Estimation of Genetic Diversity in Rice (Oryza sativa L.) Genotypes using Simple Sequence Repeats  

Muhammad Jamil1 , Iqrar Ahmad Rana2 , Zulfiqar Ali1 , Faisal Saeed Awan2 , Zaigham Shahzad1 , Abdus Salam Khan1
1. Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture Faisalabad, Pakistan
2. Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
Author    Correspondence author
Molecular Plant Breeding, 2013, Vol. 4, No. 36   doi: 10.5376/mpb.2013.04.0036
Received: 04 Nov., 2013    Accepted: 20 Nov., 2013    Published: 22 Nov., 2013
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This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Jamil et al., Estimation of Genetic diversity in Rice (Oryza sativa L.) Genotypes using Simple Sequence Repeats, Molecular Plant Breeding, Vol.4, No. 36 285-291 (doi: 10.5376/mpb.2013.04.0036)


Simple Sequence Repeats (SSRs) are co-dominant DNA markers and have a wide range of applications in the field of genetics. In the present investigation, 24 rice genotypes, belonging to Pakistan and imported from IRRI, Taiwan were examined for the determination of genetic diversity using twenty four SSRs.  Our results showed that the primers used had polymorphism when applied to the tested genotypes. The distinguishing factor with respect to both locations were primers designed from chromosome 2,3,4,5,7 and 8.  A total of 76 loci were produced by twenty four SSRs among 24 rice genotypes with an average of 3.17 loci per genotype. All markers produced polymorphic fragments among most of the genotypes. A total of 995 alleles were detected with an average of 13.87 alleles per locus. Among all the primers, RM-1 produced highest number of bands, “120” followed by RM-154 who developed 108 bands, RM-124 produced 65 bands shown and lowest number of bands (8) produced by primer RM-489. The similarity matrix clearly revealed that most closely genotypes were SRS-62 and SRS-505, securing the similarity value of 0.9234. It mean that these genotypes are 92.34 % similar, likewise genotypes Bas-370 and Bas-Pak, Bas-370 and S.S.Shaheen had the score of 0.8966 and 0.8840 respectively. The most dissimilar genotypes are IRRI-12 and EF-1-2-51-2002, scoring the value of 0.5601; it means they are 56.15% dissimilar. Similarity coefficient ranged from 0.54 to 0.9234. The average genetic similarity index was calculated as 0.73. Dendrogram divided twenty four rice genotypes into four main clusters and each cluster was subdivided into two furthers groups. Among all the genotypes, IRRI-4 showed distinct behavior in dendrogram, proving it to be useful for breeding program.

Genetics diversity; Rice; SSRs; Polymorphism
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