Inbreeding has been a hot topic within the field of genetics. It is a large and often polarizing topic. This article is not intended to advocate a specific position. Instead, it aims to provide a set of factual reference points and provide clarification for frequently used terms to help readers to think more clearly as the inbreeding discussion unfolds.
Inbreeding defined
Inbreeding refers to the mating of related individuals that increases the probability that an animal receives the same allele (segment of DNA) from both parents because of shared ancestry.
Line breeding vs. inbreeding
In the breeding of plants, a commonly used term is line breeding. Line breeding is the selective, intentional form of inbreeding used to concentrate the genes of a particular ancestor while trying to avoid obvious negative effects. This may sound familiar. It is important to realize that line breeding is not genetically different from inbreeding. Instead, there is a different management philosophy between animal breeding and plant breeding.
Inbreeding sounds accidental and risky while line breeding sounds deliberate and strategic. Both, however, increase the inbreeding coefficient in individuals. Many crop lines are more inbred than any dairy cow could ever become. However, they are fully productive, highly uniform and very genetically predictable. In crops, inbreeding is a tool rather than a concern, and it is often the goal.
This contrast is useful, not because dairy cattle should be managed like crops, but because it reminds us that we debate terms through the lens that we were taught to use. Inbreeding is not inherently bad, but it can lead to negative consequences.
Inbreeding trends are going up
Inbreeding is a normal consequence of genetic selection. Selection pressure slowly increases relatedness within a population. As genetic selection intensifies, so does the rate of inbreeding.
Animal breeders are trained to maximize genetic gain per generation for economically important traits. With the development of artificial insemination, genetic evaluation models and genomic selection, the industry has become very effective at achieving this goal. Genetic gain per generation is faster than ever and thus, so is the increase in relatedness.
Our inbreeding trends demonstrate this. These trends are often stronger in countries and breeds where genetic selection is more intense. Over time, any breeding program that applies consistent selection will increase population relatedness.
The 6.25% inbreeding limit
For years, a commonly used maximum inbreeding threshold in cattle breeding was 6.25%. This is the inbreeding coefficient of an individual whose parents have a common grandparent, based on classic pedigree genetics. The value became a convenient guideline in cattle breeding because many studies categorize inbreeding levels starting with 6.25% to assess the onset of inbreeding depression. These studies, however, were largely written before the development of genomic selection and are thus based on pedigree rather than genomic inbreeding.
Currently, the 6.25% limit has lost relevance. If producers strive to maintain this classic value, they likely seriously compromise genetic gain as the genetic merit of resulting offspring may be lower than its dams.
Another older but respected measure is the limit on the inbreeding rate, which describes how quickly inbreeding accumulates in a population from one generation to the next. The Food and Agricultural Organization of the United Nations (FAO) recommends keeping this rate at around 1% per generation to help maintain genetic diversity in livestock populations. Currently, global Holstein populations show inbreeding rates of approximately 1.2% per generation, slightly above this benchmark.
Inbreeding after genomic selection
The onset of genomic selection has increased genetic gain, but it has also helped us understand inbreeding better. Where we once had to rely on assumed relationships through pedigrees, we can now analyze the DNA and know that pedigree relationships are an average. The actual amount of relatedness per individual varies. Genomic inbreeding estimates are therefore more accurate than pedigree estimates and should be used where possible.
Old vs. new inbreeding
The onset of genomics has also taught us that there is a difference between old inbreeding and recent inbreeding. Old inbreeding – the sharing of genes from a far ancestor – means there has been repeated selection of positive traits and deleterious mutations have not surfaced or have been purged. It is therefore considered lower risk than recent inbreeding, which has not expressed itself yet in either being good or bad, and mutations could be still hidden. Breeding programs will therefore focus more on reducing relatedness between close relatives rather than worrying about co-ancestry deeper in the pedigree.
Genetic defects
Genomic data has also improved our ability to monitor, detect and manage genetic defects. Once a defect is identified, the entire genotyped population can be screened, and carrier statuses communicated, allowing breeders to avoid carrier-to-carrier matings. Gene tests also make it possible to identify specific defects and adjust breeding programs to gradually remove them from the population. Genomic selection has gone hand in hand with increased inbreeding due to intense selection, but it has also provided the tools needed to manage these side effects more effectively.
Inbreeding coefficients, EFI and GFI
The Council on Dairy Cattle Breeding (CDCB) offers producers multiple inbreeding parameters on their animals and the bulls they may be using. The CDCB also corrects for inbreeding in the statistical models of their traits. That means published predicted transmitting abilities (PTAs) are adjusted, or penalized, for the contribution of the individual animal on the inbreeding level of the population.
