Implications: levels of polymorphism

One consequence of the difference in divergence between introns and exons is that PCR primers designed to amplify orthologous sequences should target exon, not intron sequence. On the other hand, where primers are designed to identify polymorphism within a species, the amplified region should include intron(s).

An example is provided by Wu et al. (2006), who developed primers flanking exons to amplify from various Solanaceae species (tomato, potato, eggplant and others) as well as from coffee and tobacco. The figure below demonstrates how different sets of primers (denoted by arrows) can be developed to flank either exons or introns.