Rice (Oryza sativa L.) is a major ingredient in cuisines world over, in the form of breakfast cereals, staple carbohydrate, snacks, alcoholic beverage and desserts. In addition to the two major subspecies, japonica and indica,  several other minor rice types have been identified with genetic markers [2, 3] which include the upland drought-tolerant Aus germplasms of India and Bangladesh, the deep-water Ashinas of Bangladesh, and the aromatic Basmati rice of India. As a consequence of adaptations to different habitats, extensive genotypic and phenotypic diversity exists within O. sativa, resulting in about 120,000 different accessions . These accessions range from traditional rice landraces preserved by indigenous farmers to the commercially bred cultivars developed during the green revolution. According to Harlan  landraces are “balanced populations in equilibrium with both the environment and pathogens, and are genetically dynamic”. They are local varieties of a domesticated plant species which were adapted to the natural and cultural environment in which they live. Each landrace has particular properties or characteristics; early maturity, adaptation to particular soil types, resistance or tolerance to biotic and abiotic stresses, and in the expected end usage of the grains. India is home to many such landraces and the ones from the state of West Bengal and North Eastern States of the country are especially diverse morphologically and genetically, and are worthy candidates for detailed examination. This study estimates a broad overview of Simple Sequence Repeat (SSR) based genetic diversity present in 83 different rice landrace selected from the wide array available in the states of West Bengal, Assam, Nagaland, Mizoram and Manipur using 23 SSR markers.
The topography of the state of West Bengal and the seven North Eastern States of India namely, Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is one of nature’s marvels which has brought in proximity the snow capped peaks of the Himalayas, the ecological hot spots of the North Eastern foothills, the Brahmaputra valley, the fertile Gangetic plain, and the estuarine regions of the Sunderban delta. High rainfall, humidity, varied topography and altitude, heavy natural selection pressures of diseases and pests, introductions over time and space from adjoining countries, introgression from the wild and weedy relatives, tribal preferences and environmental stresses have made the region rich both in floristic and crop diversities .
Molecular markers, especially DNA-based markers, have been used extensively for the study of genetic diversity, unambiguous identification of germplasm and their protection under the trade related intellectual property rights (TRIPS) of the World Trade Organization (WTO). Mackill  classified 134 japonica rice cultivars (both traditional and modern) using RAPD and was successful in separating the temperate and tropical japonica genotypes. Glaszmann  quantified the genetic diversity of 289 rice cultivars from various parts of Northeast India at 14 isozyme loci and was able to segregate the cultivars into the varietal groups I to VI. The gene diversity index  for that study was 0.341 for Northeast Indian rice which was close to that calculated for all Asian rice (0.346), and thus very high considering the small size of the area under survey. SSR or Simple Sequence Length Polymorphism (SSLP) markers have been used for evaluating rice genetic diversity by a number of groups [10–14] for estimating variation between the indica and japonica subspecies  and classifying Oryza sativa L. genotypes . Blair et al.,  differentiated indica and japonica rice genotypes using Inter Simple Sequence Repeat (ISSR) polymorphism data. ISSR polymorphism has also been used for genetic diversity and phylogenetic analysis in 42 genotypes including 17 wild Oryza species . ISSR and SSR markers have been used to study genetic diversity of Oryza nivara Sharma et Shastry, genotypes collected from different geographical regions . Herrera et al.  used 48 simple-sequence-repeat (SSR) markers to assess the genetic diversity of 11 Venezuelan rice cultivars released by the National Rice Breeding Program between 1978 and 2007 and detected 203 alleles. Pervaiz et al.,  used 35 SSR markers to detect genetic diversity in 75 rice landraces and identified 142 alleles. The polymorphism information content (PIC) ranged from 0.124 to 0.836, with an average of 0.569. Maytinee et al.,  used InDel (Insertion/Deletion), ISSR and SSR markers to detect genetic diversity among 126 Thai rice accessions. Behera et al.,  used 36 microsatellite markers to assess genetic diversity in a set of 33 medicinal rice genotypes and detected 166 polymorphic loci. The PIC values ranged between 0.24 and 0.956 with an average of 0.811 per locus. However a thorough SSR based genetic diversity analysis, of the landraces of West Bengal and North Eastern States is yet to be undertaken.
Previous workers like Ge et al.,  have reported the linkage of SSR loci on rice chromosome 2 with cooked kernel expansion and the same for chromosome 3 with width expansion of rice kernels. Quantitative Trait Loci (QTL) mapping of rice by Bai et al.,  have indicated the linkage of rice grain shape (grain length/ grain breadth ratio) to SSR loci RM112 and RM530 on chromosome 2. Ahmadi and Fotokian  have indicated the linkage of markers RM251 and RM282 on rice chromosome 3 to potassium ion concertration. Lin et al.,  have shown linkage of RM112 and RM530 on chromosome 2 to leaf rolling in rice plants due to water stress. QTL mapping of rice indicated the linkage of rice grain and kernel length, breadth, length/breadth ratio kernel length after cooking and aroma to 18 different SSR markers [28, 29]. The set of markers used in this study to assess genetic diversity included 18 markers from the references above along with 5 more (a total of 23 markers) with linkage to Sheath blight and Blast resistance  HSP 80 gene  and Beta amylase gene. Only the most popular landraces that are regularly cultivated by small farming communities were chosen for this study. Each of the landraces had some special characteristic like aroma, disease resistance, yield etc for which they have been cultivated by farmers down the ages. Keeping the above in view, the present study was conducted with the aim to (i) calculate the genetic distances among 91 rice germplasm using 23 mapped SSR markers; and (ii) examine the population structure among the accessions using model-based clustering approach.