Molecular and Pathological Characterization of Colletotrichum falcatum Infecting Subtropical Indian Sugarcane

Abstract

Red rot, caused by Colletotrichum falcatum, is the most significant problem of sugarcane worldwide. Pathological studies and three different marker systems were used to characterize 25 C. falcatum isolates collected from 18 subtropical sugarcane cultivars from 15 different sugarcane-growing regions of three north-eastern states of India to assess pathogen diversity. Of these 25 isolates, three were new (RR2A, RR15, RR83) from cultivars Co 7717, Co J83 and Co S88230, respectively, pathologically characterized on 13 standard differential hosts. Isolates Cf 01, Cf 08 and RR15 were the most, and Cf-07 the least virulent. Molecular characterization using random amplified polymorphic DNA, universal rice primers (URP) and inter simple sequence repeat markers amplified a total of 161 alleles of which 159 were polymorphic (98.76%). Unweighted paired group method with arithmetic averages analysis of combined data of all the DNA markers obtained by three marker systems classified 25 isolates into six clusters at 34% genetic similarity with high Mantel matrix correlation (r = 0.83). The principal component analysis (PCA) of marker data explained 68% of the variation by first three components. Molecular diversity as revealed in these isolates is very high, but non-structured. Isolate Co Pant 84212 was found to be genetically most diverse. We demonstrated for the first time that URPs derived from weed rice could successfully assess genetic diversity in C. falcatum. Molecular characterization of the C. falcatum isolates prevalent in north-eastern India would enable red rot management strategies, selection for resistance genes and development of resistant cultivars.

Current status of Colletotrichum capsici strains, causal agents of Brown blotch disease of cowpea in Burkina Faso

“…All the four clusters were representative of the three agroecological zones and the distribution of the isolates was not depending on the geographic area indicating a high genetic diversity at all locations. Kumar et al (2010) observed the same results; working with C. falcatum from sugarcane in India. Such variations could be due to similar climatic conditions, which might favor the coexistence of the isolates.…”

Variations in random amplified polymorphic DNA profile and toxin production among isolates ofColletotrichum falcatumWent from sugarcane in Tamil Nadu, India

“…Genetic variabilities in C. falcatum isolates have been reported earlier using RAPD (Madan et al 2000;Mohanraj et al 2002;Suman et al 2005), analysis of ITS sequences (Malathi et al 2010), Universal Rice Primers (URP) and Inter Simple Sequence Repeat markers (Kumar et al 2011). The analysis of genomic DNA using PCR-based methods has proven to be a fast, sensitive and reliable method for determining genetic relationships among strains of the same phytopathogenic organisms (Ma and Michailides 2007).…”

A Review on Red Rot: The ?Cancer? of Sugarcane

“…The key morphological identification features of C. falcatum fungus are: its mycelium which is both intracellular and intercellular, asexual fruiting bodies known as acervuli (minute, velvety and formed on the surface of the host part), often with setae (dark-pigmented, unbranched, thick-walled sterile hyphae usually pointed at the tip), having hyaline, linear or club shaped conidiophores producing elongated, single celled, thin walled, uninucleate, colourless, sickle shaped (Falcate), slimy conidia having granular protoplasm with a large oil globule, thick walled, greenish black chlamydospores and the presence of appressoria (thick-walled swellings at the end of a hypha or germ tube useful for attaching the fungus to the host surface before penetration of the tissue), presence or absence of the telomorph, colony colour and growth, production of pigments and growth rate which are mostly used for genetic characterization [9,10,44,45].…”

“…The characterization of pathogen has primarily been based upon variation in colour, conidial size and shape, appressoria, colony characters, host association and sporulation [60][61][62][63][64]. But this phenotypic identification is time consuming, expertise specific and not always fully discriminative [45].…”

“…Variability in C. falcatum isolates have been characterized by using arbitrary marker system such as RAPD [74][75][76][77]. Kumar et al [45] used inter simple sequence repeat (ISSR), universal rice primers (URPs) and RAPD markers to characterize variability among C. falcatum isolates. ITS primers were also used to study the variability among pathogen [78,79].…”