Inbreeding coefficients that are produced based on an animal’s recorded pedigree are estimates of the expected degree of inbreeding by descent. They are calculated as half the additive relationship between the parents. For example, a non-inbred father and daughter share half their DNA in common, and so have an additive relationship of ½. An offspring generated from a father-daughter mating would have an inbreeding coefficient of half of this, i.e. ¼ (or 25%).
An inbreeding coefficient can be interpreted as meaning that 25% of the DNA in the inbred offspring will be identical by descent. The pedigree based inbreeding coefficient is an estimate because not all offspring from a father-daughter pairing will exhibit 25% DNA identical by descent – some offspring of such a mating may have a slightly higher amount, and other offspring a slightly lower amount, but if the pairing were repeated a number of times, on average the inbreeding will be 25%. The following table gives these estimates for how much inbreeding by descent happens when related animals are mated, for various common matings:
|Relationship||Inbreeding Coefficient (%) *|
|Animal mated to its own parent (e.g. sire & daughter)||25%|
|Mating between full brother and sister (i.e. mates are full siblings – share both their sire and dam in common)||25%|
|Mating between half brothers and sisters (i.e. mates are half siblings - share either a sire or a dam in common)||12.5%|
|Animals have a single great-grandparent in common||3.1%|
Inbreeding causes a measurable negative impact on cattle performance. Inbreeding will not exist if the sire and the dam do not share any near or distant ancestors. Therefore inbreeding can be minimised by avoiding matings between related animals.
Why should inbreeding be avoided?
Inbreeding typically causes a measurable negative impact on cattle performance.
Genetic material can randomly mutate at any time, and these mutations can lead to compromised gene function. Fortunately, individuals carry two copies of every gene, and the second copy can often compensate if the first is mutated so as to be non functional. Because of this compensation, mutated genes can be passaged through many generations without being phenotypically observed. Mutated genes can often remain hidden until two relatives each carrying the mutation are mated together. When two carrier animals are mated, there is a one in four chance that the offspring will inherit two versions of the mutated gene, causing the corresponding phenotype to be compromised.
If an animal’s parents are related, there is a chance that a mutated gene from their common ancestor(s) could be present in both the mother and the father. If both parents have the mutation, then the animal could inherit two impaired versions of the gene. The level to which any one gene is impaired may be small, but over the whole genome these effects will add up to a measurable reduction in the animal’s performance, known as inbreeding depression.
What are the effects of inbreeding on cattle performance in NZ?
The following table shows the estimated inbreeding depression for each additional percent of inbreeding. A positive value indicates that the trait will increase as an animal becomes more inbred (for example, stature). A negative number indicates that the trait will decrease as the animal becomes more inbred (for example, liveweight).
Estimated Performance Change Due to Inbreeding (NZAEL January 2020 estimates)
|Trait||Expected performance change per 1% of Inbreeding||Expected performance change for an animal with 12.5% inbreeding coefficient|
|Body Condition Score (score)||-0.0037||-0.047|
|Somatic Cell Score (log SCC)||0.0058||0.073|
|Total Longevity (Days)||-0.0787||-0.984|
|TOP Capacity (score)||-0.0090||-0.112|
|TOP Dairy Conformation (score)||0.0030||0.038|
|TOP Fore Udder (score)||0.0037||0.046|
|TOP Front Teat (score)||0.0019||0.024|
|TOP Legs (score)||0.0053||0.066|
|TOP Milking Speed (score)||0.0097||0.121|
|TOP Overall Opinion (score)||0.0003||0.004|
|TOP Rear Teat (score)||0.0017||0.021|
|TOP Rear Udder (score)||0.0050||0.063|
|TOP Udder Support (score)||-0.0044||-0.055|
|TOP Rump Angle (score)||0.0158||0.198|
|TOP Rump Width (score)||-0.0020||-0.025|
|TOP Shed Temperament (score)||0.0056||0.071|
|TOP Stature (score)||0.0231||0.288|
Why don't breeding values incorporate inbreeding depression?
A breeding value represents additive genetic merit. This value reflects only the portion of an animal’s genome that will have a “direct and independent effect” on the performance of its progeny—that is, genes that are expressed by progeny, irrespective of what other DNA the progeny inherit.
The size of an animal’s inbreeding depression will depend on what they inherit from both parents. Because inbreeding depression is pairing specific in this way, it cannot be accurately captured in a breeding value.
If inbreeding is not properly accounted for within a genetic evaluation system, it can create a bias in Breeding Values (i.e. systematic under-estimation of genetic merit). Recent research has found that such a bias was developing in the NZ genetic evaluation system. As a result the models used to calculate Breeding Values have now been improved to adequately account for inbreeding effects.