I am trying to find the genes responsible for trait variation in a yeast population. The population was produced by several generations of interbreeding starting with the F2 descendants of a cross between four inbred lines.
Strain A and Strain B were bred to produce Population 1 (F1 generation). Strain C and Strain D were bred to produce Population 2 (F1 generation). Individuals from Population 1 were bred with individuals from Population 2 to produce Population 3 (F2 generation), which contains genetic contributions from all four founder strains. Population 3 was interbred to produce Population 4, which was then itself interbred to produce Population 5, and so on for several generations.
This is similar to the population type "Heterogeneous Stock", or an Advanced Intercross Line with four founder strains.
We have enough density of markers (~100,000), that we can perform a GWAS rather than QTL.
I am trying to find an analysis program that will take the population structure (potential relatedness between individuals) into account. I understand the way to do this is with a linear mixed model.
All the programs that I have found so far (e.g. QTL-Rel, FaST-LMM) seem to expect that there will be only two alleles at each locus. We have four founder strains, so four different alleles per locus is a possibility.
Does anybody know of a program which will allow me to perform GWAS/QTL analysis with compensation for population structure and the possibility of more than two alleles per locus?