Haplotype probabilities in advanced intercross populations

G3 (Bethesda). 2012 Feb;2(2):199-202. doi: 10.1534/g3.111.001818. Epub 2012 Feb 1.


Advanced intercross populations, in which multiple inbred strains are mated at random for many generations, have the advantage of greater precision of genetic mapping because of the accumulation of recombination events across the multiple generations. Related designs include heterogeneous stock and the diversity outcross population. In this article, I derive the two-locus haplotype probabilities on the autosome and X chromosome with these designs. These haplotype probabilities provide the key quantities for developing hidden Markov models for the treatment of missing genotype information. I further derive the map expansion in these populations, which is the frequency of recombination breakpoints on a random chromosome.

Keywords: Collaborative Cross; Mouse Genetic Resource; advanced intercross lines; diversity outcross; heterogeneous stock; map expansion.