Mapping quantitative trait loci by genotyping haploid tissues

Mapping strategies based on a half- or full-sib family design have been dev eloped to map quantitative trait loci (QTL) for outcrossing species. Howeve r, these strategies are dependent on controlled crosses where marker-alleli c frequency and linkage disequilibrium between the marker and QTL may limit their application. In this article, a maximum-likelihood method is develop ed to map QTL segregating in an open-pollinated progeny population using do minant markers derived from haploid tissues from single meiotic events. Res ults from the haploid-based mapping strategy are not influenced by the alle lic frequencies of markers and their linkage disequilibria with QTL, becaus e the probabilities of QTL genotypes conditional on marker genotypes of hap loid tissues are independent of these population parameters. Parameter esti mation and hypothesis testing are implemented via expectation/conditional m aximization algorithm. Parameters estimated include the additive effect, th e dominant effect, the population mean, the chromosomal location of the QTL in the interval, and the residual variance within the QTL genotypes, plus two population parameters, outcrossing rate and QTL-allelic frequency. Simu lation experiments show that the accuracy and power of parameter estimates are affected by the magnitude of QTL effects, heritability levels of a tl a it, and sample sizes used. The application and limitation of the method are discussed.