Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers

A method is presented to estimate the biometric parameters of a quantitative trait locus linked to a genetic marker when both loci are segregating in the F-2 generation of a cross between two inbred lines. The method, which assumes underlying normal distributions, is a combination of maximum likelihood and moments methods and uses the statistics of the genetic marker genotype samples for the quantitative trait to estimate the recombination frequency between the two loci and the means and variances of the genotypes of the quantitative trait locus. With this method, the genetic parameters of a locus affecting plant height linked to an electrophoretic marker for esterase were accurately estimated from a sample of 1596 F-2 progeny of a cross between two species of Lycopersicon (tomato). Linkage distance between the two loci was 38 map units and the effect of the quantitative trait locus was 1.6 phenotypic standard deviation units. Accurate estimates of the genetic parameters and linkage distance for populations of 2000 individuals simulated with a segregating codominant locus with an effect of 1.63 standard deviations linked to a genetic marker with .2 recombination were also derived by this method. The method is not effective in distinguishing between complete and partial linkage in samples of only 500 individuals or for quantitative loci with effects less than a phenotypic standard deviation. The method is more effective for codominant than for dominant loci.