Int.J.Curr.Microbiol.App.Sci (2018) 7(6): 1190-1197 1190 Original Research Article https://doi.org/10.20546/ijcmas.2018.706.141 Determination of Genetic Diversity among Sclerotium rolfsii Isolates Causing Collar Rot of Chickpea Using Simple Sequence Repeat (SSR) Markers Epsita Swain 1* , Archana A. Gadekar 1 , S.S. Mane 1 and Jhumishree Meher 2 1 Department of Plant Pathology, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, India 2 Department of Plant Pathology, Jawaharlal Nehru Krishi Viswa Vidyalaya, Jabalpur, Madhya Pradesh, India *Corresponding author ABSTRACT Introduction In India, chickpea accounts for about 45% of total pulses in the country. Among the soil- borne diseases of chickpea, collar rot caused by Sclerotium rolfsii is seen at the seedling stage (up to 6 weeks after sowing). Seedling mortality ranged from 54.7 to 95.0% in chickpea due to infection of S. rolfsii has been reported by Mathur and Sinha (1968, 1970) and Kotastthane et al., (1976). The genetic variation of S. rolfsii isolates has previously been assessed based on the analyses of RAPD, RFLPs, AFLP profiles by earlier workers like (Harlton et al., 1995; Okabe et al., 1998; Sarma and Singh 2002), however isolates of S. rolfsii have not been investigated using Simple sequence repeat (SSR) markers. Simple sequence repeats (SSRs) are highly informative, codominant, multi-allele genetic markers that are experimentally reproducible. These markers are enormously useful in studies of population structure, genetic International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 06 (2018) Journal homepage: http://www.ijcmas.com Six isolates of chickpea collar rot fungus of Sclerotium rolfsii were collected from different locations of Maharashtra were investigated for genetic diversity under present experiment. We employed five SSR of MB- series to construct a genotype-specific DNA fragment profile of field isolates of this fungus. The PCR amplified product of each primer was resolved on 10 % Polyacrylamide gel electrophoresis. The 5 SSR primers screened produced a total of 60 reproducible and scorable amplicons. The size of amplicons produced ranged from 115bp to 800bp. The percentage polymorphism generated by the SSR markers was 77.6% among all the 6 isolates of Sclerotium rolfsii. The result from the UPGMA based dendrogram generated for Sclerotium rolfsii isolates revealed that they were divided into two main clusters, Cluster-A and B which were further subdivided into sub-clusters. The isolates in the two clusters have an overall Jaccard's similarity coefficient of 35%. The similarity coefficient range varied from 0.27 to 0.83. The SSR markers suggest that there is genetic differentiation among the population. Keywords Chickpea, Sclerotium rolfsii, PAGE, Dendrogram, PCR, SSR marker Accepted: 06 May 2018 Available Online: 10 June 2018 Article Info