Putting Inbreeding Into Perspective
by Charles Sattler, vice president, dairy progeny testing and genetic research
When inbreeding is mentioned, it usually conjures up unpleasant thoughts.
But, as with most things, reality is not as extreme as perception.
Improving dairy cattle genetics starts by increasing the percent of
good genes in the population and replacing bad ones. We also have goals
for consistency and uniformity. To do this, we make use of the
highest-performing cow families. As more animals become descendants of
these family lines, however, the chance that we are mating distantly
related animals goes up, leading to a gradual increase of inbreeding.
This isn't all bad, because clearly we have improved productivity and
uniformity. The challenge is to continue selection intensity without
"too much" inbreeding.
A closer look at the genetic process shows that an animal has two copies
of every gene, one each from her sire and dam. Inbreeding is what happens
when identical genes are inherited from the parents. For this to occur,
the sire and dam must have a common ancestor. If parents are completely
unrelated, there is no inbreeding (this is unlikely among animals of the
same breed). The chance of inheriting identical genes from both parents
increases as they are more closely related.
When mating two related animals, we never know exactly how inbred the
offspring will be, since only a full DNA analysis can tell us. However,
inbreeding probability can be estimated through pedigree analysis. This
number, the inbreeding coefficient, estimates the percentage of identical
genes that are inherited. Inbreeding coefficients are estimates, not
guarantees. Although we use estimates daily (e.g., genetic evaluations),
inbreeding coefficients are a bit different because they never are backed
up by real data. Typically genetic evaluations start with a Parent Average
(PA) and then track offspring’s performance to establish genetic merit.
Inbreeding coefficients remain PAs forever, since we don't know exactly
which genes are transmitted. If we mated the same parents 100 times, the
inbreeding coefficient is a good indicator of how often identical genes
would match up in the offspring for the group. But, individually, some
offspring will be less inbred than the estimate and others more so.
Also, the inbreeding coefficient does not identify whether the genes matching
up are undesirable or desirable. If an animal inherits good identical genes,
then inbreeding is beneficial. Results of individually mating related animals
vary based on the number of identical genes that get matched up by chance,
and the quality of those genes that happen to be identical.
The key to the inbreeding dilemma is to find a balance between genetic
selection and control of inbreeding. In fact, inbreeding can be a wise
way to make rapid gains in a single generation for A.I. organizations and
herds that are working to develop a particular cow family. The Jersey,
Golden MBSB of Twin Haven-ET, is an example (Table 1). She has a high 9.0
percent inbreeding coefficient, but is a genetically elite, profitable
producer. This shows the reward/risk of inbreeding. While some inbred
matings result in terrific performance, on average, inbred matings perform
below expectation due to inbreeding depression.
Table 1. Performance measures for Golden MBSB of Twin Haven ET.
| |
Genetic Values |
Actual Performance |
| Milk |
+1,174 |
30,380 |
| Fat |
+71 |
2,084 |
| Protein |
+53 |
1,251 |
| Type |
+2.5 |
Excellent (94) |
| Other |
+331 JPI
(10th in breed) |
National |
November 2002 data
Research conducted by Virginia Tech estimates that for each 1 percent
increase in the inbreeding coefficient, there is a corresponding loss of
$22 net income. This came from tracking performance of more than 2.6 million
cows after they entered the milking herd, and shows that inbreeding depression
reduces production, reproductive performance and longevity (Inbreeding losses
occurring before first calving are not in this estimate). Table 2 shows the
value that is lost due to inbreeding or gained due to genetic improvement
for several important traits.
Table 2. Values for genetic change in various traits.
| Trait |
Value |
| Inbreeding* |
-$22 per 1% increase in inbreeding coefficient |
| Milk+ |
+$24 per 100 pounds PTA Milk |
| Udder composite+ |
+$29 per 1 point of UDC |
| Feet-and-Legs composite+ |
+$15 per 1 point of FLC |
| Productive Life+ |
+$28 per 1 month of PTA PL |
| Somatic Cell Score+ |
+$15 per 0.1 point of PTA SCS |
| Calving Ease |
+3 per 1% DBH
(when breeding heifers) |
*Source: Smith et al., Virginia Tech. +Source: USDA.
