Our analysis package will ultimately support the following experimental designs:

1) Phenotype homozygous RILs directly

This design is simple and only involves measuring the focal phenotype on one or more individuals from each genotyped RIL. In this case, all individuals scored are homozygous for nearly all loci (not typically the case for diploid organisms). Because the lines are inbred, this design carries with it the risk of mapping QTL for inbreeding depression in addition to QTL for the focal trait.

2) Phenotype RILs from matched crosses between the two populations

This design utilizes heterozygous individuals. These
individuals are created by crossing the set of RILs derived

from synthetic population A with the set of RILs derived from synthetic population B. These crosses are done both with females from set A crossed to males from set B and vice versa such that the effect of sex-linked QTL can be determined in both sexes. With this design, inbreeding depression should be less of an issue, as the crosses are done between the two synthetic populations which share only one founder in common. In addition, because three genotypes will be present at each locus (AA, Aa, aa) the degree of dominance at mapped QTL can be assessed via this design. However, one drawback is reduced power relative to using RILs directly.

3) Phenotype RILs from round-robin crosses within synthetic populations

In this design, RILs are crossed in a within-population round-robin design (RIL1 x RIL2, RIL2 x RIL3, ... RIL750 x RIL1). Once again, individuals are heterozygous, and inbreeding depression should not be a major issue, as on average each round-robin test individual is identical by descent (IBD) for only 1/8th of the genome. Like the above cross between synthetic populations, the degree of dominance at mapped QTL can be assessed though power is reduced relative to using RILs directly.

4) Phenotype the progeny from each RIL crossed to a standard strain

In this design, females of each RIL and males of a standard, inbred strain of Drosophila (RIL1 x STD, RIL2 x STD...RIL750 x STD) are crossed. The cross is performed in this direction (RIL females x standard strain males) such that the effect of X-linked QTL can be determined in both sexes. In this “backcross” type design all individuals are phenotyped as heterozygotes, although only two genotypes will be present at each locus (AA and Aa, or Aa and aa). An advantage of this approach is that the level of inbreeding depression is equivalent to that in a natural population, since a given fragment of a recombinant chromosome is always against the same region from an unrelated strain. In this panel genetic variation is reduced because every individual scored has a common chromosomal complement, however the background genetic variance (a contributor to the error variance) is also reduced. A particular concern with the approach is the selection of the “standard” strain that all the RILs are crossed to: Detection of fully recessive autosomal, or female-specific X-linked QTL is only possible if the standard strain harbors the recessive allele. Similarly, detection of partially recessive QTL will depend on the magnitude of the departure from straight additivity, and the allele harbored by the tester strain – some combinations will increase, and some will decrease power to detect the QTL relative to other designs.