Journal of Agricultural Science; Vol. 9, No. 6; 2017 ISSN 1916-9752 E-ISSN 1916-9760 Published by Canadian Center of Science and Education 239 Assessment of Genetic Diversity in Wild Rice of Eastern India Using SSR Markers Rosalin Swain 1 , Shibani Mohapatra 2 , Pritesh Roy 2 , D. Swain 2 , O. N. Singh 2 , J. Meher 2 , S. K. Dash 2 , G. J. N. Rao 2 & H. N. Subudhi 2 1 Department of Biotechnology, KIIT University, Bhubaneswar, India 2 Crop Improvement Division, National Rice Research Institute, Cuttack, India Correspondence: H. N. Subudhi, Crop Improvrment Division, National Rice Research Institute, Cuttack, India. E-mail: dr_hatanath_subudhi@yahoo.co.in Received: November 8, 2016 Accepted: January 17, 2017 Online Published: May 15, 2017 doi:10.5539/jas.v9n6p239 URL: https://doi.org/10.5539/jas.v9n6p239 Abstract Wild rice is an important reservoir of valuable and useful genes. O. rufipogon and O. nivara contain AA genome andare the progenitor of cultivated rice which makes them compatible with the cultivated rice for cross breeding to incorporate the genes for stress tolerance. SSR markers were used to assess the extent of diversity of 26 accessions of O. rufipogon and O. nivara collected from different districts of Orissa, West Bengal and Tripura. The Principal Co-ordinate Analysis (PCA) clearly indicates the clustering pattern and inter-relationships among different accessions. Mantel Z-testexhibitedacorrelation between cophenetic matrix and Jaccards’ similarity coefficient in 26 accessions and 4 CRRI released varieties using 54 STMS (SSR) markers which showed significant correlation (r = 0.8249) between them. O. nivara accessions and O. rufipogon accessions were grouped different clusters. O. nivara collected from Midnapore is placed in different cluster. It is concluded that the SSR markers used were found to be equally informative for the genetic diversity study between and among the accessions of two wild species such as O. rufipogon and O. nivara collected from different locations of Orissa, West Bengal & Tripura. Highlysignificant morphological variations were also observed among O. nivara and O. rufipogon accessions. Keywords: diversity, wildrice, morphology, SSR marker, Eastern India 1. Introduction Rice is the world’s most important cereal crop and is a primary source of food for more than half of the world’s population (Khush, 1977). More than 90% of the world’s rice is grown and consumed in Asia. Oryza sativa L. is a diploid species having 24 (2n = 24) chromosomes. It belongs to genus Oryza of family Poaceae. The genus Oryza includes 24 species of different genome (AA, BB, CC, DD, EE, FF, GG, HH) of which 22 are wild species (2n = 24, 48) and two species namely Oryza sativa and Oryza glaberrima are cultivated in Asia and Africa respectively. The Asian cultivated rice (Oryza sativa) originates in South and South-East Asia (Chang, 1985) and is grown world wide. Where as the African cultivated rice, Oryza glaberrima, is domesticated in West Africa. All the wild species played a significant role in rice breeding by contributing genes valuable to resistance for diseases, insect and pests and tolerant to abiotic stresses (Chang et al., 1975; Stich et al., 1989; Khush, 1977). A number of useful traits such as Cytoplasmic male sterility, resistant to Grassy stunt virus, Bacterial blight, Blast and Brown Plant blast hopper, have been introgressed from wild species into cultivated rice (Brar & Khush, 1997; Yuan, 1993). The wild species exhibit tremendous diversity in morphological traits. Besides these, it constitutes an exceptionally valuable genepool for rice improvement (Lu, 1996; Bellan et al., 1988; Zhong et al., 2000). Recently many diseases and pests resistant genes, high yielding genes and abiotic tolerant genes have been found in wild Oryza species (Khush et al., 1990; Jena & Khush, 1990; Brar et al., 1996). All the AA genome species are the most accessible genetic resources because transfer the alien gene to O. sativa can be achieved through sexual hybridization (Jena & Khush, 1990). The fuller exploitation of the wild rice species gene poolessentially relies on the better understanding of the genetic diversity and relationship of the rice production (Sharma, 1983) through assessment of genetic diversity and relationship of rice and its wild relatives. O. rufipogon and O. nivara are the closely related species of Asian cultivated rice and considered as the progenitor of cultivated rice (Okha, 1988; Khush, 1997). O. rufipogon is perennial, photoperiod sensitive, largely