Genomics rapidly evolving; unanswered questions remain

The latest USDA genetic evaluations ushered in numerous changes just three months after January's major base change. Among them were imputed female evaluations and cow evaluation adjustments which put genomically tested female evaluations on a more even playing field with genomically tested male counterparts.

While all these changes might have been scientifically sound, they came as a surprise to most breeders since there was little advance notice regarding the changes prior to the April release. The lack of notice combined with the fact that the majority of genomically tested females dropped due to the corrections caused a great deal of frustration for owners of elite cattle. On top of that, cow adjustments created a multiple currency system which now sees genomically tested cows on a different genetic scale than those with traditional genetic evaluations. In our May 10 issue, AIPL scientists answer some questions regarding imputed proofs and cow adjustments. We are attaching a PDF of that article to help answer these questions.
hdm-2010-05-10-0-343.pdf

At the latest Council on Dairy Cattle Breeding meeting in Baltimore, Md., on April 27 and 28, genomics continued to be a leading topic of conversation. Information shared with industry partners included:

• Full sibling do not share equal amount of genes from parents. In the past, it was thought that 50 percent of the genes came from the dam and 50 percent came from the sire. Genomic testing tells us that the number of genes in common between full siblings can range from 35 to 65 percent.

• The genomic evaluations for bulls with 99 percent reliability will change over time because scientists are learning more about the relationships within the Brown Swiss, Holstein, and Jersey breeds every month as more genomic data comes into the system.

• There are 50,119 animals with genotypes as of April 2010.

•North America is no longer in the lead for accuracy of genomic evaluations. A group of European countries (Germany, Holland, France, and Scandinavia — Denmark, Sweden, and Finland) have each contributed 4,000 genotypes for Holstein bulls to create a database of some 16,000 animals. The sharing system has created higher reliabilities — 5 percent higher — than those in the U.S. and Canada. German reliabilities are even a bit higher than other European countries because they tested an additional 1,000 bulls.

• The cow adjustments allowed genomically tested females to contribute to young bull evaluations. In Holsteins, the improvement in reliability went up 2.6 to 3.1 percent for yield traits. The improvement was greater for Jerseys at 7.7 to 9.4 percent. No adjustments were made in the Brown Swiss breed due to smaller population size.

To view the actual presentations from USDA scientists, click on the title to this blog and it will take you to the AIPL presentations.

Who are the best genetic sources in Holsteins?

For nearly four decades, Penn State's Larry Specht has been evaluating which farms and sires have been the best contributors to genetic progress in the Holstein breed. For his efforts, Specht was named a pioneer by the National Dairy Shrine. The Sire-Son Report ranks a bull based on the average of his son's predicted transmitting ability (PTA) for 11 traits. "The report has long been a valuable educational tool to demonstrate that the bulls with the best daughters are generally those with the best sons," says Penn State's Chad Dechow. "Thought of another way, bulls with the best daughters are also those that are likely to have the best granddaughters," says Dechow. "This seems pretty logical to us now, thanks in large part to Dr. Specht's work, but hasn't always been thought to be the case. There are occasionally those bulls that do not fit the mold and his lists help to identify them."

The Prefix Report is based on a similar concept. "A bull's registration name most often begins with the prefix of the farm that bred him," notes Dechow. "This allows us to summarize the performance of a herd's bulls that have gone to stud. The report has been a valuable tool for buyers of elite genetic stock," says Dechow. "It helps them determine those herds that provide them with the best odds of purchasing a bull or cow that will go on to have outstanding genetic merit.

A recent addition to Specht's work is the Bull-Mother Report. The report is identical to the Sire-Son Report, except that it tracks how well a cow's sons perform once they enter stud.

Only sires and herds with at least 20 sons in A.I. during the past 25 years are considered. Cows are required to have 10 sons to be listed. Genomic selection has added a new wrinkle to genetic selection programs. Currently, only bulls with a progeny test are considered for the lists. However, plans are underway to expand the list to include bulls with genomic-only information.

So, which bull, cow, and farm topped the last list?

Bull: O-Bee Manfred Justice-ET
Cow: Pen-Col Mtoto Dima-ET
Farm: Shadeycrest-H

Four bull proofs slated for 2010

Sire evaluations currently are published three times a year — January, April, and August. In 2010 that will change for one year with evaluations released four times — January, April, August, and December. The extra December evaluation is intended to balance future publication dates moving forward. With that said, there will no longer be January genetic evaluations in 2011, and genetic evaluations will be published in April, August, and December in future years.

That decision was reached earlier this winter when over 100 representatives of national evaluation centers, A.I. organizations, breed associations, and genomic researchers met at an Interbull workshop in Uppsala, Sweden. Interbull is the international body that works to harmonize genetic evaluations across all countries with populations of dairy cattle.