Inbreeding in Dairy Cattle

By Bennet G. Cassell, Extension Dairy Scientist, Genetics and Management, Virginia Tech.
calendar icon 22 September 1999
clock icon 11 minute read
Table of Contents

Performance of inbred dairy cattle
Inbreeding in today's dairy populations
Consequences of inbreeding
Identification is essential


The mating of related individuals is called inbreeding. New dairy animals created by AI or natural service inherit a random sampling of the genetic makeup of each parent. If the parents are related, some of the genes transmitted to offspring by each parent will be copies of the same genes found in the common ancestor(s) which caused the parents to be related. As the genetic relationship between parents increases, the likelihood that pairs of genes in offspring are copies of a single gene in an ancestor generations back increases. Such genes are said to be "identical by descent."

The most extreme form of inbreeding is selfing, that is the mating of an individual to itself. This process is possible in many plant species because each individual produces both male and female germ cells. Suppose a plant has genotype Bb for some part of its chromosome structure. Since germ cells contain a sample half of the plant’s genetic material, half of all germ cells would carry B and half would carry b for both male and female cells. If the plant were "selfed," offspring would be BB, Bb, or bb in ratios of 1:2:1. BB individuals are called "homozygous" for the B allele, while bb individuals are homozygous for the b allele. Bb individuals are called "heterozygous" as they carry both B and b in their genetic material. If offspring of the selfed plant were also selfed, only BB offspring would result from the BB individuals and bb offspring from the bb individuals. The Bb individuals would again produce BB, Bb, and bb offspring in ratios of 1:2:1. The process, continued over several generations, would continue to increase the frequency of BB and bb (homozygous) individuals and reduce by half in each generation the number of Bb individuals. Selfing is not possible in mammals such as dairy cattle, but the same process of increased homozygosity and decreased heterozygosity occurs with inbreeding in all species.

Inbreeding does not change gene frequency, that is the total number of B or b genes in a population. It only changes the arrangement of those genes in pairs of BB, Bb, or bb. If some of those combinations are non-fertile, a selection process will occur which will change gene frequency.

Performance of inbred dairy cattle

Inbred animals become homozygous at more chromosome locations than non-inbreds. The positive aspect of inbreeding is that the genotypes of sperm or egg cells from inbred individuals are more predictable than for outbreds. BB or bb individuals can only produce B or b sperm and egg cells. The heterozygote, Bb, can produce either B or b sperm or egg cells. If the inbred animal were superior and transmitted its superiority with regularity, the advantages would be obvious. Inbreeding can also be used to "purge" a line of cattle of undesirable recessive genes.

Unfortunately, inbreeding produces many undesirable side effects as well. When undesirable recessive genes appear in the homozygous state (bb), the condition is often fatal. The fatality may occur very early in embryonic development and look like a failed conception to a dairy producer. If the genes are semi-lethal, and the individual does survive, it may be totally unprofitable. Most animal species (including dairy cattle and humans) carry low frequencies of lethal or semi-lethal genes hidden in the heterozygous state (Bb). Inbreeding, by increasing the frequency of homozygous individuals (BB or bb), removes the protective cover of the non-lethal, dominant gene (B), exposing more offspring to the lethal combination of genes (bb). For dairy cattle, inbreeding reduces the profitability of individual animals which is unacceptable for most producers.

The effects of inbreeding have been so much more negative than positive in animal breeding that the term "inbreeding depression" was coined. Table 1 shows inbreeding depression for lifetime and individual lactation traits of Holsteins from a recent study by Smith, et al. at Virginia Tech. The changes are expressed "per 1% increase in inbreeding." This means that the lifetime economic loss for a mating producing 6.25% inbreeding would be $24 X 6.25 = $150 expected loss from such a mating. Notice that, with the exception of somatic cell score where inbreeding has no apparent effect, all consequences of inbreeding in Table 1 are undesirable. Age at first freshening goes up, length of productive life goes down, all production traits are reduced, and first calving interval is lengthened as inbreeding increases.

