Genomic testing has role in elite and commercial herds

Several years ago genomics burst onto the dairy scene and has been bringing changes to the science of breeding top quality dairy cows and bulls. The science has continued to advance in the last few years and many farmers are wondering if there is a way they can use it on their farms.

Dr. Tom Lawlor, director of research and development with Holstein Association USA, spoke to an audience of dairy producers at World Dairy Expo, and noted that genomic testing is quickly becoming more cost-effective.

Over 115,000 animals have so far been genomic tested, he said, and with cheaper tests coming down the road, that number is certain to grow. The genomic test, he explained, identifies a set of genetic markers along each chromosome that an animal received from its parents. By tracking these segments and then matching up those markers with the actual performance of an animal and its offspring, science is able to establish the value of a particular set of markers.

Another use of the science, he said, is that it allows people to determine how closely related two animals are. Tests measuring 3,000 markers (the 3K test) are now available for about $43, Lawlor said and soon that same price range will cover a 6K test for 6,000 genetic markers. A 50K test that once cost $250 is now down to $125 and a 770K test now retails for $250.

Top genetic animals will likely continue to be tested with the higher density tests, he said, while the 3K test will be discontinued in favor of the test with double the markers - the 6K test. Those lower density tests will have their greatest value for screening programs and commercial dairies.

The key benefit of a genomic test, said Lawlor, is to get an earlier and more accurate measure of genetic merit. Knowing where an animal ranks in the herd and within the breed allows the producer to make important management decisions on how much money to invest in an animal and which ones to consider culling.

The genomic test can help the farmer determine which heifers are better than might have been expected, given the performance of their parents, and which ones have a lower genetic potential than their parentage would suggest. "Almost always, the best time to test an animal is as early as possible," he said.

Most testing of females is done prior to 15 months of age. Which animals to test and which test to use will depend on the planned use of the information. Farms that are planning to find the elite animals so they can be used for sires, for flushing and embryo transfer will test differently than a commercial herd manager who is looking to maximize the value of his herd replacements.

Lawlor said that the best testing strategy for finding an elite animal will involve sorting animals by TPI (total performance index) or NM$ (net merit) and selecting animals within the top 20 to 25 percent of the breed. That would be a PTPI or 1700 or NM$ of $300, he said. Depending on the number of animals owned and the financial resources at hand, the herd owner could plan on spending about 60 percent of the budget on the low density genomic test - the soon-to-be released 6K test - and then re-test the best animals from that screening with the 50K test.

Several hundred Holstein operations are already using this kind of process to select their best animals, he said. "But you need to think of it as a program you will routinely use rather than cherry picking certain animals now and then," he said. "It must be continued."

But for commercial farms, routine testing of heifer calves and yearlings can be a cost-effective strategy for enhancing the genetic potential of replacements, he said. Early culling of inferior replacements will save all the money that would have gone into feeding and housing those animals. Lawlor explained that the value and profitability of genomic testing increases with greater culling opportunities.

This may be the case on farms where there is an outstanding calf rearing program or where sexed semen is used, resulting in an oversupply of heifers needed as replacement for the farm. Lawlor said 73 percent of the genomic testing is done on animals that are less than 15 months of age.

Sometimes a herd owner may not have any parentage information on a group of heifers. "Without any information they all appear the same," he said, "but genomic testing will pull them apart." Culling the lowest animals, based on genomics, will raise the average net merit of the others significantly.

If the opportunity exists to cull more heavily, that net merit value rises even more, resulting in extra revenue from the remaining animals that have been selected to keep. "The more selective you can be, the more profitable it becomes," he said. "That way you're not spending money on the poor ones."

Another value to genomics is that it can definitively identify a sire. Many times animals are not from the genetics they are supposed to be from. "If a sire is genotyped we'll find him. In commercial settings without sire information 47 percent of the time the correct sire will be identified." As time goes on, and genomic testing improves, that number will rise even higher, Lawlor said.

Roughly half the time, he said, the sire will be identified and the genomic prediction will become more accurate. "It's very profitable to genotype animals if we don't know anything about them," he said. The decision to genotype animals with no pedigree is a "no-brainer," he said.

Gains in genetic merit, in those cases, will more than pay for the genotyping costs, he said.

But if a farm has good pedigree information is it still cost effective to genotype them? Lawlor said the parent average is a good initial sorting tool in such herds, but genomic testing adds refinement. It is valuable if the herd owner is looking to cull low-end animals and to make precision breeding decisions.

"Genetic testing gives you a better prediction," he said. For heifers with known sires, genotyping the bottom 50 percent was the most profitable strategy, if a 20 percent culling rate was available.

The testing of 100 percent of the animals was recommended only if a 30 percent culling rate was available. "If the culling opportunity is low, target the low-end animals to test," Lawlor said. "If a high culling rate is available, the return to testing all animals is best."

Genetic testing will only improve, as time goes on, he said, but each new generation will need new Dairy Herd Improvement (DHI) data on things like type and herd health, he said. "It won't replace performance testing."

In the five years since genomics became available, all bulls going into the commercial breeding system are now genotyped. By the year 2013, bull owners will be able to test their own bulls.

Lawlor said there is no doubt that genomics has changed the industry and there are concerns that it will reduce DHI testing. It has already reduced progeny testing through young sire programs. "If there is a reduction in the amount of information we have geneticists will have to take another look," he said. It's the information on daughters that allows the genetic tests to be matched up with certain performance traits.

"If the volume of information doesn't meet that need, the U.S. genetics industry will have to find a way to pay for that information," Lawlor said. "We need a continuous supply of new information."

The Holstein breed has the largest reference population and this makes genomic testing the most reliable for Holstein animals. There is also a pretty good base of information for Jersey animals, he said, and slightly less for Brown Swiss cattle.

In order to test crossbred dairy animals the genetic test would have to be able to relate to the actual gene on the chromosomes and science isn't at that point yet, Lawlor said. The fact that 5,000 or so Holstein animals are tested per month makes the genomics in that breed so much more reliable.

There are some concerns that genetic testing will narrow the breed (or breeds) and Lawlor said that this is where it will be valuable to the industry to have various groups in different countries, since that will allow some opportunities for outcrossing.