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Genomics - FAQ

Why are there so many new high genetic merit bulls?

With genomic selection now available, new Holstein sires graduated that would not have been available for another two or three years if we had continued to use the old sire evaluation system.  The advantage we gain from genomics is that we can now predict the genetic merit of our you animals at a much higher reliability earlier than we could with simply the use of traditional parent averages.  This gives dairy producers the potential to make significant genetic progress in their herds.


What is genomic selection?

Genomic selection is predicting the performance of an animal's offspring based on the DNA of that animal. Recent breakthroughs from industry-supported research have resulted in new tests that look at thousands of DNA markers of an individual bull or cow. The DNA markers of the individual animal are compared to the marker profiles of thousands of bulls and cows with millions of offspring with known performance for the various traits of interest. This allows an estimation of breeding values of an animal based on associations between DNA marker profiles and milk yield, Somatic Cell Score, Productive Life and other important traits.


What is a genomic genetic evaluation?

A genomic genetic evaluation includes the information from the DNA marker testing of that individual. The evaluation also considers parent or pedigree information and may also include progeny information or, for females, performance information. The USDA-AIPL began calculating a genomic Predicted Transmitting Ability (genomic PTA) for Holstein and Jersey animals with the January sire summaries.


How can I tell if a bull is genomically proven?

If a bull is genomically proven and has no daughter information in his proof.


Can I determine what portion of a bull's proof is based on genomics? 

No. You will see only one PTA or Standardized Transmitting Ability (STA) for each trait. These PTAs and STAs will consist of parent, genomic and daughter information depending on which type(s) of information the bull has available. USDA-AIPL weights each of these appropriately.


What is the expected reliability of a genomic proof?

We can expect most bulls with genomic proofs to range between 62 and 72 percent reliability for all traits.


Is it safe to use bulls at these reliability levels?

Yes, it is safe to use bulls at these reliability levels. Reliability level should determine the amount of use each bull receives. Also, it is important to use a group of genomically-proven bulls.


How does genomic reliability compare with number of milking daughters?

The genomic breeding value for a bull without any milking progeny has an average reliability of 68 percent. This is comparable to a normal progeny tested bull with 50 milking daughters. It is anticipated that the reliability levels will increase for bulls with no milking progeny as more animals are genotyped in the future.

For bulls with milking progeny, the genomic contribution to the PTA increases overall reliability of the PTA. The amount of increase in reliability varies by bull and is mostly dependent on how many milking daughters the bull has. Typically for a bull with 100 milking daughters, the increase in reliability is equivalent to approximately 10 more daughters.


Are all breeds utilizing genomics?

Currently only the Jersey and Holstein breeds have published genomic proofs. Other breeds such as Brown Swiss and Guernsey have genomic projects underway.


How does genomics impact crossbreeding?

Several who considered or tried crossbreeding did so for immediate impact on some "challenging" traits for the Holstein breed. For example, many producers have been frustrated with the lack of progress in Daughter Pregnancy Rate (DPR). This trait is relatively new in dairy genetics time (first reported in 2003) so procurement staff have not had ample time to procure sires specifically for it. DPR has also "lagged" due to low heritability and low reliability. Therefore, in some instances crossbreeding has been used as a quick fix.

Now, with genomics, procurement staff can realize the true effect of traits like DPR sooner. When selecting a mating sire or dam of future sons, genomic tests on those animals reveal an accurate description of their DPR at a much higher reliability. Holstein procurement staff that select intensely for these kinds of traits can utilize genomic evaluations to produce faster genetic improvement. So does genomics erase crossbreeding? Most likely not, but it does allow the Holstein breed to address a few troublesome traits that prompted some to start crossbreeding in the first place.


Why should I use genomic bulls?

The answer to this question is the same as the question, why use A.I.? Quite simply, a producer should use genomic bulls to use the best genetics available. Many of the best bulls for a particular trait will now have evaluations based on genomic tests and not on progeny test information.  Many genomically-proven sires will have lower reliabilities, so that should be considered and usage spread over more bulls. After that, use the best bulls to make the fastest genetic progress.


Why do the PTA numbers look so big?

Right now, genomics identifies the superior bulls that would typically have received daughter proofs in 2013, 2014 and 2015.

It is also important to remember that every five years the USDA-AIPL performs a base change. In simple terms, this re-adjusts the proof numbers for genetic progress. It keeps the numbers in a "normal" range or prevents PTAs from getting too large. Therefore, genomically-proven sires should have large PTA numbers as they represent genetic progress.


Will reliabilities stay the same or go up?

Currently most reliabilities range from 62 to 72 percent for genomically-proven sires. With that in mind, you may wonder why the reliabilities differ. The answer is some bulls come from more "popular" families. If more of the sire's family members have been genomically tested, the reliability of the sire is higher. If pedigree information was not recorded and no direct family members were genomically tested, his reliability is lower.

The reliabilities of genomically-proven sires continue to increase based on the number of animals in the breed that have been genomically tested. However, the increase in overall reliability is now small due to diminishing returns. For instance, the 1,000th animal tested increased the overall reliability for genomic evaluations more than the 31,000th. Without improvements to the calculation methodology and/or larger marker panels, I do not foresee the average reliability increasing much over 75 percent.

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