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. 2015 Jan 12;3(1):apps.1400092. doi: 10.3732/apps.1400092

Fig. 6.

Fig. 6.

Developing molecular markers for fine mapping. Examples of indel (A), CAPS (B), and dCAPS (C) markers. Three hypothetical scenarios after sequencing the same genomic regions in A619 and B73. In (A) a deletion is present in B73 but not in A619. Designing primers flanking the deletion allows the detection of a size difference in PCR products. (B) In this scenario, an SNP (in bold, underlined) is present between the two inbred lines. The SNP creates a restriction enzyme site (boxed) in A619 (TCGA, TaqI). A size difference will be detectable upon digestion of the PCR product with TaqI. In (C) the SNP (in bold, underlined) does not create a restriction site, but can be used to develop a dCAPS marker. By using the italicized oligonucleotide carrying an artificially introduced mutation (in bold) as a forward primer for PCR, the PCR product will contain a restriction enzyme site (boxed) in B73 (GAATTC, EcoRI), but not in A619. A size difference will be detectable following a restriction enzyme digest of the PCR product.