African Journal of
Agricultural Research

  • Abbreviation: Afr. J. Agric. Res.
  • Language: English
  • ISSN: 1991-637X
  • DOI: 10.5897/AJAR
  • Start Year: 2006
  • Published Articles: 6578

Full Length Research Paper

Comparison of two PCR-based DNA markers with high resolution melt analysis for the detection of genetic variability in selected quality protein maize inbred lines

  Demissew Abakemal1*, Gregory Watson2, Shimelis Hussein3, Derera John3 and Twumasi-Afriyie4        
  1Ethiopian Institute of Agricultural Research, Ambo Plant Protection Research Center, P. O. Box 37, West Shoa, Ambo, Ethiopia. 2Department of Genetics, University of KwaZulu-Natal, Private Bag X01, Scottsxille 3209, Pietermaritzburg,  South Africa. 3African Centre for Crop Improvement, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg, South Africa. 4International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, P. O. Box 5689, ILRI Sholla Campus, Addis Ababa, Ethiopia.
Email: [email protected]

  •  Accepted: 25 September 2012
  •  Published: 30 November 2012



Molecular markers are fast, efficient and reliable in detecting distinct differences between genotypes at DNA level. In particular, polymerase chain reaction (PCR)-based markers are widely preferred for genotype characterization in diverse crop species, including maize. It is impossible, however, to obtain the entire information required in plant breeding and conservation programmes solely from a single marker system without integration with other technique(s). The current study was, therefore, initiated to compare results from random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers in combination with high resolution melt analysis for effectiveness in detecting genetic variability or similarity among selected QPM inbred lines. Eight fresh leaf samples (two per line) were collected from each line for DNA extraction. The genomic DNA extracts were subjected to polymerase chain reaction (PCR) and high resolution melt analyses which involved three RAPD primers and three SSR primer pairs using a Real-Time PCR System. The curves of the HRM analysis showed fairly similar melt patterns among the lines for both types of marker systems. Results obtained from the gel-electrophoresis and genetic distance measures for RAPD markers were also in agreement with the HRM analysis. In general, both marker systems in combination with HRM analyses were able to detect genetic variations within and between the inbred lines, thus justifying the potential use of HRM analysis and indicating the possibility of excluding the use of gel-electrophoresis at the early stage of screening of large number of samples of newly developed inbred lines in order to save time and resources.


Key words: Genetic variability, polymerase chain reaction, quality protein maize, random amplified polymorphic DNA, simple sequence repeats.