www.pelagiaresearchlibrary.com t Available online a Pelagia Research Library European Journal of Experimental Biology, 2013, 3(1):380-387 ISSN: 2248 –9215 CODEN (USA): EJEBAU 380 Pelagia Research Library Comparative analysis of RAPD and ISSR marker assays for detecting genetic polymorphism in Tilletia indica Shabana Parveen, M. S. Saharan, Ajay Verma and Indu Sharma Directorate of Wheat Research, Karnal, Haryana, India _____________________________________________________________________________________________ ABSTRACT Karnal bunt of wheat, caused by Tilletia indica Mitra is an important disease prevalent in several countries. The pathogen due to its heterothallic nature shows high variability. In the present study, genetic relationships among ten isolates of T.indica collected from different locations of India and 15 monosporidial lines raised from these isolates were investigated by using 34 RAPD and 28 ISSR primers. RAPD and ISSR primers revealed 92.82 and 98.4 % polymorphism, respectively. Similarity coefficient values ranged from 0.61 to 0.97 for RAPD and 0.61 to 0.96 for ISSR primers. The dendrogram developed by RAPD and ISSR primers based analysis grouped the isolates and monosporidial lines in different clusters. Mental test employed for detection of goodness of fit established cophenatic correlation value for both the primer systems and it was significant at P 0.01. Clustering of isolates within groups was also similar based on RAPD and ISSR derived dendrograms. In our study, both marker systems were similar except for the percentage polymorphism which was found to be greater using ISSR, thus indicating the greater effectiveness of ISSR primers for estimating genetic diversity of Tilletia indica. Key Words: Karnal bunt, Tilletia indica, Wheat, DNA polymorphism, Variability _____________________________________________________________________________________________ INTRODUCTION Tilletia indica Mitra [synonym Neovossia indica (Mitra) Mundkur], the causal agent of Karnal bunt of wheat was first described on wheat near Karnal, India in 1931(13). Tilletia indica a floret infecting basidiomycetes causes a partial bunting of wheat seeds and infected seeds have a trimethyleamine odor (5). Karnal bunt is viewed as a serious disease for international trade in wheat because it reduces grain quality. The pathogen has a very restricted distribution, being limited largely to the Indian subcontinent and a small area of Mexico and the south-western United States of America (4). The pathogen is heterothallic and undergoes sexual reproduction after teliospore germination. Primary and secondary sporidia or hyphae as compatible mating types must fuse to form a dikaryon which readily increases the chances of variation due to heterozygosity and plays an important role in the production of new variants. Karnal bunt of wheat became an important disease of wheat after the introduction of dwarf wheat varieties in North West India, where it was of minor importance earlier (17). Knowledge of diversity of the Karnal bunt pathogen in the form of distinct monoteliosporic and monosporidial cultures is essential for its effective management. The variability in T. indica has been documented on the basis of pathogen morphology, cultural characteristics, temperature response and pathogenicity tests (15-21-7). Understanding the genetic variability in the pathogen is extensively achieved through the use of genetic markers (3- 10) , but these approaches are not yet very efficient for genetic variability studies in T. indica. Hence the present investigation was undertaken to compare RAPD and ISSR assays for their utility in generating polymorphic DNA profiles and genetic variation studies in T. indica isolates and monosporidial lines to understand the degree of congruency between the two marker systems.