Characteristics of genetic markers: Genomic abundance
The number of markers that can be generated is determined mainly by the frequency at which the sites of interest occur within the genome. RFLPs and AFLPs generate abundant markers due to the large number of restriction enzymes available and the frequent occurrence of their recognition sites within genomes. Within eukaryotic genomes, microsatellites have also been found to occur frequently. RAPD markers are even more abundant because numerous random sequences can be used for primer construction. In contrast, the number of allozyme markers is restricted due to the limited number (about 30) of enzyme detection systems available for analysis. To investigate specific genomic regions by PCR sequencing, SSCP, CAPS or SCAR, sequence data of the sites of interest (structural genes mainly) are required for primer construction. Although, in principle, many sites of interest may occur within genomes, the proportion of the genome covered by PCR sequencing, SSCP, CAPS and SCAR in studies reported to date is limited. However, this is expected to change due to the wealth of sequence information that is becoming increasingly available for different crops. Genomic abundance is essential to studies where a large fraction of the genome needs to be covered, e.g. for the development of high-density linkage maps in gene mapping studies. If, in addition to genomic abundance, genome coverage is also sought, caution should be taken in marker selection. While some markers are known to be scattered quite evenly across the genomes, others, such as some AFLP markers, sometimes cluster in certain genomic regions. For example, clustering of AFLP markers has been reported in centromeric regions of Arabidopsis thaliana.