Some of the changes shown in Table 1 are larger than other estimates in the literature. Wiggans, et al. reported slightly smaller milk yield losses in Holsteins of 65 lbs. per 1% increase in inbreeding. His work also showed that first lactation milk losses of 67 lbs./1% increase in inbreeding for Ayrshire, 43 lbs. for Guernsey, 47 lbs. for Jersey, and 54 lbs. for Brown Swiss.

Table 1. Effect of inbreeding on lifetime and individual lactation performance in registered Holstein cows
Inbreeding depression per
1% increase in inbreeding
Lifetime net income ($)
Age at first freshening (days)
Days of productive life
Lifetime total milk production (lbs.)
Lifetime total fat production (lbs.)
Lifetime total protein production (lbs.)
First lactation milk production (lbs.)
First lactation fat production (lbs.)
First lactation protein production (lbs.)
First lactation average somatic cell score
First calving interval (days)

Inbreeding in today’s dairy populations

Selection for higher production and improved type of dairy cattle has reduced genetic diversity. The diversity eliminated included undesirable genes for the traits we have selected to improve which was, of course, our purpose. Today, a limited number of animals in each breed serve as parents of highly influential sires in each generation. Wiggans, et al. found average inbreeding of 4.7% in Ayrshire cows, 3.0% in Guernsey, 2.6% in Holstein, 3.3% in Jersey, and 3.0% in the Brown Swiss breed. Are these numbers alarming? The critical issue is whether inbred dairy cows are functional under today’s management conditions and whether that functionality is compromised by less genetic diverstiy in the population. Cattle today are more inbred than their ancestors, but they are also much more productive. It would not be accurate to say that current levels of inbreeding are alarming.

A 1996 study by Young and Seykora looked at inbreeding changes in Holsteins throughout the 20th Century. Holstein cows were first imported to the United States in 1884. Young and Seykora’s work showed that today’s Holstein cow was about 5% inbred relative to that original importation date. The average relationship (percent of genes in common between any two animals) increased from about 3.4% in 1928 to approximately 10% (twice the average inbreeding value of 5%) in 1990. This increased relationship indicates the effects of selection for more productive, functional cattle and reflects a narrowing of the genetic base. Young and Seykora reported that Pawnee Farm Arlinda Chief and Round Oak Rag Apple Elevation accounted for nearly one fourth of all genes segregating in Holstein cattle in 1990. Holstein pedigrees without one of these two patriarchs in the first six or eight generations would often be a product of unusual breeding decisions.

Consequences of inbreeding

Table 2 presents the results of three specific matings which could be made in dairy cattle. Most dairy farmers would avoid mating a sire to his own daughter and many would recognize that a selected AI bull should not be mated to daughters of his sire. However, the mating of a bull to a daughter of a half brother would be more difficult to recognize. In Holsteins, for instance, mating daughters of Mattie to another son of Mascot such as Javlin would produce the 6.25% inbreeding indicated in the Table 2. Dairy farmers might make such matings because they did not recognize the relationship between Mattie and Javlin. NAAB short names don’t reveal much about pedigrees!

Table 2. Expected change in lifetime economic merit and individual lactation performance from matings producing inbred offspring
Mating of a bull to
Percent inbreeding Expected change in
    Lifetime net income First lactation milk (lbs) First lactation protein (lbs)
His own daughter
25% $600 2,050 75
His own half sister
12.5% $300 1,025 38
A daughter of a half brother
6.25% $150 513 19

