Sugarcane (Saccharum spp.) is a monocotyledon and member of the family Poaceae, tribe Andropogoneae. Sugarcane contributes approximately 80% of the global sugar requirement[1]. Red rot is one of the most serious and oldest diseases of Sugarcane. The first appearance of the disease was in Java in 1893. Currently, the disease occurs in all the sugarcane-growing continents, and it is reported in 77 countries, including India, Pakistan, Bangladesh, Thailand, Myanmar, Nepal, and Vietnam[2].

Sucrose content, the main economic produce, was reduced in the range of 31%–75% at different infection levels[3]. Red rot–affected canes show a decline of 29 to 83% in cane weight and 24 to 90% in juice extraction [4].

Sugarcane has some red rot resistant varieties. However, in countries, especially in Asia, varietal breakdown to red rot has caused severe epiphytotics, by which the resistant varieties failed in the field at regular intervals. New pathogenic strains with higher virulence were found responsible for the varietal breakdown in Sugarcane. Extensive cultivation of a single variety over large areas led to extensive crop damage due to the vertifolia effect in different decades in India. The current epiphytotic on the ruling variety Co0238 has caused a loss of more than one billion US dollars to India in the 2020-21 season[1].

Colletotrichum falcatum is a fungal pathogen that causes red rot disease in Sugarcane. The morphology of the fungus includes conidia that are crescent-shaped or falcate (curved), which is why the species name is falcatum, conidiophores which produce conidia in clusters, and sclerotia which are hard, dark-coloured masses that help the fungus survive in unfavourable conditions. This pathogen is a facultative parasite. It occurs in anamorphic and teleomorphic forms, but the amorphic stage, which infects standing canes, is the most important stage. The distinctive morphological and cultural characteristics of C. Falcatum include the development of acervuli with setae, the presence or absence of teleomorph, the pinkish appearance of the colony, sporulation and growth rate[5].

Diversity in virulence within pathotypes revealed that a red rot pathogen undergoes adaptive changes in host cultivars. It was reported that isolates are virulent in susceptible varieties but not in resistant and moderately susceptible varieties[6]. Virulence frequencies of isolates range from 21.3–40% on mildly susceptible varieties compared with 62.9–97.9% on susceptible varieties. This suggests that C. falcatum isolates differ in their host infectivity. Thus, it is very important to identify the extent of pathogen diversity and the way infection occurs to develop effective disease control and planting management [5].

Of the 5.2 M ha land in cultivation in India 2.6 M ha (50%) area of sugarcane production is done in the state Uttar Pradesh(UP). The sugarcane variety Co 0238 grown in UP, known for its moderate resistance to disease, saw a significant rise in popularity, with its cultivation area increasing from 19.8% in 2015-16 to 86.67% in 2020-21. However, during this same period, the incidence of Red Rot in Co 0238 escalated dramatically, from 5% in 2015-16 to 100% by 2020-21. The rapid spread of this disease was primarily attributed to infected soil and setts used in farmer fields.

CoS8436 was a popular moderately disease-resistant variant of Sugarcane in Bihar, India. The cane production dipped almost 1/3rd over 3 seasons of Sugarcane Production as Variety CoS8436 succumbed to Red Rot.

Many sources of inoculum are involved in the transmission of Red Rot. C. falcatum is primarily spread through soil and diseased setts, whereas secondary distribution is through irrigation water, rainfall splashing, midrib lesion dew brushing, wind dispersal and other field vectors[7]. The relative importance of how inoculum is spread depends on the time of the year and the conditions under which the cane grows; in monsoon season, the secondary distribution will be active.

The pathogen infects stalks through nodes, leaf scars, growth rings, root primordial and buds. The pathogen enters the nodes of a sugarcane plant through the inner epidermis of the lower part of the leaf sheath of this plant. In an unfavourable condition, the fungus produces appressoria on the rind and leaves. Late in the season, the infection restarts with the placement of healthy plants.

During soil-borne transmission, latent fungal structures, namely appressoria, dense-walled hyphae chlamydospores, and setae play important roles in the dispersal of disease [8]. Colletotrichum falcatum thrives on unhealthy stalks or stubble fragments. Although C. falcatum is not a definite soil-inhabitant pathogen, there is enough evidence to suggest that fungal propagules are perpetuated by debris-borne inoculum [9].

