Theoretical and Applied Genetics

, Volume 91, Issue 4, pp 582-588

First online:

Template mixing: a method of enhancing detection and interpretation of codominant RAPD markers

  • T. M. DavisAffiliated withPlant Biology Department, University of New Hampshire
  • , H. YuAffiliated withPlant Biology Department, University of New Hampshire
  • , K. M. HaigisAffiliated withPlant Biology Department, University of New Hampshire
  • , P. J. McGowanAffiliated withPlant Biology Department, University of New Hampshire

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Ten codominant RAPD markers, ranging in size from about 300 to about 1350 bp, were identified in mapping populations of chickpea (Cicer arietinum L.) and diploid strawberry (Fragaria vesca L.). A distinguishing feature of all ten markers, and perhaps of codominant RAPD markers in general, was the presence in heterozygous individuals of a non-parental, heteroduplex band migrating more slowly than either of the respective parental bands. This non-parental band could also be generated by mixing parental DNAs before PCR (template mixing). As a means of identifying primers likely to detect codominant RAPD markers, parental and mixed-template (parent-parent) PCR-product gel lanes were compared for 20 previously untested RAPD primers (10-base oligomers). Four primers that produced a total of five non-parental, heteroduplex bands in mixed-template reactions were selected, and then used to detect a total of five segregating, codominant markers and nine dominant markers in the respective F2 mapping population, a codominant marker frequency of 35.7%. When closely migrating fast and slow bands of codominant RAPDs were difficult to differentiate, parent-progeny template mixing was used to deliberately generate heteroduplex bands in fast- or slow-band F2 homozygotes, respectively, allowing confirmation of marker phenotype.

Key words

RAPD markers Codominant Template mixing Heteroduplex DNA Genome mapping