Nonselective inbreeding is directly related to a depressed fertility rate, an increase in abortion and stillbirth. Some basic principles of genetics show why these traits are directly related to inbreeding. When two unrelated horses are mated, the chances of unidentical alleles combining within the resulting embryo are high. Although the reason for this allelic interaction is not clear, geneticists believe that its presence contributes to the overall quality of an individual. Therefore, as homozygosity increases within the inbred herd, physical quality controlled by overdominant alleles declines.
Many undesirable genes affecting the horse's overall vigor and fertility are recessive.
Fortunately, they have no influence in the heterozygous state, since the effect of the recessive allele is completely hidden by the effect of the corresponding dominant allele. Because of the overall effect of inbreeding is an increase in homozygosity, it increases the number of homozygous recessives. Hence, the effects of undesirable recessive genes begin to surface. Inbreeding does not create undesirable trait, it exposes recessive alleles for hidden weaknesses which are present within the sire and dam. Not only is the time factor impractical for most breeders, the intense culling often necessary may be an economic problem.