Regression on markers with uncertain allele transmission for QTL mapping in half-sib designs

Recently, regression of phenotype on marker genotypes was described for quantitative trait loci (QTL) mapping in F-2 populations and shown to be equivalent to regression interval mapping (RIM). In this study, regression on markers was extended to half-sib designs with uncertain marker allele transmission, and properties of QTL parameters were examined analytically. In this method, offspring phenotypes are first regressed on the probability of transmission of a given allele from the common parent at flanking marker loci. Resulting regression coefficients can then be interpreted based on an assumed genetic model. With presence of a single QTL in the marker interval, it was shown that expected values of regression coefficients for the flanking markers contained all information about position and effect of the QTL and were independent of the probability of marker allele transmission. Through simulation, it was shown that regression of phenotype on marker allele transmission probabilities is equivalent to RIM under the same assumed genetic model. Regression on marker genotypes is computationally less time consuming than QTL interval mapping, as it eliminates the need to search for the best QTL position across marker intervals. This can form the basis for more efficient methods of analysis with more complex models, including threshold or logistic models for the analysis of categorical traits. (C) Inra/Elsevier, Paris.