With each replacement heifer so important to profitability, ignoring
inbreeding is not a good strategy. Neither is avoiding all inbreeding,
because you sacrifice more genetic improvement than what is gained by
minimizing inbreeding depression. The best strategy is to make sire choices
based on current genetic evaluations, and then mate these sires to specific
cows considering the inbreeding these matings may cause. For specific
guidelines you can use to manage inbreeding in your herd, visit www.selectsires.com
and watch for the next issue of Selections.
Weigel at the University of Wisconsin-Madison studied different strategies
for using inbreeding estimates in mating decisions. He used real data from A.I.
sires available at the time and cows from 25 registered-Holstein herds and 25
registered-Jersey herds. The results from this research showed that the optimum
strategy is to calculate a genetic value for each prospective mating, adjust
for the level of expected inbreeding and then use the mating with the highest
adjusted value. This strategy slightly reduced the amount of genetic progress
made but did the best job of controlling inbreeding. This study did not
consider any potential gains from corrective mating.
This seems like a fairly obvious solution but it is one that is easier to
describe in research settings than to carry out in real-life situations.
First of all it requires sophisticated calculations to produce a genetic
value for each animal and then adjust it for inbreeding depression. It also
requires complete pedigree information; which isn’t available in most cases.
This level of information does exist for herds with registered cows. This
would be the best strategy for mating registered cattle and would be one way
for these herds to more fully capture the investment they have made in
maintaining these pedigree records. These values come from a population of
cows where nearly all of them are healthy revenue-producing individuals.
Table 3. Results from Holstein Association USA’s Inbreeding Calculator for
Potential Sire Choices for a cow with a sire stack of
Durham x Emory x Ambition x Bell Rex.
| Potential Mate |
Pedigree |
Actual TPI |
Inb. Coefficient of Mating |
TPI adjusted for Inb.Depression |
| 9HO2575 BRET |
Formation x Exquimau |
1609 |
4.5% |
1609 |
| 7HO6055 BRIGHT |
Rudolph x Roebuck |
1557 |
3.9% |
1570 |
| 7HO5682 SAUNDERS |
Bellwood x Aerostar |
1569 |
4.7% |
1569 |
| 7HO5687 FORBIDDEN |
Emory x Mascot |
1626 |
10.3% |
1506 |
The Holstein Association website provides an inbreeding calculator that does a
good job of demonstrating this procedure one cow at a time. We used this feature
to find the best mate for a cow with a sire stack of Durham x Emory x Ambition
x Bell Rex. The bulls we considered were 7HO5687 Forbidden, 9HO2575 Bret,
7HO6055 Bright, and 7HO5682 Saunders. The results are in Table 3. This exercise
shows that inbreeding does have an impact on the mating choice. If inbreeding
was ignored, Forbidden would have been chosen because he has the highest TPI.
But he is closely related to the cow being considered and, after accounting
for inbreeding depression, Bret becomes the best mating choice. This example
also shows that the best choice does not have 0% inbreeding and isn’t even
the one with the least inbreeding. This strategy finds the balance between
genetic gain and inbreeding depression.
The inbreeding values we get when mating this cow to Bret, Bright or Saunders
are typical of what we see in current Holsteins when complete pedigree
information is available. The average for Holsteins born in 2000 that are
included in USDA genetic evaluations is 4.5%. The corresponding average
for Jerseys is 6.2.
In most situations, however, complete pedigree information is simply not
available. Going through all these calculations when little pedigree
information is available is overkill. Weigel’s research showed that a second
strategy which only allowed matings that were below a fairly strict level of
inbreeding did a good job at controlling inbreeding and produced results
that were close to the more sophisticated methods described above. The advantage
of the sophisticated approach likely would become smaller when less pedigree
information is available. This threshold strategy is the one used by the
Select Mating Service (SMS) program. SMS uses a default inbreeding threshold
of 3.125% inbreeding when four generations of pedigree information is available.
