Genetic linkage maps are often based on maximum-likelihood estimates of recombination fractions which are converted into map units by mapping functions. This paper presents a cost analysis of linkage analysis for a segregating F-2 population with codominant or dominant molecular markers and a qualitative monogenic dominant-recessive trait. For illustration, a disease-resistance trait is considered, where the susceptible allele is recessive. Three sub-populations of the F-2 can be used for linkage analysis [susceptible (= recessive) individuals, resistant (= dominant) individuals, complete F-2]. While it is well-known that recessive individuals are more informative than dominant individuals, it is not obvious a priori, which of the three sub-populations should be preferred, when costs of phenotyping and genotyping are taken into consideration. A comparative economic analysis of alternative procedures of linkage detection based on these three sub-populations does exhibit a clear economic superiority of the sub-population of susceptible (= recessive) individuals, when costs of genotyping are high. This cost-effectiveness is due to the higher information content of this sub-population compared to the sub-population of dominant (= resistant) individuals and also compared to the complete F-2. Our final conclusion/recommendation is as follows: If the cost to genotype an individual is sufficiently large compared with the cost to phenotype an individual, then linkage analysis and genetic mapping should be only based on susceptible (= recessive) individuals. Conversely, if the cost of phenotyping exceeds that for genotyping, it may be preferable to genotype all plants. The exact conditions under which a strategy is preferable are described in the paper.
