African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12191

Full Length Research Paper

Simple sequence repeat (SSR) marker-based DNA fingerprinting of some varieties of rice (Oryza sativa L.) released in Nigeria

Ishaq, M. N.
  • Ishaq, M. N.
  • National Cereals Research Institute Badeggi, P. M. B. 8 Bida, Niger State, Nigeria.
  • Google Scholar
Ehirim, B. O.
  • Ehirim, B. O.
  • National Cereals Research Institute Badeggi, P. M. B. 8 Bida, Niger State, Nigeria.
  • Google Scholar
Nwanyanwu, G. C.
  • Nwanyanwu, G. C.
  • National Cereals Research Institute Badeggi, P. M. B. 8 Bida, Niger State, Nigeria.
  • Google Scholar
Abubaka, R. I.
  • Abubaka, R. I.
  • National Cereals Research Institute Badeggi, P. M. B. 8 Bida, Niger State, Nigeria.
  • Google Scholar


  •  Received: 14 June 2018
  •  Accepted: 12 September 2018
  •  Published: 13 March 2019

Abstract

Over time, precise, specific and rapid identification of variety have been achieved via fingerprinting with molecular markers. In this research, 13 out of 45 screened simple sequence repeat (SSR) markers were employed to fingerprint 27 rice varieties (22 are commercially released while five are suspected duplicates from the hands of marketers with different names) in Nigeria. The SSR primer pairs (13) were polymorphic and were found to generate 81 allele distinct reproducible bands with an average of 6.233 bands per primer pair. Primer RM400 had the highest allelic frequency of 0.94 resulting from 20 alleles. The polymorphic information content (PIC) values of each primer pair ranged between 0.31 and 0.93 with an average of 0.54. The unweighted pair group method with arithmetic (UPGMA) cluster analysis helped to separate the 27 varieties into 13 major groups indicating wide range of diversity. A large number of the closely related varieties were identified by means of the fingerprinting on the basis of the polymorphic SSR primer pairs. The findings showed a broad genetic variation among the test varieties giving a first-hand insight on how related some of the commercially released varieties are and also disproving the duplicity suspected from the materials with marketers.

Key words:  Cultivar, DNA, fingerprinting, rice, simple sequence repeat (SSR) marker, variety verification.