B. Chaudhary et al / Research Journal of Biology (2012), Vol. 02, Issue 04, pp. 117-125 ISSN 2049-1727 Available online at www.scientific-journals.co.uk 117 Research Paper Genetic Characterization of Selected Medicinal Dendrobium (Orchidaceae) Species Using Molecular Markers Pritam Chattopadhyay 1 , Nirmalya Banerjee 1 and Bhupendra Chaudhary 1,2 * 1 Department of Botany, Visva-Bharati, Santiniketan 731 235 WB, India 2 School of Biotechnology, Gautam Budhha University, Greater Noida 201 308 UP, India *E-Mail: bhupendrach@gmail.com Abstract Molecular characterization of orchids is imperative for the prevention of elite germplasm erosion in breeding programs mainly during development of synthetic hybrids. The Indian Dendrobium species comprise the third largest genus in the family Orchidaceae and have their remarkable value in horticultural, agricultural and medicinal realms. The present study is focused on the latter characterizing five selected medicinal Dendrobium species from North-eastern India, using Random Amplified Length Polymorphism (RAPD) as well as Simple Sequence Repeat (SSR) markers. The RAPD genotypes were determined using the Polymerase Chain Reaction (PCR) followed by electrophoresis in agarose gel and the genetic relationship among studied species was estimated using Nei’s genetic distance. Five successful random primer-pairs generated a total of 124 RAPD fragments containing 25 species-specific fragments. On an average each primer-pair produced 28 amplified DNA fragments and the amplicon size varied between 250 to 800 base pairs (bp). Using multiple nucleotide repeat loci, 30 individuals from different species were studied using as biological replicates. The size of amplified DNA varied between 152-230 bp. A total of 27 highly reproducible DNA fragments showed polymorphism with average frequency of 5.4 allele per locus. The number of SSR alleles detected per locus ranged from 4 to 7. The highest number of 7 alleles were scored with DO-03 primer and observed to be the most polymorphic marker (100%). The expected heterozygosity varied between 0.0788 (with primer set DO-12) to 0.7209 (with primer set DO-07) with an average expected heterozygosity of 2.805. The cluster analysis based on both type of molecular markers grouped all species into two different clusters, however, genetic relationships at inter-specific level comparable to their morphological sections could be established with SSR marker. Thus the preliminary study using UPGMA method showed that SSR markers are superior in the detection of polymorphism among Dendrobium species segregating them into their respective pre-defined morphological sections, than RAPD markers. Further studies of other species using more microsatellite loci with larger sample sizes can reveal the intricate genetic relationships of Indian orchids. Keywords: Dendrobium, Phylogeny, RAPD, SSR, Molecular Markers 1. Introduction Orchids belong to the largest and most diverse group among the angiosperms. The genus Dendrobium is the third largest in the family Orchidaceae comprising of about 1184 species worldwide (Leitch et al, 2009). Till date, more than 103 species of the genus Dendrobium have been reported from India mainly from North-East region (Singh et al, 2001) (Figure 1). The Dendrobium species are broadly categorised into horticultural, agricultural, medicinal or dual purpose species depending upon their utility per se, however, the latter got limited exploration so far. The medicinally important species have specific qualities of tonic, disease resistance and anti-depressant.