Although the RI approach requires less initial work than the F2 approach because sets of RI lines are commercially available, the method is limited by the number of available RI lines. Thus, for a given progenitor cross, typically 20 to 40 RI lines exist, meaning that an investigator has a sample of 20 to 40 different genotypes at a particular locus to assess for the trait of interest. In contrast, the F2 approach requires substantially more work, because both the phenotype and genotype must be determined for each animal as each F2 animal has a different genotype. The benefit of this approach is that the resulting sample size available for QTL studies is much larger than with RI strains, often in the hundreds or thousands. This large sample size allows for more powerful QTL mapping analyses.
