaturation, DNA repair and genome stability, alteration of membrane structure and composition, altogether ensuring sustained growth and cane yield under adverse environmental conditions. Further characterisation of the differentially expressed proteins and their gene functions might provide novel information to decipher the molecular mechanisms leading to the adaptation of sugarcane to high-temperature stress.

Sugarcane wilt caused by Fusarium sacchari is a destructive and widespread disease globally. In the present era of intensive agriculture system, huge quantities of fungicides are being applied to manage diseases to get high crop yields. However, these fungicides have many non-target effects. For sustainable agriculture, there is a need for eco-friendly methods of growth promotion and crop protection. In this context, a total of 30 endophyte Chaetomium globosum isolates were isolated and evaluated for their antifungal potential against sugarcane wilt caused by Fusarium sacchari. The isolates of C. globosum showed large variations in colony colour, growth rate, colony diameter, ascospore shape, sporulation of F. sacchari time, and ascomata hairs. The most promising CGSR13 strain inhibited colony diameter, spore germination, and sporulation by 66.39, 55.17, and 75.00, respectively. The collective sett and soil treatment with CGSR13 showed 60.09 and 46.37

National Hybridization Garden (NHG) at ICAR-SBI, Coimbatore, India, is the national resource for sugarcane breeding and varietal development in India. The parental clones are being maintained under disease free conditions to utilize them in sugarcane hybridization and varietal development in the country. Recently, wilt struck some of the parental clones, that affected their utilization in breeding programme. Hence, a detailed study was conducted to assess the impact of wilt on flowering and ratoon establishment in about 225 parental clones at NHG. Of the 225 clones, 108 remained free from wilt and the remaining 117 clones exhibited varying incidences of wilt. Majority of wilt-free clones recorded more than 75 to 100

Stalk rot is one of the important diseases of sugarcane - caused by Phaeocytostroma sacchari. Survey and monitoring was done during 2020-2022 to assess the status of stalk rot in the sugarcane germplasm and molecular identification of the associated pathogen. During the study period, 15 clones from the Saccharum officinarum recorded stalk rot incidence followed by two foreign hybrids. The clones affected were generally weak and were already affected by sugarcane bacilliform virus (SCBV). The clones 28 NG 10 and 57 NG 140 were severely affected by stalk rot. In addition, the association of Fusarium spp. was also recorded in these clones. The pathogen was studied for morphological and cultural characters and identified through molecular methods using ITS and LSU primers and in the BLAST analysis, the amplified nucleotide sequence of the pathogen shared more than 98% similarity with other already submitted nucleotide sequences of P. sacchari. As there are no reports available on the molecular identification of this pathogen, this is the first record of molecular identification of P.sacchari from India.

Sugarcane is an important cash crop that is severely affected by red rot caused by the fungal pathogen Colletotrichum falcatum Went in India. The management of this economically important disease with mustard biofumigation was tested under in vitro and in vivo conditions by considering its effect on other soil microbiota and most importantly, the popular biocontrol agent Trichoderma harzianum , which is widely accepted and adopted by most of the farmers. In vitro studies on the effect of volatiles from mustard seed meal gave 100% inhibition of C. falcatum at 0.5% concentration (w/v), whereas T. harzianum was not inhibited even up to 1% concentration. In another study, using mustard seed extract in poisoned food technique, 56.16% mycelial inhibition was shown at 2.5% concentration, while beneficial organisms like T. harzianum , Metarhizium anisopliae and Nomuraea rileyi were not affected by it. However, Beauveria bassiana and Paecilomyces lilacinus showed about 40% mycelial growth inhibition. Under in vivo conditions, incorporation of 5% chopped mustard in sterile or unsterile soil drastically reduced C. falcatum population. The in vivo study on the effect of mustard biofumigation on sugarcane sett germination and plant growth proved that the biofumigant increased the rate of germination by reducing the per cent disease incidence (i.e. 17.65—41.17%) and plant growth by reducing the effect of C. falcatum . Moreover, it did not show any harmful effect on sugarcane sett growth.

