Inbreeding results when two related animals, with a shared ancestor in their pedigree, mate. The degree of inbreeding, or homozygosity, is a measure of how closely related the ancestors were along the sire and dam lines. Mating two closely related animals will result in a higher homozygosity compared to mating animals more distantly related. Traditionally, inbreeding has been measured using pedigree information, tracing back from the animal to common ancestors found both on the sire and dam side. The correctness of pedigree inbreeding values is therefore highly dependent on the depth and completeness of the records used; a low inbreeding value may simply be a result of a shallow or incomplete pedigree missing the shared ancestor.

Inbreeding levels are increasing

Inbreeding is expected to occur in a population under selection. The rate of inbreeding in dairy cattle, however, has increased in past generations. This is due to several factors, including the increased use of reproductive and genomic technologies, particularly in the Holstein breed. For instance, artificial insemination (A.I.) allowed the widespread use of a small number of popular bulls and their large contribution to the following generation. Furthermore, improvements in genetic evaluation methodologies enhanced the ability to identify elite individuals and families for the breeding goals, which were previously centered around a small number of traits like production and type.

The introduction of genomic selection has brought faster rates of genetic gain and enabled more expansive breeding goals including feed efficiency, fertility and health traits. At the same time, the use of genomic selection has also accelerated the annual increase in homozygosity. This inbreeding trend is mainly a result of a shorter generation interval, a consequence of the growing use of genomically tested young sires (and younger animals in general). Although genomics has helped deliver a larger palette of sires than previously used, many bloodlines are still closely related, and it is typically only a small number of elite related individuals contributing to the next generations.

Consequences of inbreeding

There is still a lot to learn about the consequences of inbreeding, and there is no set limit for how much inbreeding is appropriate or when issues are likely to develop. The reduced performance that results from homozygosity – known as inbreeding depression – typically impacts fitness traits (like fertility and health) the most, although production can also suffer. The magnitude of such effects with each percent increase in inbreeding have been found to be subtle but significant, and notable economic losses can be observed in extremely inbred animals. The most apparent impact of close inbreeding is the increased probability that an individual will receive two copies of the same undesirable gene. This type of detrimental homozygosity can result in calf malformation or even death of the embryo or calf.

Managing homozygosity

Not all inbreeding is harmful, and specific areas of the genome where homozygosity has either negative or positive effects on traits of interest have already been identified. This knowledge could lead to more advanced mating plans.

Lactanet has developed an inbreeding calculator – an online tool to predict the pedigree inbreeding level of progeny from the mating of specific females in a herd to various sires. The Relationship-value (R-value), which represents the percentage of genes a potential bull has in common (i.e., its genetic relationship) with active females within the breed, is also available. The use of genomics provides even more insight into relationships between individuals. While pedigree-based inbreeding is based on probabilities and is limited by pedigree depth, genomic inbreeding measures can provide a more detailed look at the actual homozygosity in the DNA.

Genomics has also made the discovery of detrimental haplotypes with notable effects possible. Holstein Canada, Lactanet and researchers at the University of Guelph will be working towards developing an improved recording scheme for these detrimental haplotypes. For these efforts to be successful, producer involvement via proper identification of each animal, its sire and dam, as well as strict recording of all births, including stillbirths and abortions, will be necessary. In the case of stillbirth or abortion, taking a tissue or blood sample for further analysis will be imperative for identifying carrier animals in the population.

Some degree of inbreeding is largely unavoidable in a purebred population, but it can be managed. It will become more difficult to avoid inbreeding as the relatedness of animals within a breed increases. Inbreeding in Canadian Holsteins has been gradually increasing over time and will continue to do so, which will lead to greater inbreeding depression and possibly an increased occurrence of recessive haplotypes or disorders in the population. Monitoring homozygosity in the breed and within herds therefore has a growing importance for our industry, and genomic information can help guide individual mating decisions.