Read the Progressive Dairyman Canada digital edition
advertisement

Inbreeding: A consequence of life on the genomic highway

Sophie Eaglen for Progressive Dairyman Published on 29 November 2018
winding road

The rapid rate of genetic progress may leave some dairy producers questioning the risks and rewards of inbreeding and how to manage it at a herd level.

Imagine yourself on the Autobahn. There is no speed limit, so you can drive as fast as you desire. What car would you want to drive? Would you feel comfortable driving your current car at max speed?

advertisement

advertisement

Now picture yourself on the NASCAR racetrack. Are you still in your current car? Or did you change to a car that was made for speed? Perhaps you’d choose one with all the tools that allow you to ramp up while staying safe.

Speaking of safety, wouldn’t you want to wear a helmet and have an expert team monitoring your every move? Although we all like a certain amount of risk, most of us will choose to assess the risk and manage it to protect ourselves from injury.

Genomic selection has put us on the Autobahn. We may even be on the NASCAR racetrack already.

Fact is: We are going fast. Very fast. It’s fantastic, but it comes with certain risks. And those risks have to be assessed and managed so we keep our industry safe.

As yet another proof run concludes, the Council on Dairy Cattle Breeding (CDCB) has made updates to the genetic and phenotypic trends for U.S. dairy cattle.

advertisement

The August 2018 trendlines for all Predicted Transmitting Abilities look impressive. The Net Merit PTA trend shows an almost exponential growth since the implementation of genomic selection in 2010 (Figure 1).

Net merit PTA values for Holstein or Red & White

It demonstrates selective breeding is going at a faster pace than ever before, which isn’t news to anyone working in dairy cattle.

We certainly have our foot on the gas. But an equally fast-climbing trendline is shown by a measure we aren’t always sure how to interpret: inbreeding (Figure 2).

Inbreeding trend for Holstein or Red & White genomic bulls

Genomic inbreeding coefficients of young bulls, especially in the Holstein breed, are climbing at a remarkable rate since 2015, leaving us with a group of young genomic sires that are, on average, 13.27 percent inbred.

advertisement

Let’s say while driving on that racetrack, we see the temperature of our engine rising rapidly. Is that bad, or is it simply a consequence of driving fast?

What is inbreeding?

Anyone who has had a biology class or two will know the common definition of inbreeding: the interbreeding of (closely) related individuals. The percentage of inbreeding increases depending on how closely related the parents are to each other.

For instance, if a female is bred back to her sire, she has a high coefficient of inbreeding. If her sire is also related to her cousin, that’s an even higher percentage of inbreeding than the original sire-daughter mating.

While we previously predicted inbreeding based on pedigree, DNA genotyping now allows us to observe the actual inbreeding of the animal at DNA level.

We call this genomic inbreeding, and it is a more accurate estimate of inbreeding than pedigree inbreeding.

Is inbreeding bad?

Most people will have an instant negative connotation when they hear the word “inbreeding.” After all, we were taught inbreeding leads to the expression of undesirable genetic defects.

That said, geneticists will tell you inbreeding isn’t always bad. In fact, inbreeding or its milder form, linebreeding, is a common practice in crop, poultry and pig breeding. How does that work?

On a DNA level, selective breeding and inbreeding have the exact same effect: It leads to more genes having the same identical forms of a gene (a so-called allele) on both chromosomes. We call the state of these identical alleles “homozygous.”

If this occurs in a good gene which positively affects a certain performance, the inbred or selected animal will show increased performance.

However, if a bad gene gets two identical copies of the same allele, this may lead to decreased performance, illness or death. So inbreeding, or the creation of identical segments of DNA, can actually lead to very positive results – if it occurs at the right locations in the genome.

The issue with inbreeding, or mating relatives who have large proportions of their genome in common, is: One increases the chance of creating homozygosity at both the good and bad genes alike.

So inbreeding could be good or bad; it depends where the chips fall. The issue is: Currently, we don’t know where they fall. In fact, to a large extent, we don’t even know where the chips should fall yet.

How did we get here?

By selective breeding (the mating of two individuals with high genetic merit), we aim to increase the homozygosity of the “good” genes. This has worked well for us.

Since the introduction of A.I., and especially genomic selection, genetic progress in dairy cattle has rapidly increased.

With the introduction of genomic selection, it was predicted genetic progress would increase due to the considerable reduction of the generation interval as well as the increase of accuracy. And this prediction certainly came true.

