A large family size is required to detect sexual heterogeneity of the recombination fraction using dominant and codominant DNA-markers

Abstract

Maximum likelihood methods for testing sexual heterogeneity of the recombination fraction using dominant and codominant DNA-markers are developed. The methods are tested by Montecarlo computer simulation. Two crosses were investigated 1) Ab/aB x Ab/aB and 2) Ab/aB x Ab/alphaB in which A, a, and alpha are alleles at a codominant marker and B and b are alleles at a dominant marker. Estimates of the recombination fraction are biased by more than 6 cM if family size is small (50) for the first cross. Also, the empirical rate of type I error under homogeneity ranged between 0.0 and 3.7 when using the tabulated values corresponding at 5%. Even for large family sizes, the rate of type I error was close to 0 when the expected rate was 1 or 5%. Empirical power was very low for the self-fertilization cross requiring large family sizes (2,000) and large differences in the recombination fraction in the two sexes (differences larger than 20 cM). For the second cross (Ab/aB x Ab/alphaB), both parents were heterozygous but they do not have identical genotypes at the codominant marker. Estimates of the recombination fraction for the two sexes were nearly unbiased in the presence of heterogeneity. The rate of type I error was similar to their expected values for this cross. For a low recombination fraction, empirical power for this cross was higher than 50% for a family size of 500 and a true difference in recombination fraction in the two sexes of approx. 10 cM.