Electronic Journal of Plant Breeding, 1(4): 512516 (July 2010) 512 Research Article Molecular characterization of rice land races using SSR markers A.Prabakaran, K.Paramasivam, T.Rajesh, D.Rajarajan Abstract Genetic improvement mainly depends on the extent of genetic variability present in the population. The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. The objective of this study was to evaluate the genetic divergence of 12 rice land races using five SSR markers. A total of 11 alleles were detected in 12 land races and the number of alleles per locus ranged from 2 to 3 with an average of 2.2 per locus. Among the primers used RM 481 indentified more number of alleles and average PIC was 0.43. The dendrogram based on SSR marker analysis grouped the 12 rice accession into six clusters, where cluster VI was the largest with three accessions. The similarity coefficient through Jaccard’s revealed that Anna samba and Chettivirippu were ascertained to be the genetically diverse from the other land races. The study also highlighted use of more number of markers for efficient characterizing the land races used for the present study. Key words: Genetic divergence, Rice land races, SSR markers, Dendrogram Introduction: Rice (  L.) is the principal staple food for more than half of the world’s population. Landraces of rice played a very important role in the local food security and sustainable development of agriculture, in addition to their significance as genetic resource for rice genetic improvement (Tang  ., 2002). Landraces provided “adaptability genes” for specific environmental conditions. Incorporation of adaptability genes from landraces only could ensure optimum grain yield for the region. According to Food and Agricultural Organization (FAO, 1997), about three quarters of original varieties of agricultural crops have already been lost from the farm fields between 1950 and 1995. Therefore, to maintain crop diversity, collection, characterization and conservation of traditional landraces are vital. Genetic diversity is a ubiquitous feature of all species in nature. Narrow genetic base in rice cultivars continues to limit the productivity of Department of Biotechnology, A.R.J College of Engineering and Technology, Mannargudi – 614001. Tamil Nadu. bioacter@gmail. com rice which has been cultivated for more than 9000 years. Genetic divergence among the genotypes plays an important role in the selection of parents having wider variability for different characters. Genetic diversity can be evaluated with morphological traits, seed proteins, isozymes and DNA markers. Molecular marker technology is the powerful tool for determining genetic variation in rice varieties (Xu and Wang, 1974). In constrast to morphological traits, molecular markers can reveal abundant difference among genotypes at the DNA level, providing a more direct, reliable and efficient tool for germplasm characterization, conservation, management. and untouched by environmental influence. Among various PCR based markers, SSR markers are more popular in rice because they are highly informative, mostly monolocus, codominant, easily analyzed and cost effective (Gracia  , 2004). SSR markers are class of repetitive DNA sequences usually 2.6 bp that are distributed through out whole genome and are flanked by highly conserved region. (Chambers and Avoy 2000). The objective of this present study was to