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Journal: Vegetos- An International Journal of Plant Research

Article DOI :10.5958/2229-4473.2017.00084.2
Year :2017, Volume : 30, Issue :special
First page : (284) Last page : (292)
Print ISSN : 0970-4078. Online ISSN : 2229-4473.


Genetic diversity analysis using microsatellite based simple sequence repeats (SSR) markers in Basmati Indica Rice (Oryza sativa L.)

Chandra Harish*, Yadava Yashwant K.1, Bishnoi Payal, Kumar Pushpendra

Department of Agriculture Biotechnology, Sardar Vallabhbhai Patel University of Agriculture & Technology, Meerut, India
1Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India

*Corresponding author: Harish Chandra, Department of Agriculture Biotechnology, S V P University of Agriculture & Technology, Meerut, India, Email:

The microsatellite (SSR) markers were used to determine the allelic diversity and relationship among 30 genotypes of Basmati rice. Genetic polymorphism among 30 genotypes of Basmati rice was assessed using 20 co-dominant microsatellite i.e. Simple Sequence repeats (SSR) markers. A total of 50 alleles were found for the 20 SSR loci with an average of 2.5 per locus, reveal that all the tested primers showed different level of polymorphism among the genotypes indicating the robust nature of SSR markers. Among all these microsatellite primers, RM 107 produced highest number of alleles (5 alleles) followed by RM 127, RM131, RM154 (four alleles), RM11, RM85, RM128 (three alleles), RM5, RM17, RM30, RM38, RM55, RM84, RM130, RM156, RM335 RM338, RM341 (two alleles), and lowest number (single) of alleles were observed in RM18 and RM273. Polymorphic information content (PIC value) ranged from 0.556 (RM273) to 0.995 (RM 273). Clustering analysis based on UPGMA grouped these genotypes into 3 main clusters I, II and III comprised of 9 (Pusa Basmati 1, CSR 30, Vallabh Basmati 22, Bindli, Annada, Type 3, Sarbati, Jeerakasala, and Kalanamak), 7 (Basmati 386, Vallabh Basmati 21, Centuri Patna, PusaSungandha 2, PusaSungandha 3 MAUB-13 and Super Basmati), 14 (Taraori Basmati, Pusa Sungandha 4, Nagina-22,(N-22), Haryana Basmati, Ranvir Basmati., Pant Sugandha 15, Punjab Basmati 2, Pusa 1460, Pant Sugandha 17, Tilak-Chandan, RR-564, Basmati 370, Pusa Sungandha 5 and MAUB- 57) genotypes respectively and was found to be distinct from other clusters in dendrogram, indicating that it will very useful for diversity analysis and breeding programmes.