Analysis of diversity in rice (Oryza sativa L.) using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers

Abstract

Molecular markers are useful tool for assessing genetic variations and resolving genotype identity. In the current study, genetic diversity among 20 rice genotypes was assessed using the random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR). In RAPD analysis, 20 primers generated a total of 116 bands of which 114 were polymorphic. The number of amplification products produced by each primer varied from 4 to 7 with an average of 5.8 bands per primer. Twenty (20) SSR primers generated a total of 65 alleles with an average 3.2 alleles per primer. Genetic diversity of 20 genotypes estimated by polymorphic information content (PIC) value ranged from 0.62 to 0.97 in SSR and 0.33 to 0.88 with RAPD analysis. The cluster dendrogram by SSR revealed two major clusters. Rajeshwari was the only genotype in cluster I. The cluster II further divided into two sub clusters IIA and IIB. II A consisted of 17 genotypes while II B consisted of two genotypes (Apo and Kalakeni). The information generated from this study can be used to maximize selection of diverse parents and broaden the germplasm base for the future rice breeding programs.

Keywords: Genetic diversity, molecular markers, rice, markers based estimation of genetic diversity in rice.

African Journal of Biotechnology Vol. 12(35), pp. 5404-5412