It was also predicted, however, that inbreeding would decrease. After all, bull studs could now obtain DNA profiles from every dairy calf they’d want, giving them the opportunity to seek out animals with high genetic merit yet low relatedness.

This would increase the chance of proliferating the good genes while avoiding the bad. That prediction wasn’t as accurate. What happened?

What researchers had not taken into account was the incredible rise in economic value of young, high-merit genomic animals.

Genomic selection worked so well for dairy cattle the dollar value of elite animals rose to levels previously unimaginable. Quickly, the race for the highest GTPI animals led to a higher degree of mating close relatives.

This wasn’t just a matter of economic value outweighing the risk of inbreeding as much as it was the consequence of a highly competitive market.

Interbreeding family members became a fast track to high-merit animals, as accepting a genetic lag with the competitor wasn’t an option.

The current factual situation is: Where genetic theory recommends an inbreeding level of 6 percent, we are more than double that in young genomic bulls and have just passed 7 percent in the national U.S. cow population.

By comparison, the current average level in the Dutch cow population, with a much less competitive market, is only 4.5 percent.

When do the bad things happen?

So we are finding ourselves on the Autobahn going 320 kph. When does our car break down?

Some people will say it isn’t a problem that the bulls are inbred, as long as their daughters are at a reasonable level of inbreeding.

With the current cow population at 7 percent, that is still a possibility but requires each producer to manage the inbreeding in his herd.

Others say the increased performance of high-merit animals outweighs the negative effects of inbreeding. That may be so, but most studies on this topic are either simulations or stem from periods in which inbreeding levels were much lower.

The honest answer to the question here is: We don’t know.

We know significantly more about genetics than we did 10 years ago, and we are learning more each day.

However, to say we should just proliferate the very best genes so we can see a bigger genetic gain would be the same as saying we should just keep our foot on the gas and hope for the best.

We have learned enough about the genomes of our cattle to do amazing things, but we don’t have all the answers yet. The rate of inbreeding has surpassed the rate of research, which currently puts us in unknown territory.

Can we avoid inbreeding?

No. If we want to keep breeding elite animals and keep our current rate of genetic progress, it is very hard to take our foot off the gas.

As a dairy producer, any bull in the current active sire list of any stud will likely be related to your herd, and inbreeding is almost unavoidable without a severe hit to genetic progress.

If you do genomic testing, you will probably see your higher-tested animals will also have higher genomic inbreeding coefficients, and that is OK. If we have to keep going at 320 kph, the key is that we do so in a car with the tools to manage that speed.

The great thing about the genomic era is: It provides plenty of opportunity for genetic companies and dairy producers to manage issues like inbreeding.

The solution is management

All genetic companies employ geneticists who know inbreeding does not have to be bad as long as it’s managed.

The current rate of inbreeding leads to discussions within companies as well as among universities and companies on how to create tools that allow us to keep our foot on the gas while driving safely.

These will become available to dairy producers. As a producer, it’s important to understand inbreeding is currently present, but you can keep your car on course if you take control of the steering wheel. Here are a few recommendations to do just that:

  • Ask your genetics sales rep for the current inbreeding levels in your herd so you are aware of the current situation.

  • Ask your genetics sales rep for tools to manage the inbreeding levels in your herd. Genomic testing is an example of one such tool. Visualized trendlines can help you manage herd inbreeding levels even when genomic inbreeding coefficients of young genomic bulls increase.

  • Use a mating program to keep your average inbreeding level steady. You can also ask your rep which sires are cleaner to your herd than others. Often, sire books only list two generations of bulls, while the co-ancestry may be at deeper levels. Mating programs can help you find the bulls most and least related to your herd.

  • Consider bringing in foreign genetics such as Dutch or New Zealand genetics. Besides the benefits of adding more genetic diversity to your herd, heterosis could also be a positive effect of foreign genetics.

In conclusion, enjoy breeding cattle in an era where genetic progress is at incredible speed. Just make sure to keep your eyes on the road and your herd in the safe zone.

Ask your genetics rep about the average inbreeding in your herd and what tools are available to manage it.

Educate yourself and keep control. This ensures your herd remains healthy and sustainable so that the next generation of producers can be race champions as well.  end mark

PHOTO: Winding road. Photo courtesy of Getty Images.

  • Sophie Eaglen

  • Sales and Marketing Manager
  • CRV USA

Before commenting on our articles, please note our Terms for Commenting.

LATEST BLOG

LATEST NEWS