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Improved genomic selection for health and other traits

Jen Bradley for Progressive Dairyman Published on 31 December 2018
genomic profiles

In August 2018, six new health traits – milk fever, displaced abomasum, ketosis, mastitis, metritis and retained placenta – were introduced to the Net Merit index (NM$), adding to a growing list of low heritability traits available in the last few years.

Paul VanRaden, a research geneticist at the USDA-AGIL, says much of the talk in the industry now is how to estimate the economic value of these traits, especially since as more traits are added, producers have to make decisions on which way to go when selecting ones that will be most important in their genomic profiles.

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Current research has been published by VanRaden and his colleagues Kristen Parker Gaddis and John Cole last year. VanRaden presented it to a full crowd at the 2018 World Dairy Expo in October. He said the data he shared at the seminar was produced using up to 2 million records from more than a million cows from the Council on Dairy Cattle Breeding’s (CDCB) database.

Records needed

Developing practical traits for genetic selection requires accurate records to be kept at the farm level and for the resulting data to be shared.

“If you don’t send in records saying your cows in your herd have mastitis, that data is not usable until we have a certain incidence rate,” VanRaden said.

Dairy producers have been concerned about the security of and access to data from their farms. He explained it’s not stored at the USDA but, instead, at the CDCB. “They do not release that to third parties,” he assured the crowd. “We only have 10 percent of the records for health traits and hope more people will be contributing.”

VanRaden noted additional records on the same cows are also very helpful. The highest heritable traits (mastitis and metritis) also had the highest incidence rate, he said, adding that more records will help get better, more accurate predictions. The traits are available only for Holsteins as of now but, as more data becomes available, VanRaden said that will change too. Jersey herds have been sending in more data, which has been encouraging.

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Data is put through similar equations as used for the other traits, to test for traditional reliability and genomic reliability. He said some of the health traits are showing up to 50 percent reliability, which isn’t as high as other traits but better than not having it at all.

Economic impact

VanRaden said the estimated cost per case is $38 for milk fever, $178 for a displaced abomasum, $28 for ketosis, $72 for mastitis, $105 for metritis and $64 for each retained placenta.

Overall, he said, genomic selection is a very successful tool for producers, adding that “genetic gains are cumulative, but progress is permanent. That’s a nice feeling.”

The next step, he said, is the multi-trait evaluation, mixing the new health traits with the ones they have been measuring for a long time to have even more reliable data.

In these new traits’ research on economic impact, the team did include costs such as vets, farm labor, drugs and discarded milk. In addition, some expenses are already accounted for in other traits, such as declines in production, fertility and longevity.

The total direct cost was used as a percentage of the health traits. Of these six, the mastitis Predicted Transmitting Ability (PTA) accounted for 33 percent of the value in total genetic cost but, as a percentage of net merit, all of them had less than 1 percent each. Compared to other traits, these direct costs do not seem to be so large on most farms, VanRaden said.

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He did add putting mastitis resistance in as a trait as a reminder that positive PTAs are favorable.

“We went for 60 years before adding new traits in the old days, and now we’re adding new traits every year,” VanRaden said. “Genomics has made this possible.”

What we’ll see next

Age at first calving, residual feed intake and heat tolerance are the next three traits being studied to add to the NM$. VanRaden explained many people have been taught to select a profile for the highly heritable traits and manage the traits that have lower heritability rates.

“With genomic selection, however, we can get accurate rankings early in life and do the selection with greater than 30 percent reliability of these new traits with genomics versus what we could get from just pedigrees,” he said.

Data collection costs can be shared across millions of animals, too, he explained. Instead of privately testing each group of animals, the data now can be translated and predicted for the whole population because of genomics.

For example, for age at first calving, a large database of 23 million records is available already, and genomic reliability is 66 percent for Holsteins. “That’s certainly worth selecting from,” VanRaden said.

Heat tolerance is being looked at, using 79 million lactations to estimate. He said genetic rankings may change if the climate is different for the daughter than her mother or for daughters of the same sire in different regions of the country.

The cost of evaluating this is minimal, however, based on the data he and his team already have.

He explained the more expensive trait to collect data on is feed intake. The University of Wisconsin has been a leader in that, VanRaden noted. It took a lot of money to collect about 5,000 records for 4,000 cows, and he stressed again it really takes new data coming in to go live with the trait.

“That’s the focus at the moment, to get more data,” he said. “The moral of the story is we’re all in this together to make more genetic progress. Genomic selection is a very successful tool.”  end mark

Jen Bradley is a freelance writer in Chilton, Wisconsin.

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