Generally, it is believed that sugarcane grows normally in the absence of stalk infecting pathogens causing red rot, wilt, smut or fungal diseases. Although degeneration occurs in sugarcane due to systemic build-up of non-fungal pathogens, the canes are harvested as healthy canes. The degenerated canes showed 30–50

Life cycle of the dimorphic sugarcane smut fungi, Sporisorium scitamineum , involves recognition and mating of compatible saprophytic yeast -like haploid sporidia (MAT -1 and MAT -2) that upon fusion, develop into infective dikaryotic mycelia. Although the dimorphic transition is intrinsically linked with the pathogenicity and virulence of S. scitamineum , it has never been studied using a proteomic approach. In the present study, an iTRAQ-based comparative proteomic analysis of three distinct stages was carried out. The stages were: the dimorphic transition period - haploid sporidial stage (MAT -1 and MAT -2); the transition phase (24 h post co -culturing (hpc)) and the dikaryotic mycelial stage (48 hpc). Functional categorization of differentially abundant proteins showed that the most altered biological processes were energy production, primary metabolism, especially, carbohydrate, amino acid, fatty acid, followed by translation, post -translation and protein turnover. Several differentially abundant proteins (DAPs), especially in the dikaryotic mycelial stage were predicted as effectors. Taken together, key molecular mechanisms underpinning the dimorphic transition in S. scitamineum at the proteome level were highlighted. The catalogue of stage -specific and dimorphic transition -associated -proteins and potential effectors identified herein represents a list of potential candidates for defective mutant screening to elucidate their functional role in the dimorphic transition and pathogenicity in S. scitamineum . Biological significance: Being the first comparative proteomics analysis of S. scitamineum , this study comprehensively examined three pivotal life cycle stages of the pathogen: the non-pathogenic haploid phase, the transition phase, and the pathogenic dikaryotic mycelial stage. While previous studies have reported the sugarcane and S. scitamineum interactions, this study endeavored to specifically identify the proteins responsible for pathogenicity. By analyzing the proteomic alterations between the haploid and dikaryotic mycelial phases, the study revealed significant changes in metabolic pathway -associated proteins linked to energy production, notably oxidative phosphorylation, and the citrate cycle. Furthermore, this study successfully identified key metabolic pathways that undergo reprogramming during the transition from the non-pathogenic to the pathogenic stage. The study also deciphered the underlying mechanisms driving the morphological and physiological alterations crucial for the S. scitamineum virulence. By studying its life cycle stages, identifying the key metabolic pathways and stage -specific proteins, it provides unprecedented insights into the pathogenicity and potential avenues for intervention. As proteomics continues to advance, such studies pave the way for a deeper understanding of plantpathogen interactions and the development of innovative strategies to mitigate the impact of devastating pathogens like S. scitamineum.

Plant diseases significantly threaten global food security, with numerous historical instances of devastating epidemics. This risk is particularly acute in key agricultural and food crops, such as sugarcane. Although recent advancements in molecular diagnostics have improved the detection of sugarcane viruses, these methods are largely confined to lab settings due to their reliance on sophisticated, costly equipment. To overcome this limitation, we have developed a more accessible and cost-effective solution: a magnetic nanozyme-enhanced colorimetric ImmunoFlow-through assay designed for the ultrasensitive detection of sugarcane yellow leaf curl virus (ScYLV). This innovative technique allows for clear optical identification of viral concentrations as low as femtomolar levels. The assay employs cationic magnetic nanoparticles for virus isolation and colorimetric immunolabels for diagnosis, enhancing sensitivity and providing immediate results, comparable to those of established methods like quantitative real-time-polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA). Our assay offers a one-step detection process and a two-step semiquantitative analysis, marking a major breakthrough in plant virus diagnostics. Extensive research into the assay's design, including its sensing platform, blocking agents, antibody conjugation chemistries, sensitivity, quantification, potential for multiplexing, and field applicability, was carried out. This diagnostic research utilizing Magnetozyme in a flow-through assay represents a pioneering approach to rapid and sensitive diagnosis within plant disease diagnostics. It introduces a promising alternative to traditional molecular diagnostics, potentially transforming plant disease management and enhancing food security globally.

