DGGE-RAPD analysis as a useful tool for cultivar identification

Abstract

Denaturing gradient gel electrophoresis- random amplified polymorphic DNA (DGGE-RAPD) was used
to overcome the main drawbacks of RAPD (i.e., the low levels of reproducibility and polymorphism). As
a model, six barley cultivars of known origin were tested for RAPD markers using DGGE methodology
with 29 arbitrary primers. Among a total of 418 bands observed, as high as 99 were polymorphic.
Comparison between agarose-RAPD and DGGE-RAPD revealed that the latter was highly reproducible
and gave higher level of polymorphism and consequently more markers. The relationships among
barley cultivars derived from this study based on DGGE- RAPD are consistent with the known lineage
of these cultivars. In conclusion, we recommend the use of DGGE-RAPD as an alternative tool to the
more costly DNA-based analysis in cultivar identification in laboratories with limited funds.