Development of a mapping population in allogamous species
In allogamous species, the situation is often more complicated than in self-pollinated species. Forced and repeated self-fertilisation often leads to inbreeding depression, i.e. inferior and stunted plants. As a consequence, RIL populations cannot be developed. Due to the poor tolerance of homozygosity, also DH populations are often not an option either. However, notable exceptions exist, for example maize, which is naturally cross-fertilizing but can be selfed without problems. Other outcrossing organisms, like animals (e.g. mice or Drosophila) can be inbred by brother-sister matings.
In allogamous species, mapping populations are created developed by crossing two heterozygous parents, or by selfing one single (heterozygous) plant. Since in cross-fertilizing species often F1 hybrid cultivars are developed, or highly heterozygous plants are clonally propagated (apple, potato), one selfing of such plant will result in segregation of all the marker and gene loci that were heterozygous in the parental plant.
Due to the high level of heterozygosity, there is a much greater need for co-dominant markers in allogamous crops. This situation is very different from the autogamous crops treated on the previous section, since in autogamous crops,
RIL and DH populations can be used and co-dominance of markers is not so important (only homozygotes need to be distinguished).