Aug. 25 2015 11:28 AM
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For genomics to pay, you must use the information to keep or produce a larger supply of genetically superior heifers and remove the genetically inferior. That goal cannot get lost in the shuffle.



by Patrick C. Hoffman
The author is a dairy technical specialist, Vita Plus Corp., Madison, Wis., and a former member of the University of Wisconsin Extension team.

calf in straw bed

Genomic information can also be used to assess long-term inbreeding and to make sure heifer matings to improve production are not at the expense of productive life and future reproductive performance.


Herd scale genomic testing of dairy calves and heifers became commercially available in late 2009 with the advent of the low-cost, low-density genomic test. At the same time, just about everybody in the dairy industry, with the exception of a few geneticists, did not have a clue exactly what the technology entailed. Genomics was an all-new vocabulary, filled with terms like SNP (single nucleotide polymorphism) markers, genomic PTAs (predicted transmitting abilities) and genomic proofs.

We have learned a lot about the practicalities of commercial genomic testing in the last six years. This is especially true at the University of Wisconsin's Integrated Dairy, which started genomic testing its herd of 550 cows and equivalent number of heifers in early 2010.

The wow factor is real


The UW Integrated Dairy has had an open education policy, so all who wish to learn about the advantages and challenges of genomic testing may do so. In addition, a multitude of commercial dairy herds have implemented whole-herd (all replacement heifers) commercial genomic testing and now have lactating cows that were genomically tested as calves. These experiences have given us a lot of practical knowledge about genomic testing.

We're all entitled to our own opinions, but the wow factor of genomic testing is very real.

In its simplest terms, imagine looking at two dairy heifers, trying to sort out in your mind which dairy heifer will be the best in your herd. Then someone hands you a piece of paper that says that heifer A has an 80 percent chance of being one of the top cows in the breed and heifer B is forecast to be below average at best. Clearly, it is very difficult to look at those heifers the same way again.

A second wow factor is that genomic testing gives us an inside view of the genetic diversity within our dairy herds. In some ways, the long-term use of artificial insemination has given us a false sense that all cows in our dairy herds have high genetic potential. Genomic testing and records paint a very different genetic picture.

For example, genomic PTAs for milk yield in our top herds (rolling herd averages greater than 30,000 pounds) commonly range from -1,200 pounds of milk to +2,500 pounds of milk. Because genomic PTAs are only half of the expected expressed breeding value, we would expect milk production of these animals to range from -2,400 pounds of milk to +5,000 pounds of milk or 7,400 pounds total.

Do these genetic principles play out in a real dairy herd? The answer is yes and, thus, the second wow factor.

In a recent genetic audit of the UW Integrated Dairy, the top third of cows had a genomic PTA for milk yield of +972, and the bottom third of cows had genomic PTA for milk of -372. Actual milk yield varied more than 4,800 pounds per cow between the genomic top third and the genomic bottom third of cows in the herd. What is somewhat surreal is that these differences in future milk yield were projected by the genomic test when the calves were 4 months old.

Animal ID challenges abound


One would think that animal identification would be the simplest part of genomic testing, but, in fact, it is one of the greatest practical challenges of genomic testing. Why?

First, a frequent misconception is that the genomic results are only derived from laboratory DNA test. This is not true. Genomic results are a combination of DNA information and parent information. As a result, when heifers are genomically tested, the animal identification system not only has to identify the calf or heifer itself, but also must be able to track and find its sire, maternal grandsire and dam.

Genomic testing services accept three forms of animal identification, which include registration number, USDA AIN or RFID number, or a unique metal ear tag number. But those numbers must be properly cross-referenced to find the animal's sire and/or dam and so forth. The problem is that animal identification numbers are long, easy to improperly record, get lost or are not available at the time of testing.

Challenges are further heightened because part of the genomic test itself is conformation of parents using the DNA information. Thus, a common day-to-day part of genomic testing is receiving information from the laboratory that says, "The parents of your calf are not right." It is not uncommon to have 10 to 20 percent sire or dam conflicts and a resolution is required to get proper genomic information.

So, what have we learned? To implement genomic testing, excellent animal identification and records systems are absolutely required.

Genomics guide decisions


The dairy industry is filled with diverse opinions of how to use genomic information to manage dairy replacement heifers. When making decisions, it is probably better to ask someone who has actually used genomics for a period of time.

Because genomic testing reports on more than 50 different traits for each calf or heifer, it is easy to become overwhelmed with all of the possibilities. Those using genomics will clearly advise on using a very simple approach because you just can't use all of the information at once. In the end, the concept on how to capitalize on genomic testing of heifers is very simple.
For genomics to pay, a dairy herd must use the information to keep or produce a larger supply of genetically superior heifers and get rid of genetically inferior replacement heifers.

Because that's the bottom line, management concepts of using genomic information is ultimately pretty simple. Dairy herds using genomic testing commonly pick a key indicator, such as the PTA of net merit dollars (NM$), and cull any heifer not meeting a minimum requirement prior to breeding. Or, in contrast, they may use embryo transfer to produce more heifers from elite animals.

It is at this juncture in which talking to someone with genomics experience really pays off because using a laboratory number to cull heifers can feel risky. But dairies with genomic experience have shown us that dairy heifers with negative PTAs for milk yield have less than a 15 percent chance of being above average cows in our herds.

Likewise, we have learned that culling genetically inferior animals as extremely young calves is not always necessary. Many dairies prefer to cull genetically inferior heifers somewhere between 6 to 12 months of age. The extra time allows for a more complete assessment of future heifer inventory. Waiting a few months to cull heifers allows dairies to assess genetic potential, calf health events and heifer inventories all at one time.

After the culling decisions have been made, genomic information on each heifer can be reexamined for use at breeding. Genomic results are extremely valuable in mating heifers for specific traits. It also helps you avoid using haplotype carrier bulls on haplotype carrier heifers, which greatly elevates the rate of early pregnancy losses.

Although the science of genomic testing may seem complicated, what we have really learned at the farm level is that keeping it simple leads to the best success.

This article appears on page 529 of the August 25, 2015 issue of Hoard's Dairyman.


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