Determining the sample size for co-dominant molecular marker-assisted linkage detection for a monogenic qualitative trait by controlling the type-I and type-II errors in a segregating F2 population.

Tests for linkage are usually performed using the lod score method. A critical question in linkage analyses is the choice of sample size. The appropriate sample size depends on the desired type-I error and power of the test. This paper investigates the exact type-I error and power of the lod score method in a segregating F(2) population with co-dominant markers and a qualitative monogenic dominant-recessive trait. For illustration, a disease-resistance trait is considered, where the susceptible allele is recessive. A procedure is suggested for finding the appropriate sample size. It is shown that recessive plants have about twice the information content of dominant plants, so the former should be preferred for linkage detection. In some cases the exact alpha-values for a given nominal alpha may be rather small due to the discrete nature of the sampling distribution in small samples. We show that a gain in power is possible by using exact methods.