Evaluation of genetic diversity in rice (Oryza sativa L. ssp. Indica) accessions using SSR marker

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Research Articles | Published:

Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Pub Email: contact@vegetosindia.org
Doi: 10.1007/s42535-022-00378-3
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Keywords: SSR, PIC, Structure, AMOVA


Genetic relationship among 25 rice accessions have been evaluated using 21 SSR markers. A total of 87 alleles were produced by 21 polymorphic SSRs with an average of 4 alleles per SSRs. The SSR RM514 produced maximum number of alleles (9) followed by RM125 (7) and RM271 and RM447 (6). The PIC value varied from 0.07 (RM507) to 0.83 (RM514) with an average of 0.46. Jaccard’s dissimilarity coefficient ranged 0.10–0.89 with an average of 0.65. The highest genetic dissimilarity was observed between Dub Raj & IPB—1 (0.89), and Pant—12 & IPB—1 (0.89) and minimum dissimilarity observed between Kalanamak and CSR—10 (0.10). By evaluating data from clustering, dissimilarity and admixture nature the most diverse accessions were IPB—1, Pant—12, Dub Raj, Ram Raj, NDR 2064 and Sobhini. The accessions IPB—1, NDR—8002, BPT—5204, NDR—2065, PB—1, PUSA Basmati, and NDR—359 was found highly diverse as these accessions showed highest dissimilarity with respect to rest of the accessions. The NJ clustering pattern revealed 3 clusters and supported by 3 subpopulations determined from STRUCTURE analysis. The analysis of molecular variance (AMOVA) showed that 85% of allelic diversity was found within the population.

SSR, PIC, Structure, AMOVA


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The authors would like to thank the Director, CSIR-National Botanical Research Institute, Lucknow for the support and facilities to conduct the experiment. The funding from Department of Science and Technology (DST), New Delhi, India is also acknowledged.

Author Information

Naaz Sharfa
Plant Genetic Resources and Improvement Division, CSIR, National Botanical Research Institute, Lucknow, India