Haplotype probabilities in advanced intercross populations

Abstract

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.

Figure 1

Frequency of a two-locus haplotype being recombinant, as a function of the recombination fraction at meiosis, for the diversity outcross population at s = 5 (solid curves), heterogeneous stock at s = 10 (dashed curves), and balanced AIL at s = 12 (dotted curves), for the autosome (black), male X (blue), and female X (red). The green dashed curve is the recombinant frequency for HS at s = 10 assumed in Mott et al. (2000).