Estimation of recombination parameters between a quantitative trait locus (QTL) and two marker gene loci

Abstract

A new method is described to obtain maximum likelihood estimates of recombination frequencies between quantitative trait loci (QTL) and marker gene loci; it is based on Fisher's method of scoring and numerical differentiation. The method is applied to data from chromosome-doubled monoploid lines of barley originating from the F1 generation of a cross between two well-adapted barley varieties. The lines segregated for marker gene loci ddt (DDT resistance) and s (short rachilla hairs) on chromosome 7. The quantitative trait of single-kernel weight was found statistically significantly associated with locus s, but not with locus ddt. The association is ascribed to a QTL designated Kw1. It could not be ascribed to pleiotropism at locus s since the recombination frequency between s and Kw1 (0.26±0.09) differed significantly from zero. The recombination frequencies between Kw1 and ddt and between ddt and s were 0.42±0.07 and 0.31±0.03, respectively, suggesting the locus order ddt, s, Kw1. The segregation ratio for alleles in locus Kw1 was estimated to be 43∶57, which is not significantly different from a 1∶1 ratio. Means and standard deviations of single-kernel weight for lines with either of the two Kw1 alleles were estimated; the Kw1 locus accounted for 25% of the variance of the single kernel weight.