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How stable are genomic proofs?

Most progressive dairy producers have now adopted and embraced genomics as the best way to make rapid genetic progress.

Yet, we don’t blame you if the recent base change has left you wondering. Are genomic proofs as stable as they once were? Are genomic-proven bulls your best option, even when many daughter-proven sires still offer a great genetic package.

With these questions in mind, we look for answers in the real proof data on bulls across the entire AI industry.

WHAT HAVE WE LEARNED ABOUT GENOMICS?

To illustrate the stability of genomic proofs, PEAK geneticist, Ashley Mikshowsky, analyzed proof figures on nearly 7,800 industry Holstein bulls. These bulls were initially released as genomic-proven sires between January 2010 and December 2016 – and they all have a current daughter proof.

You can find the results in Graphs 1 and 2 below. The darker-colored line on each graph charts the average GTPI or NM$ by initial genomic release date. The lighter-colored line shows the average April 2020 daughter proven TPI or NM$ for those same bulls. The space between the two lines represents the average change for TPI or NM$ from initial genomic release to daughter proof.

Graph 1 illustrates TPI while Graph 2 illustrates NM$

Click image to view larger

As you can see on the left side of the graph, the bulls first released in January 2010 changed 200 TPI points from their genomic debut to their April 2020 daughter proof.

Let’s compare that to the newer daughter-proven bulls, including those released as genomic sires in December 2016. For these bulls, you see only a 91-point TPI difference from their first genomic proof to their April 2020 daughter proof.

This means the stability in GTPI from genomic release until daughter proofs has more than doubled – or the change is less than half! You also see the added bonus of genetic levels on a continual rise!

Click image to view larger

The same goes for Net Merit $. Check out those results here in Graph 2.

Industry bulls first released as genomic-proven sires in January 2010 dropped, on average, 112 NM$ from their first release until their April 2020 daughter proof. Whereas, the most recent bulls to get a daughter proof – those first released as genomic sires in December 2016 – only changed a mere 37 NM$ from their initial release.

Looking at these results, your argument might be that dairy genomics are still inflated. Yes, and while that may still be true, the gap between genomic and daughter proofs has clearly improved since the start of genomics.

LET’S DIG DEEPER INTO GENOMIC PROOF STABILITY

Because two graphs may not have you convinced on the stability of genomics, let’s check it out from another perspective.

Graph 3 and Graph 4 are based on additional proof data analyzed by PEAK geneticist, Ashley Mikshowsky. She evaluated 971 industry bulls released as genomic-proven sires in 2016. This is to see the distribution of change from genomic proof to daughter proof – for both TPI and NM$. She uses this age group specifically because those bulls released in 2016 now have daughter proofs for production, health, and conformation traits.

Graph 3 shows the distribution of change for TPI and Graph 4 shows the distribution of change for NM$. The orange bar is in place to show the reference to a change of 0.

Click to view larger

The bulls released in 2016 changed an average of -115 TPI points from their first release in 2016 to their daughter proof in April 2020.

More than 140 of these bulls have a daughter proven TPI within just thirty points of their original genomic TPI. And only thirty bulls from the entire group of 971 changed more than 300 TPI points.

Click to view larger

We see the same trend for NM$ in Graph 4, based on analysis of the same 971 industry bulls. The average sire released in 2016 changed just -70 NM$ from their first genomic proof in 2016 to their daughter proof in April 2020.

Nearly 160 of the 971 bulls held steady within the small 20-point swing from genomic to daughter-proven NM$. Just 13 bulls changed more than 300 NM$.

WHAT ABOUT YOUR GENETIC OPTIONS TODAY?

Still debating whether your best bet is to go with the higher reliability daughter-proven sires? Or do you prefer to accelerate your genetic progress with genomic-proven sire groups? Take a look at the tables below, using NM$ for a neutral comparison between daughter proven and genomic proven sires.

The top daughter-proven sires currently average a highly reliable 621 NM$. Whereas, the top, readily-available genomic-proven group offers a much more enticing 776 NM$ average. That’s a $155 advantage over the daughter-proven choices!

Even the top-ranking daughter-proven sire, AltaTOPSHOT, who is among the top daughter-proven sires in the entire breed, still doesn’t match up to the average of the genomic-proven group.

Some bulls will gain points and some bulls will lose points between their genomic proof and daughter proof. That is inevitable, and the data proves it. Yet we can also see that the stability of genomics continues to improve.

Keep in mind that your odds are essentially zero that every single bull atop the genomic-proven list would drop to rank lower than the current list of daughter-proven sires.

