Quantitative trait locus mapping based on selective DNA pooling

Concepts of a simple method to map quantitative trait loci (QTL) based on selective DNA pooling in half-sib family, backcross, and F-2 designs were developed. Tt is shown that the position of a QTL can be estimated from differences in allele frequencies for two flanking markers between individuals with high and low phenotypes and does nor depend on the phenotypic means of the selected groups. An estimate of the QTL effect was obtained by relating group differences in phenotypic means to differences in QTL frequencies, which can be estimated from the QTL position and marker allele frequencies. Simulation of a half-sib family and a F-2 family of 2000 individuals showed that the method gives close to unbiased results when power is high. Biases increased when measurement errors on marker allele frequencies increased and when the effect of the QTL was small. Similarities of QTL mapping based on selective DNA pooling data and on individual genotyping data are discussed, as are opportunities to extend the selective DNA pooling method to the use of multiple markers and multiple half-sib family designs. This study shows that the use of selective DNA pooling can be extended from the detection of marker associations to the mapping of QTL. Selective DNA pooling can greatly reduce the number of genotypings required.