Research Journal of Biotechnology Vol. 12 (4) April (2017) Res. J. Biotech 14 Morphological, Pathological and Molecular Diversity of Colletotrichum Capsici inciting Fruit Rot in Chilli (Capsicum Annuum L.) Srideepthi R. 1 , Lakshmisahitya U. 1 , Peddakasim D. 1 , Suneetha P. 2 and Krishna M.S.R. 1* 1. Department of Biotechnology, KL University, Green Fields, Vaddeswaram, Guntur- 522502, AP, INDIA 2. Jayashankar Telangana State Agricultural University, Hyderabad, INDIA *msrkrishna81@gmail.com Abstract Anthracnose is a well-known disease caused by Colletotrichum capsici/truncatum resulting in both qualitative and quantitative yield loss of a commercial vegetable crop chilli. Variability among the C. truncatum species with respect to geographical distribution remained as a major constraint to chilli production. Hence present study was aimed at identifying the genetic variability existing among the species within Andhra Pradesh region. Eight different isolates were characterized and confirmed as C. capsici with species specific marker. Variations among the isolates exist in their cultural and morphological features including aerial fluffy cotton to submerged felty type colonies at a growth rate of 3.8-9.8 mm per day while conidial size varied from 18.1-22.36 μm in length to 2.8-4.0 μm in width. Mode of virulence and pathogenic ability of eight isolates were clustered into high (C.c1, C.c4 and C.c7), moderate (C.c2, C.c5 and C.c6) and least (C.c3 and C.c8) based on their disease score. Genetic relationship was analyzed using 40 randomly amplified polymorphic DNA (RAPD) primers. Based on similarity coefficient by un-weighted pair group method with arithmetic average (UPGMA), isolates were distributed into two clusters (I and II) confirming their genetic diversity. No correlation among pathological and RAPD grouping of isolates was observed. Results showed that RAPD-PCR is a valuable technique for evaluating inherited variation within C. capsici species. Keywords: Anthracnose, Capsicum annuum, Genetic diversity, RAPD markers, Variability within species. Introduction Chilli (Capsicum annuum L.) is an indespensible fourth most important vegetable crop grown worldwide for its exceptional nutritional and therapeutic values. India is the largest producer, consumer and exporter of chillies in the world. Andhra Pradesh ranks first in the production of chilli all over India. Yet, there are several abiotic and biotic factors limiting its production. Anthracnose is one of the devastating fungal diseases affecting chilli crop. This disease is characterized by sunken necrotic lesions at both pre-and post harvestal stages of the crop and is caused by Colletotrichum species resulting in a yield loss of about 20 to 70 per cent every year 1 . Anthracnose spreads very rapidly during moist- humid conditions leaving very less scope for farmers to protect the crop. In addition, indiscriminate usage of pesticides has been increasing the production costs to farmers even alarming the environmental issues. Hence providing tolerance to this devastating disease remained as a daunting task for the scientific community. Colletotrichum species like C. acutatum, C. coccodes, C. gleosporioides, C. atramentarium, C. dematium and C. capsici were reported to be the causative agents of chilli anthracnose globally 2 . There exists a huge variability among Colletotrichum species causing anthracnose disease. Among the existing species, C. capsici / C.truncatum is an economically important cosmopolitan fungus 3 . It is reported to infect 45 genera of plant kingdom either by multiple species occurring on a single host or single species occurring on multiple hosts leading to serious cross infection problems. 4 C.capsici is most commonly found to occur in India and causes prominent yield losses in chilli production 5 . Existence of variability within the species and its pathogenic ability with respect to different hosts, inadequate taxonomic details of the species, remained as a major constrain to develop efficient strategies against C. capsici. Earlier taxonomic identification was done based on cultural characteristics described by Smith and Black 6 , yet this method is no longer adequate in the present-day situation as morphological characters vary with environmental conditions. Considering the variability of this species with respect to its geographical location and environmental conditions, present research work was surveyed to identify variability among C.capsici from different locations of the state to study their morphological, pathological and molecular characteristics. Pathogenic variants of taxonomic complexity in a given pathosystem can be identified by application of molecular techniques like RAPD markers 7 . Molecular techniques combined with morphological studies have proven to be effective for characterization of Colletotrichum species. 23 In this study totally forty different RAPD markers were utilized to find out the variations existing among the eight Colletotrichum species collected from different locations of the state. The genetic relationship/diversity among the species was analyzed from the data obtained from RAPD