Variety identification and genetic diversity analysis in rice (Oryza sativa L.) using STMS markers

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Year 2015 Vol 4 Issue 3
Document Type : Original article
¹Anjana Bora ² Partha Ray Choudhury ³ Veena Pande ⁴Asit B. Mandal
¹Directorate of Seed Research, Indian Council of Agricultural Research, Mau-275101, Uttar Pradesh, India 2Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital- 263136, Uttarakhand, India
²Directorate of Seed Research, Indian Council of Agricultural Research, Mau-275101, Uttar Pradesh, India
³Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital- 263136, Uttarakhand, India
⁴Directorate of Seed Research, Indian Council of Agricultural Research, Mau-275101, Uttar Pradesh, India
Abstract
In the present study, 14 rice specific sequence tagged microsatellite site markers (STMS) were used to develop fingerprints and to determine the genetic relatedness among 48 rice genotypes/cultivars.

Ten of the 14 SSR primer pairs were found to be polymorphic, generating a total of 39 distinct reproducible alleles with an average of 2.79 alleles per primer pair and 22 (56.41%) of the 39 bands amplified emerged as polymorphic.
The number of alleles per primer ranged from one to six. The polymorphic information content (PIC) value ranged from 0.03 to 0.7 with an average of 0.35. Cluster analysis based on Jaccard’s similarity coefficient using unweighted pair group methods for arithmetic mean (UPGMA) grouped the 48 rice cultivars into five major clusters with an average similarity index of 0.87. A diagrammatic representation of DNA fingerprints of the rice cultivars based on 10 informative SSR markers was developed for ready reference, which are expected to be key in varietal identification as well as provide IPR to halt biopiracy.
Keywords
Oryza sativa rice DNA fingerprinting genetic diversity STMS
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