Exploiting quantitative information in the analysis of dominant markers

Dominant genetic markers such as AFLPs and RAPDs are usually analyzed based on the presence or absence of a band on an electrophoretic gel. This type of analysis does not allow a distinction among dominant homozygotes and het erozygotes. Such a distinction is possible based on the quantitative measur ement of band intensities. In the present paper, we consider the problem of analyzing dominant markers based on band-intensity data. The basic step fo r mapping a marker is to assess its recombination frequency with other mark ers. Ordering markers on a map can then be done using a number of standard procedures. For this reason estimation of the recombination frequency is th e main focus of the present paper. The method is demonstrated for the case of an F-2 population. By simulation we investigate its accuracy and compare it to the standard estimation based on dominant scoring for band presence/ absence. There are a number of potential applications. For example, the map may be used to locate quantitative trait loci (QTLs), applying standard pr ocedures modified to account for uncertainty of the marker genotype. Moreov er, map information can be used to determine the most likely genotype at a marker, given its band intensity and the band intensities at flanking marke rs.