Inbreeding: manage it to maximize profit

Dairy cows at feedbunk. A discussion on inbreeding

Inbreeding is a hot topic…

Are you concerned about whether genomics is creating too much inbreeding in the dairy cattle population? Many producers express their concern that sire options to prevent negative inbreeding effects continues to dwindle. We certainly don’t want to mate an animal to her father or brother, but we do need to ask what the real goal is in terms of inbreeding. Should we aim for zero percent inbreeding or rather manage it to maximize profit?


The linear effect of inbreeding depression

As animals become more related to each other, inbreeding depression, or sub-par productive performance, can occur. Inbreeding depression is not ideal. Yet you should still weigh the negative effects against the added profit you could see from greater genetic gains.

Many producers buy in to the common misconception of a magic level of inbreeding that we should never exceed. In reality, we’ve seen results from numerous studies over time that show the effects of inbreeding depression to be linear.

For every 1% increase in inbreeding for a mating, you will realize $22-24 less profit over the life of the resulting offspring. You will see the same cost, or loss, when going from 9% to 10% inbreeding as you see between 1% and 2%.


Genetic progress

It’s well-documented that inbreeding has risen each year since the mainstream adoption of AI. Despite this increase, dairy cattle have made significant strides in production traits like milk, fat, and protein. It’s safe to say that producers would not trade today’s high producing cows for the less inbred, but also lower producing, cows of the 1960’s.


Real-herd examples

Let’s look into the records of a random cross-section of 10 upper Midwest dairies averaging 1,500 cows, who implement a mating program on their farm. This analysis shows how cows with superior genetics are more productive than cows with inferior genetics, despite the more highly productive group also being more inbred.

In this analysis, cows born between 2005 and 2010, with at least one lactation on record were included. Each individual herd was first analyzed separately, and cows were split into quartiles based on their individual level of inbreeding.

Here, you can see the difference in genetics, 1st lactation milk production, and NM$ between the top 25% most inbred from each herd and top 25% least inbred animals from each herd. The most highly inbred quartile of cows was also the most genetically superior group of cows in each of these ten herds.

When we measure actual performance, genetics more than make up for inbreeding depression. The NM$ levels, pounds of milk and milk deviations were all favorable for the more highly inbred, but also more genetically superior group.

This doesn’t mean that a mating resulting in 25% inbreeding is the best option. Rather, when managed properly as part of a program, excellent genetics can outweigh the results of inbreeding depression.

You may not realize that current proof values already account for the bull’s level of predicted future inbreeding. Outcross sires see favorable adjustments. Whereas, PTA’s on sires that are more closely related to the average population are negatively impacted because of these adjustments.


Determining matings

Let’s check out an example to see how managing, rather than avoiding, inbreeding is the best route.

The example below shows three sire options to use for a mating in your herd. Sire 1 and sire 2 both offer high Net Merit $ levels. However, their 8% and 6.5% inbreeding levels would be above the suggested 6.25% industry standard. That alone could eliminate them as potential mating sires in many breeding programs. Sire 3 would be a logical outcross mating in this example, resulting in a mere 1% inbreeding.

Above-average inbreeding levels would result if you mated this female with sire 1 or sire 2. Yet both of these choices would still produce a much more profitable mating over the life of the resulting offspring than a mating to sire 3. This even accounts for the inbreeding depression adjustment within the bull’s proof!

So while 6.25% is often considered the industry norm inbreeding limit, there are often cases when a mating beyond that level of inbreeding still produces the best potential for future profit.


Two ways to manage your herd’s inbreeding

Within your herd, a two-part approach to record management and mating can help maximize your future profit potential.

  • Maintain accurate animal identification

You won’t be able to manage inbreeding if you cannot measure it. If your records are not accurate, it’s impossible to prevent excessive future inbreeding. If an animal is misidentified, a mating you thought would result in a 1%-2% level could easily become 12% or more.

  • Make the right mating program work for you

With accurate identification in place, a mating program can offer a solution to manage inbreeding. Yet, the first step is actually to select which bulls best fit your genetic plan. Select the best bulls available that meet your goals, and keep only those bulls in your tank.

After you’ve selected the best bulls for your genetic plan, the more traditional mating method suggests a 1st, 2nd, and 3rd choice sire from that group of bulls. Each of the three choices would ensure a mating below your set maximum inbreeding level.

When simplicity is also your goal, a “pen mate” is a logical option. This takes the opposite approach of a traditional mating program. Instead of showing the “perfect” mating for each cow and heifer, a pen mate lists the bulls in your tank that should not be used on any given female. This helps you avoid the matings that exceed your set inbreeding maximum.

A pen mate also increases efficiency and accuracy for technicians on big breeding days. A technician can forego the stress of loading five AI guns with five different bulls for five different cows, and then hope to record it all accurately. Instead, s/he can head to the pen to breed with five AI guns all loaded with the same bull that appropriately manages inbreeding for all five cows. The pen mate aids in accurate record-keeping. It gives you peace of mind that your herd’s inbreeding is properly managed.


Inbreeding takeaways

With all of this in mind, it’s important to ask yourself if your goal is to eliminate inbreeding in your herd, or to maximize profit potential.

  1. Dairy cattle inbreeding is on the rise, but so are genetic values and average production levels.
  2. Instead of aiming for zero, or the 6.25% inbreeding industry standard maximum, set out to simply manage inbreeding levels. This way you can capitalize on genetic progress and maximize potential future profits.
  3. Manage inbreeding best by maintaining accurate identification and records.
  4. Utilize simple pen mates for added peace of mind that inbreeding levels will stay below your desired maximum.
  5. Use a group of sires that fit your genetic plan to ensure no mating is a bad one.


Want to improve your mating programs and optimize inbreeding on your farm? Then check out Alta BLUE LINK, the next-generation of dairy genetic planning software that empowers you to make more strategic decisions and directs the course of your best future herd using your real-time data directly from DairyComp. Talk to your Alta advisor to learn more. 



  1.  Smith LA, Cassell BG, Pearson RE. Effects of Inbreeding on Lifetime Performance of Dairy Cows. Advances in Dairy Technology. Volume 11. (1999) 13.
  2. CDCB. Trend in Milk BV for Holstein or Red & White, calculated August 2014. Web. 1 Oct 2014.

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