Journal of
Plant Breeding and Crop Science

  • Abbreviation: J. Plant Breed. Crop Sci.
  • Language: English
  • ISSN: 2006-9758
  • DOI: 10.5897/JPBCS
  • Start Year: 2009
  • Published Articles: 409

Full Length Research Paper

DNA fingerprinting and estimation of genetic diversity among hybrid rice parental lines (Oryza sativa L.) using simple sequence repeats (SSR) markers

Nirmala Rajendran1,2*, Lipi Mukherjee1,3, K. Kamalnath Reddy1 and H. E. Shashidhar1,4
  1Barwale Foundation, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad, A.P., India. 2Directorate General of Agriculture and Livestock Research, Ministry of Agriculture, Muscat, Sultanate of Oman. 3Biocon Pharmaceuticals, Bangalore, India. 4Department of Biotechnology, University of Agriculture, GKVK, Bangalore, India.
Email: [email protected]

  •  Accepted: 24 September 2012
  •  Published: 31 December 2012



Molecular fingerprinting and genetic distance analysis of twelve commercial hybrid rice parental lines were carried out using simple sequence repeats (SSR) markers. Out of hundred SSR markers screened, sixty two were found to be polymorphic. A total of 203 alleles were recorded as 0 to 1 data set (presence-1 and absence-0) with an average of 3.2 alleles per loci. Most of the primer sets generated fingerprint markers for rice lines used in this study which would be useful in their hybrid detection with an example. Commercial rice hybrid KRH-2 can be detected using its male parent KMR-3 specific markers RM297, RM442, RM541, RM584 and RM107 and female parent IR58025A specific markers RM529, RM489, RM589, RM533 and RM182 identified in this study. NTSYS cluster analysis of genotypic data set distinguished maintainer and restorer groups into two different clusters with the mean genetic distance value of about 22%. The results indicated the low level of genetic diversity exists among the commercial hybrid rice parental lines, suggesting the need to broaden the genetic base in order to maximize heterosis in hybrid rice breeding program.


Key words: Cultivar identification, genetic diversity, hybrid rice, simple sequence repeats (SSR) markers.