WITH YOUR GENETIC CHOICES, KEEP THESE POINTS IN MIND:

  1. Genomic proofs are still slightly inflated. Yet, even with a recent base change update, we see less change from genomics to daughter proven TPI and NM$ over time because of model improvements made along the way.
  2. Despite an average drop for TPI and NM$ from a bull’s genomic to daughter proof, you will still make faster genetic progress using a group of genomic-proven sires than a group of daughter-proven sires.
  3. Make sure the genetic progress you make is in the direction of your goals. Select a group of genomic-proven sires based on your farm’s customized genetic plan. Emphasize only on the production, health or conformation traits that matter most to you to boost your farm’s future progress and profitability.

 

Proof analysis and graphs provided by Ashley Mikshowsky, PEAK Geneticist

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New in April 2019: Crossbred evaluations

The Council on Dairy Cattle Breeding (CDCB) will now release genomic evaluations for crossbred animals. In recent years, increased crossbreeding, paired with increased adoption of genomic testing in commercial environments, has led to the demand – and accessibility – to calculate genomic evaluations on crossbred animals.

What does this mean for you?

You can expect genetic value estimates for crossbred animals to be slightly less accurate than purebred estimates. CDCB will calculate crossbred genomic predictions as a weighted average of the respective single breed evaluations. This means that you’ll see improved accuracy for some crossbred animals already receiving evaluations. For example, animals that are about 85% Jersey and 15% Holstein, will have greater accuracy, because instead of being evaluated as only a Jersey, their Holstein proportion will now more accurately be accounted for within that animal’s evaluation.

Another result of this update is a slightly increased accuracy of purebred evaluations. This is because crossbred animals with a BBR of <=94% will not be included in individual breed evaluations.

The details

There are five main breeds of dairy cattle with genomic evaluations in the US: Holstein, Jersey, Brown Swiss, Ayrshire, and Guernsey.

Currently, BBR, which stands for Breed Base Representation, is an estimate of the percent of DNA contributed to that animal by each of these five breeds. Going forward, animals will be divided as follows:

  • BBR >= 94% will be defined as a purebred.
  • BBR >= 90% will still be evaluated with the breed of its highest BBR.
  • BBR < 90% will be evaluated in a blended group, and their predictions will be based on a weighted combination of marker effects from the different comprising breeds.

If an animal has a BBR < 90%, CDCB will most often label that animal as the breed of its highest BBR. The exception to this is first generation crossbreds with a BBR of the highest breed less than 55%.

Some traits are only evaluated within certain breeds or are difficult to compare across breeds. Because of that, crossbred animals will have type traits, calving traits (Holstein and Brown Swiss only), and health traits (Holstein only) from one breed only – they will not be blended.

There will also be no haplotypes released for the crossbred animals at the April 2019 release.

Keep this in mind…

If you implement crossbreeding as part of your genetic strategy, these new crossbred evaluations are big news. This update will provide you with more accurate information to make better decisions, regardless of your herd’s breed composition.

Want to learn more?

Check out the webinar addressing the new crossbred evaluations from CDCB.

 

Published in partnership with Ashley Mikshowsky and Doug Bjelland, PEAK Geneticists

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Haplotype & genomic reliability updates

Based on new findings from the Council on Dairy Cattle Breeding (CDCB), one new haplotype will be added, and two others removed, starting with December 2018 proofs. Alta Bull Search and Alta GPS will be programmed according to this new information.

A new Holstein haplotype, HH6, was recently identified in France, and is currently found in about 0.5% of animals in the US Holstein population. Mating two HH6 carriers is expected to yield a 7%-11% drop in conception rate.

Further research into the JH2 haplotype in Jerseys and the BH1 haplotype in Brown Swiss showed no significant fertility losses on matings between carriers. This, paired with the fact that researchers could find no causative mutation on these two haplotypes, means they will no longer be reported.

Gene test advancements

In addition to new and discontinued haplotypes, the reported haplotypes are also gaining accuracy. PEAK Geneticist, Doug Bjelland, compares the improved accuracy of haplotypes to locating a house on a map. The previous way of recognizing haplotypes essentially showed us which street a house is located on. Now, because of gene test advancements for causative mutations to determine haplotypes, we know exactly where on that street a house is located.

Upgraded genomic reliability

Improved genomic accuracy also extends beyond the gene test. Researchers are now using an 80k SNP chip. This means they are using nearly 80,000 markers on the genome, up from the previous 60,000 used since 2014.

The additional markers, combined with a new reference genome, give genomic predictions about a 1% – 2% improvement in reliability.

What does this mean for you?

We want to keep you up-to-date on the newest genetic findings. Updates on haplotypes and genomic accuracy are one part of that. Because the haplotype updates will be accounted for within the AltaGPS program, you can have confidence that potential carriers of two bulls will not be mated together. That means your clients are protected from any potential fertility losses that could result in mating two carriers of any given haplotype.

Improved genomic accuracy should give you, and your clients, even more confidence that genomics and genetics continue to advance at more rapid rate. It’s as important now as it ever has been, to ensure your clients select genetics according to their customized genetic plan so the progress they make aligns with their current situation and future goals.

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