Red Rot disease manifests in four distinct forms depending on the part of the plant affected:

Tiller Red Rot: Appears during the tillering stage, identified by stunted plant growth, dry straw-colored leaves, and overall poor plant health.

Lamina Red Rot: This type causes the lamina (leaf blade) to turn straw-colored in the middle, with dark reddish-brown edges. The leaves eventually split and hang at the lesion sites.

Mid Rib Red Rot: This form is characterized by a reddening of the midrib (central vein of the leaf), with the red color progressing throughout the entire midrib.

Stem Red Rot: Occurs in the stalk at later stages, where the internal tissues show alternating red and white patches with an alcoholic scent. The infected stalks often weaken and separate easily at the nodes.

1. Initial Infection (0-3 days): The pathogen typically enters through wounds or natural openings in the plant, which aligns with the early infection phase.

3. Inoculum Build-up (10-16 days): This is when the fungus multiplies and builds up spores (inoculum), essential for further spreading within the field.

4. Symptom Appearance (16-21 days): The yellowing of leaves and internal reddish streaks in the stalk are common symptoms during this stage.

5. Red Discoloration (21-30 days): The characteristic red discoloration of internal tissues becomes more severe, along with tissue rotting.

6. Plant Decline and Death (30-45 days): Severe infections lead to a rapid decline in plant health, including extensive wilting and tissue breakdown, often resulting in plant death if left unmanaged.

The most important requirement in any good disease management practice is the accurate identification of the pathogen.

1. Traditional Methods: Traditional methods for detecting plant diseases involve pathogen isolation and inoculation tests. Colletotrichum species are primarily identified based on morphological traits such as mycelial development, color, texture, and conidia size. While conidia can be observed under a microscope, the accuracy of this approach relies heavily on the experience of the examiner. These phenotypic methods are time-consuming and require skilled personnel. Additionally, overlapping characteristics within species make morphological identification insufficient. Pathogenicity tests are also used but take a long time and are influenced by environmental factors.

2. Serological Methods: Serological methods, such as ELISA, are used to detect Colletotrichum Falcatum, the red rot fungus in Sugarcane. Viswanathan et al. demonstrated that ELISA could quantify pathogen colonization and classify host reactions as resistant, moderately resistant, or susceptible based on fungal spread in cane stalks[10]. Other techniques like dot immune binding assay (DIBA) and western blotting have also been employed for detection. Specific polyclonal antibodies were raised against C. Falcatum with high affinity. However, serological tests risk false positives due to cross-reactivity with plant debris or unrelated organisms.

3. Image Processing Methods: Image processing techniques, including computer vision-based algorithms, have been applied to detect diseases like red rot in Sugarcane, involving steps like image acquisition, preprocessing, and segmentation. Fluorescence imaging captures chlorophyll fluorescence, providing insights into plant responses to pathogens but is limited in field applications. Thermography tracks temperature variations in plant leaves to identify diseases but struggles with environmental sensitivity and disease differentiation. Hyperspectral imagery captures plant health data across wavelengths, successfully detecting orange rust in Sugarcane, though further research is needed for broader applications. However, leaf size variability and rapid evaporation pose challenges.

1. DNA/RNA-Based Affinity Biosensor A new DNA-based biosensor has been developed for early pathogen identification, detecting diseases before visible symptoms. It relies on specific nucleic acid hybridization to rapidly identify genetic and infectious diseases. The most common assay uses single-stranded DNA (ssDNA) on electrodes with electroactive markers to test hybridization with target DNA. While promising, DNA biosensors require PCR amplification and small nucleic acid samples. However, drawbacks include high costs, single-target synthesis, and limitations in real-time detection.

Colletotrichum Falcatum nucleotide sequences are available in the public domain database. Embed this table in an Image Format like in [5].

There is a growing need for rapid, accurate, and user-friendly diagnostic methods, particularly for agricultural pathogens like Colletotrichum Falcatum, which causes red rot in Sugarcane, given the elevated virulence and frequent epiphytotics. Traditional diagnostic methods are time-consuming, require specialized equipment and skilled personnel, and are often impractical for field use. Developing a point-of-care (PoC) diagnostic tool that leverages the specificity of ITS rDNA identification combined with a home-friendly iSPR(Surface Plasmon Resonance) system can provide early, reliable detection of pathogens at the molecular level. This approach is not only faster and more accurate but also more accessible, enabling real-time monitoring and management of crop diseases, which is crucial for improving yield and reducing losses in agricultural systems.