ISSN: 1314-6246 Ullah et al. J. BioSci. Biotech. 2013, 2(2): 145-150. RESEARCH ARTICLE http://www.jbb.uni-plovdiv.bg 145 S. M. Sarid Ullah 1 Md. Amzad Hossain 2 Md. Musharaf Hossain 1 Sumanta Barman 3 Md. Mehadi Hasan Sohag 1 Shamsul H. Prodhan 1 Genetic diversity analysis of chewing sugarcane (Saccharum officinarum L.) varieties by using RAPD markers Authors’ addresses: 1 Shahjalal University of Science & Technology, Sylhet-3114, Bangladesh. 2 Bangladesh Sugarcane Research Institute (BSRI), Ishwardi, Pabna, Bangladesh. 3 Ruhr University, Bochum, Germany. Correspondence: Shamsul Haque Prodhan Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet-3114, Bangladesh. Tel.: +880-821 713491 ext. 242 e-mail: shamsulhp@yahoo.com Article info: Received: 19 April 2013 Accepted: 21 June 2013 ABSTRACT In the present study an efficient and easy method was followed for the isolation of DNA from meristem cylinder in five chewing sugarcane varieties, namely Amrita, Bomaby, Babulal (Co.527), Q83 and Misrimala. The quality and quantity of DNA were assured by visual estimation using agarose gel electrophoresis and UV spectrophotometry. The highest amount of DNA was retrieved from the Amrita (3250 ng/ml) and the lowest amount was attained from the variety Q83 (1450 ng/ml). The amount of recovered DNA was enough for PCR amplification and marker studies such as random amplified polymorphic DNA (RAPD). Using RAPD markers, bands obtained from fingerprinting (190 bp to 1200 bp) showed 73.5% polymorphism. The dendrogram, based on linkage distance using unweighted pair group method of arithmetic means (UPGMA), indicated segregation of the five chewing varieties of sugarcane into two main clusters. Amrita, Bombay and Misrimala were grouped in cluster 1 (C1) followed by sub- clusters. Babulal and Q83 were grouped in cluster 2 (C2). The results of the present investigation also revealed that the twenty RAPD primers were able to identify and classify the chewing sugarcane varieties based on their genetic relationship. Key words: genetic diversity, RAPD, PCR, UPGMA, Saccharum officinarum Introduction Sugarcane (Saccharum officinarum L.) is one of the leading crops in the world and it is the second most important cash crop, especially for the North and Southern part of Bangladesh. It provides cheap food in the form of “sugar” and “gur (zaggary)”. It is also a food crop as people use to chew and drink sugarcane juice. Northern, Southern and Central region of Bangladesh practice sugarcane cultivation and commands 2% area of total cultivated land. Twenty-five lakh metric tons (MT) from the total production of sugarcane are used for sugar production, 30 lakh MT for gur, 10 lakh MT for chewing purposes. Globally, it occupies less than 2% of the total cropped area, producing 1350 million MT of cane (FAO, 2004). DNA isolation, qualification and quantification are the prerequisite for DNA fingerprinting and genetic diversity study of varieties based on molecular markers. The genomic DNA is the base material for molecular studies. DNA genetic markers form the basis of current strategies for genome analysis, gene mapping and germplasm identification. However, DNA markers seem to be best candidates for efficient evaluation and selection of plant material. Estimation of genetic variation increasingly are being based upon information at the DNA level by various molecular markers such as, Randomly amplified polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Restriction Fragment Length polymorphism (RFLP), Simple Sequence Repeat (SSR) (Hossain et al., 2012; Sajib et al., 2012). Among them, RAPD is a PCR based technique for identifying genetic variation.