Haplotype probabilities in advanced intercross populations.

G3 (Bethesda). 2012 Feb; 2(2): 199-202
Broman KW

Advanced intercross populations, in that multiple inbred strains are mated during pointless for many generations, have the advantage of larger precision of genetic mapping because of the accumulation of recombination events across the multiple generations. Related designs include heterogeneous stock and the farrago outcross population. In this article, we 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. we further derive the map enlargement in these populations, that is the frequency of recombination breakpoints on the pointless chromosome.

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