SMS would not recommend a mating where the sire and dam have grandparents
in common.
The inbreeding considered by SMS is just for common ancestors that appear
in the most recent generations. The numeric inbreeding coefficients mentioned
in this context are not comparable to the inbreeding coefficients calculated
by USDA or the breed associations because they consider many or all the
generations of pedigree information and in these cases the inbreeding
coefficients are higher.
A key factor in the degree of inbreeding control the SMS program achieves
is the amount of pedigree information available. If the cow’s sire is unknown,
SMS (and all other mating programs) can’t provide any inbreeding control. If
only the cow’s sire is known then the effective inbreeding threshold used by
SMS is 12.5%. With known sire and maternal grand sire for the cow, the
effective inbreeding threshold for SMS is 6.25%.
The 3.125% inbreeding threshold provided in SMS is fairly strict. Producers
who are comfortable with taking on a little more risk to be able to use more
of the top-end bulls may want to relax this threshold to 6.25% (one less generation
of checking for common ancestors). SMS allows users to relax the inbreeding
controls. It is not recommended to relax the inbreeding threshold more than
this when mating cows for typical commercial herds.
Here are a few guidelines dairy producers can use to manage inbreeding in their herds:
- Record pedigree information. Nothing can be done to avoid inbreeding if a
cow’s parents are unknown. The key to controlling inbreeding is the recording
of pedigree information. Maintaining records of the cow’s parents and her
grandparents are needed to effectively manage inbreeding. With more pedigree
information, even stricter control of inbreeding can be achieved.
- Breed the type of cattle you like. It is important to know what you would
like to accomplish with your breeding program and then work to achieve your
goals. There is a degree of personal preference involved in managing inbreeding.
If you have the opportunity to practice some selection on the female side and
are willing to accept a little risk, then your breeding program can accept a
higher level of inbreeding. Also if you have high standards for level of
production, udder, feet and legs or overall conformation you will need to
accept a higher level of inbreeding. These traits do not necessarily go together
and the more restrictive your selection is, the fewer families will have
individuals that meet these standards. Also adding criteria like color or polled
will restrict pedigree choices as well. If your goal is to minimize the level
of inbreeding in your herd you will need to use lower selection criteria and
accept a little more variety in your cattle. A general rule of thumb for avoiding
inbreeding would be to limit matings to sires and dams that have no grandparents
in common.
- Use a mating program. With the widespread use of artificial insemination,
the pedigrees of dairy cattle have gotten very complicated. In most cases, a
computer along with recorded pedigree information is needed to get a reasonable
estimate of inbreeding. Keeping pedigree information on cows and A.I. sires
organized is a challenge especially as herd sizes get larger. Using mating
programs to organize the pedigree information and then to determine specific
sire recommendations for each cow is an effective way to avoid mating of
highly related animals.
- Maintain diversity in the pedigrees of your animals. Breeding a high percentage
of your herd to one bull is not a good strategy for several reasons and one of
them is that it might cause inbreeding problems. Using bulls with several different
types of pedigrees will also encourage A.I. companies to develop bulls with
different pedigrees. The responsibility for maintaining a diverse selection of
bulls primarily falls on A.I. companies and the breed associations, though. There
are many companies involved and this is difficult to control. One area that
should be monitored is to avoid the sampling of too many bulls from any one sire
father. While some bulls deserve more use than others as sire fathers there have
been instances where too many sons of a particular bull have entered A.I. sampling.
Bulls with wider variety in their sires is one way to improve the diversity
in A.I. sires.
To order product contact:
Select Sires Inc., 11740 U.S. 42 North, Plain City, Ohio 43064 / Phone: (614) 873-4683 Fax: (614) 873-5751
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