When farmers plant diverse crops, with an increased heterozygosity, plant pathogens and parasites have to adapt to each new plant in the field, and in some cases, may not be able to. Breeding closely related animals reduces the level of heterozygosity in the offspring. When inbreeding occurs within a population rare genes can be lost and the frequency of deleterious genes can increase or even become fixed, and overall genetic variability is reduced. A classic example of this is the cheetah. All cheetahs are extremely closely related, and the level of heterozygosity within the entire cheetah population is of a similar order to that of brothers and sisters.
Cheetahs are almost clones of each other.
In fact, the entire cheetah population existing today is believed to be descended from one pregnant female that survived the last glacial period around five thousand years ago. Most organisms carry many deleterious alleles, but the affect of these are covered, or masked, by the individual also carrying a fully functioning copy of these alleles. In diverse population the chance of both parents giving a deleterious allele of the same gene to their offspring is minimal. When inbreeding occurs offspring may recieve deleterious alleles of a gene from each parent. Having two deleterious alleles for that gene means that they do not have a working copy of that gene, and this can reduce fitness or even be fatal.