Individual inbreeding coefficients
The individual inbreeding coefficient of an animal indicates how inbred that individual animal (in percentage points) is or how much estimated diversity there is in the animal's genome. CDCB calculates both a pedigree-based inbreeding coefficient and a genomic one, if the animal was genomic tested. While the inbreeding coefficient says something about the level of inbreeding within the animal, it is irrelevant for mating decisions. If a highly inbred bull is mated to a nonrelative, their offspring will not be inbred. Carrier statuses of the genetic defects the bull may carry are published. Inbreeding coefficients on females could be useful to analyze trends and monitor inbreeding management.
Estimated future inbreeding
A bull can be highly inbred but have a low level of relatedness to the population. To indicate how much the animal may affect the future inbreeding level of the population, CDCB publishes estimated future inbreeding (EFI) metrics. EFI tells us how much we believe the animal may change inbreeding in the population. EFI is calculated by estimating the pedigree relatedness of the bull to all genotyped females born in the U.S. within the last 48 months. This group is reestablished every four months at the official sire evaluation. The PTA of a bull is adjusted to the difference between the EFI of the bull and the average EFI of the base population (which is currently cows born in 2020). Therefore, one can expect the EFI of a bull to change with each sire evaluation and at each base change. The percent EFI that is published also does not reflect on the relatedness of that bull with your herd. It is merely a measure that gives you an indication of how related that bull is to the youngest genotyped U.S. dairy population, within breed.
Genomic future inbreeding
Genomic future inbreeding (GFI) gives the same measure as EFI but based on the genomic relatedness of that bull to the same cohort of genotyped females born within the last 48 months. Similarly, it changes by sire evaluation and base change and is estimated within breed. Because genomic relationship coefficients are more accurate as they are not based on pedigree assumptions, this measure is more accurate than EFI. That said, both EFI and GFI are based on a cohort of genotyped females, and it can be debated if this group is representative of the entire U.S. dairy population. Like EFI, GFI does not reflect on the relatedness of that bull with the individual herd.
Why don't we take our foot off the gas?
Maximizing genetic gain has always been the goal in animal breeding for many traits, including those sensitive to inbreeding depression like fertility and health. Thanks to these efforts, genetic gains are now often greater than the cost of inbreeding depression. With current inbreeding levels, imposing a strict limit would significantly slow progress. In fact, offspring could show less genetic merit than their parents, which would reduce overall program effectiveness.
It is important to realize that breeding programs are not currently mating close relatives in pursuit of ultimate gain. They are carefully designed to balance genetic improvement with the risk of inbreeding. In theory, it is possible to implement models that slow both genetic gain and inbreeding accumulation. But just like it’s possible to drive 30 mph everywhere because it’s safer, it isn’t practical. In reality, industry business models and the demands of the food system make it nearly impossible to take our foot off the gas without significant financial loss. The solution is not slowing down; it is learning to manage inbreeding while continuing genetic progress.
Knowledge gaps and future research
Just like pedigrees, inbreeding estimates highly depend on accuracy and completeness of the pedigree. Genomic inbreeding information depends on the accuracy and completeness of our genomic data. Twenty years into genomic selection, the industry has made great progress in identifying genetic variants on the cattle genome. That said, our genomic evaluations, which include genomic relatedness, are based on one genetic variant – the single nucleotide polymorphism (SNP).
One concern of high inbreeding is the loss of genetic diversity. An argument often made is that there is still plenty of genomic variation since we are still making genetic progress, which is correct. That said, one must acknowledge that this conclusion is made looking through the lens of SNP-based genomic evaluations. It is possible that genetic diversity is lost in places of the genome that are not well mapped nor understood yet. With continued research, future genomic developments will undoubtedly give us further handles on both understanding and managing inbreeding for the benefit of our dairy population.
Conclusion
While messages in our industry about inbreeding can be mixed, the facts are clear. Published trends show a steep upward trajectory in inbreeding. This is a natural consequence of high selection intensity and rapid genetic gain. That gain has brought significant genetic progress, which, by current estimates, often outweighs the financial costs of inbreeding depression. At the same time, all our estimates are based on the current state of scientific knowledge of the animal’s genome, and that knowledge continues to improve.
Panicking about rising inbreeding isn’t productive – managing it is. There are various tools available, of which mating programs are the most effective.
EFI and GFI reflect an animal’s relatedness to the broader genotyped population, not to a specific herd. Avoiding bulls based solely on these metrics can mean missing valuable genetics. The priority should be managing inbreeding in the resulting offspring through structured mating programs and accurate pedigree records.
We can trust that ongoing research will continue to provide new insights and practical handles for understanding and managing inbreeding, just as it has in the past. With clear knowledge and good management practices, there is no reason to panic; inbreeding can be managed effectively while continuing to make genetic progress.
