Open Access Highly Accessed Research article

Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India

Basabdatta Das1, Samik Sengupta2, Swarup Kumar Parida4, Bipasha Roy1, Mrityunjay Ghosh3, Manoj Prasad4 and Tapas Kumar Ghose1*

Author Affiliations

1 Division of Plant Biology, Bose Institute, Main Campus, 93/1 A.P.C. Road, Kolkata, West Bengal, 700009, India

2 Department of Horticulture, Institute of Agricultural Science, University of Calcutta, 35, Balligunge Circular Road, Kolkata, West Bengal, 700029, India

3 Department of Agronomy, Bidhan Chandra Krishi Viswavidyala Mohanpur, District – Nadia – 741252, Kolkata, West Bengal, India

4 National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India

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BMC Genetics 2013, 14:71  doi:10.1186/1471-2156-14-71

Published: 15 August 2013



Adaptations to different habitats across the globe and consequent genetic variation within rice have resulted in more than 120,000 diverse accessions including landraces, which are vital genetic resources for agronomic and quality traits. In India the rice landraces of the states West Bengal, Assam, Mizoram, Manipur and Nagaland are worthy candidates for genetic assessment. Keeping the above in view, the present study was conducted with the aim to (i) calculate the genetic distances among the accessions of 83 landraces collected from these states along with 8 check accessions (total 91 accessions) using 23 previously mapped SSR markers and (ii) examine the population structure among the accessions using model-based clustering approach.


Among the 91 accessions, 182 alleles were identified which included 51 rare and 27 null alleles. The average PIC value was 0.7467/marker. The non-aromatic landraces from West Bengal was most diverse with 154 alleles and an average PIC value of 0.8005/marker, followed by the aromatic landraces from West Bengal with 118 alleles and an average PIC value of 0.6524/marker, while the landraces from North East ranked third with 113 alleles and an average PIC value of 0.5745/marker. In the dendrogram distinct clusters consisting of predominantly aromatic landraces and predominantly North East Indian landraces were observed. The non-aromatic landraces from West Bengal were interspersed within these two clusters. The accessions were moderately structured, showing four sub-populations (A-D) with an Fst value of 0.398, 0.364, 0.206 and 0.281, respectively. The assigned clustering of accessions was well in agreement in both distance-based and model-based approaches.


Each of the accessions could be identified unequivocally by the SSR profiles. Genetically the non aromatic landraces from West Bengal were most diverse followed by the aromatic landraces from the same state. The North Eastern accessions ranked third. Further, grouping of accessions based on their agronomic traits may serve as a resource for future studies, leading to the improvement of rice. Moreover in-situ preservation of the landraces is also a means of protection of biodiversity and cultural heritage.

Oryza sativa; Landrace; Genetic diversity; SSR polymorphism; Population structure