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Background  Hill rices ( Oryza sativa  L.) are direct seeded rices grown on hill slopes of different gradients. These landraces have evolved under rainfed and harsh environmental conditions and may possess genes governing adaptation traits such as tolerance to cold and moisture stress. In this study, 64 hill rice landraces were collected from the state of Arunachal Pradesh of North-Eastern region of India, and assessed by agro-morphological variability and microsatellite markers polymorphism. Our aim was to use phenotypic and genetic diversity data to understand the basis of farmers’ classification of hill rice landraces into two groups:  umte  and  tening . Another goal was to understand the genetic differentiation of hill rices into  Indica  or  japonica  subspecies.    Results  According to farmers’ classification, hill rices were categorized into two groups:  umte  (large-grained, late maturing) and  tening  (small-grained, early maturing). We did not find significant difference in days to 50 % flowering between the groups. Principal component analysis revealed that two groups can be distinguished on the basis of kernel length-to-width ration (KLW), kernel length (KL), grain length (GrL), grain length-to-width ration (GrLW) and plant height (Ht). Stepwise canonical discriminant analysis identified KL and Ht as the main discriminatory characters between the cultivar groups. Genetic diversity analysis with 35 SSR markers revealed considerable genetic diversity in the hill rice germplasm (gene diversity: 0.66; polymorphism information content: 0.62). Pair-wise allelic difference between  umte  and  tening  groups was not statistically significant. The model-based population structure analysis showed that the hill rices were clustered into two broad groups corresponding to  Indica  and  Japonica . The geographic distribution and cultivars grouping of hill rices were not congruent in genetic clusters. Both distance- and model-based approaches indicated that the hill rices were predominantly  japonica  or admixture among the groups within the subspecies. These findings were further supported by combined analysis hill rices with 150 reference rice accessions representing major genetic groups of rice.    Conclusion  This study collected a valuable set of hill rice germplasm for rice breeding and for evolutionary studies. It also generated a new set of information on genetic and phenotypic diversity of hill rice landraces in North-Eastern region of India. The collected hill rices were mostly  japonica  or admixture among the subpopulations of  Indica  or  Japonica.  The findings are useful for utilization and conservation of hill rice germplasm.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-016-0414-1) contains supplementary material, which is available to authorized users.

Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India