Schematic diagram of the LID-insertion PCR assay. The diagram displays the LI-insertion dimorphism assay. The L1 element is in dark green, with the flanking unique sequence regions in yellow. The 5′- and 3′-flanking unique sequence primers are in red stripe and black, respectively. The internal Ta subfamily specific primer is shown in light green. The PCR amplicons generated from the L1-occupied and empty alleles are shown as green and red lines. In the assay, two PCR reactions are utilized to genotype each L1 insertion. In the first PCR reaction, 5′- and 3′-flanking unique sequence oligonucleotide primers are used to assay individual loci for empty alleles that do not contain Ta L1 elements. In the second PCR reaction, the 3′-flanking unique sequence oligonucleotide is used for the PCR, along with Ta L1 element subfamily specific primer ACA. With this approach, the size of the PCR-based amplicons generated from L1-occupied alleles is minimized and individual loci are tested for L1-occupied sites. The expected results of the PCR reactions are shown for the three potential genotypes at the bottom of the figure.