Pokkah boeng (PB) caused by Fusarium verticillioides is an emerging and important fungal disease of sugarcane in India. A total of 30 Chaetomium globosum isolates were screened for the evaluation of their antifungal activities against F. verticillioides. The initial screening of about 30 isolates of C. globosum against F. verticillioides pathogen under in vitro conditions revealed that the C. globosum strain CGSR-13 recorded 77.38, 54.05 and 50.00

Red rot resistant varieties are deployed in the field to avoid serious losses caused by the red rot pathogen, Colletotrichum falcatum. However, frequent breakdown of resistance occurs due to the development of newer pathotypes and in certain situations, elite varieties that are moderately susceptible to red rot are being cultivated. Under such situations, adopting novel strategies to manage the disease is of paramount importance. Since protection of crop at different stages of crop growth from red rot incidence is essential to maintain good crop stand and to achieve higher productivity, attempts have been made by following conventional and molecular approaches. Conventionally, effective fungicides, bioagents and their integration were identified and also standardized effective delivery methods for successful management. In addition, attempts have been made at molecular level to identify virulence related genes of C. falcatum to monitor pathogen population under field conditions and to identify newer pathotypes with high virulence for effective screening programme. Besides, established the possibility of identifying potential target sites as genes/ proteins for fungicidal management of red rot in the field. Findings of both conventional and molecular approaches attempted for red rot management under field conditions are summarized in this review.

Seed cane treatments play a crucial role in managing the primary transmission of sugarcane diseases, ensuring the establishment of healthy sugarcane nurseries for commercial plantations. Leaf scald is one of the major diseases in sugarcane that is primarily transmitted via infected seed cane. The present study was done to test the effectiveness of the hot water treatment (HWT) and adoption of cold soak treatment (CST) to find the optimum combination of seed cane treatment for the production of leaf scald disease (LSD) free-seed cane for sugarcane nurseries. Twelve-months old LSD affected seed cane was treated at 24, 36, and 48 h CST treatments followed by another set of treatments at 54 °C for 50 and 120 min of HWT. A field trial was conducted to record germination, LSD symptoms, and yield in the plant crops. Latent infection of the LSD pathogen in the plants was detected by PCR with L1 and Ala4 primer pairs specific to the Xanthomonas genus. The results revealed that the CST at 36 h followed by 54 °C for 50 min HWT showed significantly higher germination and cane yield. Moreover, the disease incidence was significantly low compared to other treatment combinations and low pathogen titer in the plant crop. Any duration of only CST treatments was ineffective in significantly reducing the level of inoculum in the infected seed cane. Although CST was applied, the 120 min HWT combination resulted in poor germination that led to low cane yield. Moreover, our findings confirmed that neither HWT nor CST or its combination was effective in eliminating LSD pathogens from infected seed canes. Although the LSD pathogen was not eliminated from the infected seed cane, the combination of CST at 36 h followed by HWT at 54 °C for 50 min can be adopted as a new recommendation to reduce the primary transmission of leaf scald disease.

A total of 30 endophyte Chaetomium globosum isolates were evaluated for their bio-control efficacy against Colletotrichum falcatum. In vitro assay with C. globosum isolates using liquid culture filtrate (LCF) and dual culture methods showed 0.00–95.32

Sugarcane rust incited by Puccinia melanocephala (brown rust) and P. kuehnii (orange rust) becomes very severe under warm,moist climatic conditions. Though there were methods to screen rust resistance under artificial conditions where rust is prevalent, there is no method to screen the rust resistance in a place where rust occurrence is not regular and severe. To overcome this problem, a simple method was devised to screen sugarcane leaves challenged with rust uredospores and maintaining the setup under optimum relative humidity and temperature for 15-20 days for identifying the rust resistant sugarcane clones. This method of rust screening is simple and easy, fast and reliable and many clones can be screened in short period of 20 days.