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EMERGENT LIFE SCIENCES RESEARCH - Online First, June 2021

Pages: 113-123

Date of Publication: 27-Sep-2022


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Molecular diversity analysis of rice (Oryza sativa L.) genotypes using RAPD and SSR marker

Author: Vipul G. Baldaniya, Ajay V. Narwade, Pathik B. Patel, Nilima Karmakar

Category: Research Article

Abstract:

Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) molecular markers were used for detecting the genetic variability of 20 rice genotypes using 79 SSRs and 30 RAPD primers. Among primers used, a set of 16 SSR and 14 RAPD markers showed polymorphism, and banding patterns were scored as 1 (present) or 0 (absent) in the datasheet which was further analyzed by using Jaccard’s similarity coefficient and SAHN clustering. The number of alleles, PIC value, and heterozygosity for individual 16 SSR and 14 RAPD markers were used to assess the degree of polymorphism among the rice genotypes. A total of 36 polymorphic loci were found in 16 polymorphic SSR markers and 77 polymorphic loci were observed in 14 polymorphic RAPD markers. The number of alleles produced per locus ranged from 2 (RM447, RM21, RM171, RM237, RM25, RM283, RM510, RM259, RM334, RM433, RM489, and RM212) to 3 (RM263, RM152, RM413, and RM3331) in 16 SSRs markers and 3 (OPR-05) to 9 (OPR-02 and OPC-06) in 14 RAPD. In SSRs, the PIC value diverse from 0.30 (RM447) to 0.58 (RM152) with an average of 0.38 per locus and an average value of heterozygosity (0.49). RAPD analysis showed an average PIC value of 0.78. Based on the information generated, the 20 rice genotypes were grouped into two main clusters in both the analysis of the marker. In SSR markers analysis, cluster I comprised 4 genotypes and cluster II comprised 16 genotypes and in RAPD cluster I was shown 2 genotypes and cluster II show 18 genotypes.

Keywords: molecular diversity, polymorphism, RAPD, rice, SSR

DOI URL: https://doi.org/10.31783/elsr.2022.82113123