NAVIGATING THE ‘SMÖRGÅSBORD’ OF DNA MARKER METHODS FOR IMPROVEMENT OF HORTICULTURAL CROPS

About 20 years ago, attempts to discriminate among horticultural crop cultivars were, if not always successful, at least relatively straightforward: you either relied exclusively on morphological features or on a more fashionable combination of morphology and isoenzyme analysis.
At present, we instead find ourselves invited to a ’smõrgåsbord’ of delectable DNA-based marker methods.
This almost unlimited display of more or less sophisticated techniques brings its own problem, namely that of having to make choices.
The requirements for equipment, expertise, time and funding vary considerably between methods, and the bewildered plant breeder frequently finds it difficult to identify the best alternative for the ever-increasing list of achievements that we expect of our DNA-based marker methods.
Identification and discrimination is only one of these tasks; now we also demand methods for gene tagging and genetic linkage mapping, for analyses of character inheritance, for analyzing genetic relatedness, and for estimating variation in genetic resource collections.
In the last decade, Southern blotting and hybridization-based methods (RFLP and minisatellite DNA analysis) have given way to PCR-based methods, employing either arbitrary primers (e.g.
RAPD, AFLP, ISSR, RAMS, SAMPL, SRAP) or primers designed from sequencing information (e.g.
STMS, SCAR, MITES, ESTP, CAPS, RGHP, SNP). Several recent investigations have highlighted differences as well as similarities between the results obtained with some of these DNA-based markers.
For maximum cost-effectiveness, it is essential to have realistic expectancies, based on up-to-date information about the strengths and weaknesses of the different methods.