We would expect a calf by Javlin out of a Mattie daughter (6.25% inbred) to lose over $150 lifetime net income compared to a non-inbred calf of otherwise equal merit. Should such a mating ever be made? As with all breeding decisions, the answer involves alternatives. Can an outcross bull be found whose genetic merit is high enough for progeny to perform better than progeny of an inbred mating? If we make the comparison on PTA milk instead of lifetime net income, the example may be clearer. A mating to Javlin would depress first lactation milk production by over 500 lbs. That means that an alternate sire could be about 500 lbs. lower for PTA milk than Javlin and be equally useful as a mate to Mattie daughters, provided he produced no inbreeding in the mating. On the Spring 1998 proofs, Javlin was +2374 for milk. A bull unrelated to a Mattie daughter could be as low as +1861 on PTA milk and be equal to Javlin as an improver of first lactation milk. If the only unrelated sires are lower for production than that, then avoiding inbreeding entirely would cost more in lost genetic improvement than would be lost from inbreeding depression. The search for an optimum mate should not be restricted to unrelated bulls. High ranking bulls to which the cow is related should also be considered.

In managing a breeding program, be aware of the effects of inbreeding, but keep in mind that the degree of inbreeding determines its effect on an animal’s performance. Further, inbreeding only depresses additive genetic merit. Lack of inbreeding does not add to genetic merit. Breeders should not avoid the use of the best sons of a particular bull simply because the bull has female offspring in their herd. Some combinations of bulls with cows in a herd may produce more inbreeding that you find acceptable. Avoid the matings that produce unacceptable amounts of inbreeding rather than eliminating the bull from a breeding program.

Identification is essential

Inbreeding cannot be avoided unless the pedigree of the cow to be inseminated is known in depth. Extremely close matings can occur when identity is unknown, but much of the loss from inbreeding comes from common ancestors three or more generations back in a pedigree. Many producers are unaware that the animals affected are inbred at all. More than one common ancestor can affect overall inbreeding as well. This means that complete pedigree information for four or five generations back is needed to do a good job of managing inbreeding. It may well be that one of the most valuable assets of a registered cow in years to come will be the ability to assign mates for her with optimum control of inbreeding. Grade animals, particularly the increasing number of such animals from very large dairy herds, frequently don’t have complete pedigree data for several generations back. Even if a complete pedigree on a grade animal could be developed through use of historic DHI records, the information is not of much use unless it is available in a form that allows computerized mating programs to use it.

We saw how important complete pedigree information was in the inbreeding study by Smith, et al. mentioned earlier. In this work, we estimated effects of inbreeding separately for cows from entirely registered and entirely grade herds. Inbreeding depression cost over $24 per 1% increase in inbreeding in registered herds, but less than $10 per 1% increase in grade animals. For first lactation milk production, registered cows had 82 lbs. inbreeding depression compared to just 35 lbs. in grade cattle. Do genes in grade cows work differently than they do in registered cows? I doubt it. Inbreeding in grade cattle is likely larger than calculated because of missing ancestors in the known pedigree. The estimated inbreeding coefficients were three times higher in registered than in grade cows. If we can’t estimate inbreeding in a mating because of limited pedigree data, we cannot avoid inbreeding or estimate its costs.


Inbreeding will become more difficult to avoid as relationships between animals in the various dairy breeds increase. Increased relationships are a natural consequence of using only a few sires in an AI breeding program. Inbreeding can be avoided, but not without sacrifice of progress toward improved productivity. The bulls to which carefully bred cattle should be mated were selected for the same reasons as the cows themselves, and can only be expected to have many of the same genes. Optimum methods to control inbreeding will choose the sire with highest genetic merit adjusted for inbreeding in a specific mating rather than avoiding some maximum level in inbreeding. Complete, accurate pedigree data for cows to be mated and sires used as mates will be a necessary part of such mating decisions.

References Smith, L.A., B.G. Cassell, and R.E. Pearson. 1998. The effects of inbreeding on lifetime performance of dairy cattle. J. Dairy Sci. accepted.
Wiggans, G.R., P.M. VanRaden, and J. Zuurbier. 1997. Calculation and use of inbreeding coefficients for genetic evaluation of United States dairy cattle. J. Dairy Sci. 78:1584-1590.
Young, C.W., and A.J. Seykora. 1996. Estimates of inbreeding and relationships among registered Holstein females in the United States. J. Dairy Sci. 79:502-505.

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May 1999

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