April's genetic evaluations ushered in a new era

by Chad Dechow
The author is an associate professor of dairy cattle genetics at Penn State University.

Last month brought some fairly significant changes to our genetic evaluation system that will have long-term impacts on genetic selection opportunities for dairy producers. The two largest changes involve transitioning our genetic evaluations from USDA's Animal Improvement Programs Laboratory (AIPL) to the Council on Dairy Cattle Breeding (CDCB) and allowing dairy producers to genomically test their own bulls.

An agreement was signed by USDA and CDCB on March 27 that began a two-year transition of dairy cattle genetic evaluations to CDCB. The two-year period is intended to create a smooth transition and provide time to work through any challenges with the new system. The CDCB currently has a two-member staff dedicated to running genetic evaluations and expects to add additional personnel in time. Both current staff members were previously part of AIPL which has provided genetic evaluations for decades. The April genetic evaluations were generated on the same computers and in the same building as has been done previously, but it is expected that CDCB will invest in its own system over time. Genetic evaluations will be labeled as "USDA-CDCB" during the transition period.

The research scientists at AIPL will continue to be involved with dairy cattle genetic research long after the evaluations are moved to CDCB. These scientists will help to develop new traits for evaluation, continue to develop the computer software needed to facilitate genetic evaluations, develop new and improved methods of conducting genomic evaluations, and many other tasks that help our system run so effectively.

Funded by genomic testing
The funding of CDCB genetic evaluations is expected to come from genomic testing fees. These fees will be an additional charge added to the basic laboratory cost of genotyping animals. A fee structure has been developed that varies depending on the sex of the animal being tested and whether the owner of an animal contributes phenotypic data to the genetic evaluation system (see table).

Fee schedule for genomic evaluations

U.S. dairy producers that meet certain DHI testing and type classification thresholds are considered "Total Program" participants, whereas U.S. herds not participating in either DHI testing or type classification are considered "Nonmembers." There is also an intermediate "Member" category for herds that meet some, but not all, recording criteria as shown in the table. Costs for international owners vary but are generally higher than costs for U.S. breeders.

I won't go through the cost structure in great detail here, but the general costs for testing females have been kept low to encourage as many cows to be tested as is feasible. "Total Program" participants will incur no additional fees other than the lab genotyping costs, while there is a $5 surcharge for "Nonmembers." Bulls that are tested before they are 15 months of age will cost $20 ($200 for "Nonmembers"). U.S. producers or organizations selling semen from a bull will be charged an $800 fee.

Opinions still vary
There remains a strong difference of opinion relating to the transfer of evaluations from USDA to CDCB and the fee structure that has been developed. Without going into great detail, some are concerned that the structure is prohibitive to breeders who want to market their own bulls and does not reward data providers who are not involved with genomic testing.

Whether every bull that is genomically tested should have their evaluation made available has also been debated. Many of the top ranking sires are only a couple of months old and will not have semen available for some time. There are also some who believe they should be able to keep genomic PTA (predicted transmitting ability) on their own animals private if they so choose. The counterargument is that genomic predictions are facilitated by a database that no one entity owns and so genomic PTAs should be available.

Genomic PTAs were made available for all bulls following the April evaluation, including over 20,000 bulls less than two years of age. It is not yet clear how evaluations for young bulls will be handled in the future, and there are issues to resolve with how to handle foreign bulls that do not have an official proof in their home country.

Bulls and cows from the Ayrshire breed can now receive genomic evaluations. Testing by AIPL indicates that reliability will improve by an average of 8 percent across all traits for young Ayrshires that have been genomically tested, with some traits (milk yield, protein yield and stature) receiving a boost of 16 percent. This development is particularly valuable for a breed such as the Ayrshire because it simply does not have a large enough population to facilitate robust progeny testing programs.

An additional modification was made to tweak the weights applied to an animal's PA (parent average) versus their DGV (direct genomic value). DGV and PA are combined to create the official genomic PTA, and the adjustments lowered the maximum weight allowed on the DGV to 85 percent for yield traits and 80 percent for type traits from the previous maximum of 90 percent for both. This change had a relatively small influence on the ranking of young bulls but did lower Lifetime Net Merit $ for the top young bulls to some extent. This change is expected to result in more stable genetic evaluation rankings over time.

The maximum weight placed on a sire's traditional genetic evaluation, on the other hand, was raised from 99 percent to 99.9 percent which only impacts bulls with many thousands of daughters and by a relatively small amount. A final change to the genomic evaluation system involves the availability of a new genomic chip that adds a small amount of reliability to genomic evaluations . . . that will be discussed in a future column.

One subtle difference you may notice is that calving ease is now reported to a decimal point rather than integers, which provides a slight improvement in the accuracy of sire selection. See the April 25 Hoard's Dairyman Bull List for the actual ranks.

First-run thoughts
Despite some down-to-the-wire negotiations among CDCB members, our first run of industry conducted genetic evaluations appears to have gone relatively smoothly. The two-year transition period will hopefully allow us to work through any remaining challenges, and I expect there will be continued debate on some issues.

Perhaps the largest change in our genetic evaluations is that we are beginning to transition from a tax-payer-funded to an industry-funded system. I think this could be an exciting time for breeders who will know more about their young bulls than at any time in the past, but marketing bulls is not a trivial challenge and it remains to be seen how well our breeders will be able to capitalize.

This article appears on page 385 of the May 25, 2013 issue of Hoard's Dairyman

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