Simulation of population size and genome saturation level for genetic mapping of recombinant inbred lines (RILs)

Various population sizes and number of markers have been used to obtain genetic maps. However, the precise number of individuals and markers needed for obtaining reliable maps is not known. We used data simulation to determine the influence of population size, the effect of the degree of marker saturation of the genome, and the number of individuals required for mapping of recombinant inbred lines (RILs). Three genomes with 11 linkage groups were generated with saturation levels of 5, 10 and 20 cM. For each saturation level populations were generated with 50, 100, 154, 200, 300, 500 and 800 individuals with 100 replications for each population size. A total of 2100 populations was generated and mapped. Small marker numbers and small population sizes produced maps with more than 11 linkage groups. As population size and marker saturation increased, marker inversion and non-linked markers decreased, moreover, between-marker distance estimates were improved. In this study, a minimum size of 200, 300 and 500 individuals were necessary for obtaining reliable maps when they were evaluated over the saturation levels of 5, 10 and 20 cM, respectively.

Estimating the effects of population size and type on the accuracy of genetic maps

Based on simulation studies, it was shown that the type and size of experimental populations can exert an influence on the accuracy of genetic maps. A hypothetical genome map (one chromosome with nine equidistant molecular markers) was generated for the following population types: F2 with dominant and co-dominant markers, backcrossing, recombinant inbred lines (RIL) and double-haploid. The population sizes were 50, 100, 150, 200, 500 and 1000 individuals and 100 simulations were made for each population. The inaccuracies of the populations with the lowest number of individuals were shown by inversions in the order of the markers and the establishment of more than one linkage group in up to 38 percent of the simulations, depending on the population type. Stress and variance values of the distances between adjacent markers were significantly reduced with the increased size of the population. More accurate maps were obtained for the co-dominant F2 and RIL whereas the maps for the dominant F2 population were less accurate. The higher the number of individuals, the more precise was the map. In all populations, a total of 200 individuals were considered as being sufficient for the construction of reasonably accurate genetic maps. Although this paper deals with plant populations this approach is equally applicable to other organisms.