Code Busters Just Made Top Genetics Easier to Find

By Hoard's Dairyman staff

A new genomic prediction test initially raises reliability on young bulls and heifers by 18 percent which is the equivalent of nine daughters in a bull's proof or four to five lactations worth of production data for females.

Seasoned genetic enthusiasts can recall the era in the 1960s when USDA sire summaries hit the scene and forever changed sire selection by taking many minus milk bulls off sales sheets and giving them one-way tickets to the slaughterhouse. Nearly four decades later, today's genomic testing could easily have the same effect on progeny testing by allowing bull studs and producers alike to sort through the industry's genetic farm system to identify the league's top prospects.

This sorting process will combine traditional parent averages from pedigrees with genomic information provided via DNA tests. For Net Merit, a key index used in selecting future bull dams, reliabilities will go from 36 to 54 percent, on average, due to the enhanced intelligence. Overall, the 27 traits in the genomic test will improve reliabilities from 5 to 34 percent.

Scientists with USDA's Agricultural Research Service (ARS), along with four other partnering organizations, have been busy developing this new genomic test which is a generation ahead of the current, single-gene, satellite tests on the market.

"This is a significant improvement over the single- gene tests," says Curt Van Tassell, the lead USDA-ARS researcher on this project. "The new test is a full genome approach. It is a big improvement in accuracy for low heritable traits."

Nate Zwald of Alta Genetics agrees, "The current microsatellite tests do a good job evaluating differences within families but are not as capable across families," he says. "The new test is more comprehensive in its approach and is a major step forward when looking at potential bulls and bull dams for progeny test programs."

"We look forward to learning more," says Select Sires' Charlie Will. "This could be one of the most significant changes we've seen in some time, and it looks to take genetic testing to a whole new level. We are still waiting (as of press time) for actual results on our tested bulls to see the degree of changes within traits, particularly within the low heritability traits."

Began with the genetic map . . .

This technological leap became possible in 2004, when scientists from around the world collaborated to sequence the entire bovine DNA, the genetic building blocks of life. The resulting genomic evaluations were released for the first time earlier this month. The predictions are based on genotypes derived from blood and semen samples provided by the animal's owner.

This test uses a DNA chip developed by a company called Illumina of San Diego, Calif., USDAARS' Bovine Functional Genomics Laboratory, Beltsville, Md., and other research partners. The DNA chip can read more than 54,000 single nucleotide polymorphisms (SNPs) evenly distributed across all 30 bovine chromosomes.

In order to obtain the genetic comparisons needed to make the test functional, USDA-ARS scientists studied DNA samples from 5,360 Holstein bulls. Similar work is under way in the Brown Swiss and Jersey breeds. The samples were provided by members of the National Association of Animal Breeders (NAAB) which is the trade association for U.S. bull studs. In addition, the Semex Alliance also provided genetic materials.

As a part of the second research phase, A.I. studs provided DNA samples for some 800 young sires and a few females, mostly calves. Those initial results were just distributed to the owners and include genomic PTAs and official parent averages along with reliabilities for both. In addition, there are 27 traits highlighted for each animal: 5 yield, 3 health, 2 calving, and 15 type, along with final score and Net Merit.

"We are quite pleased this test will make all type traits available, not just dairy form," says Will.

The seven A.I. organizations that contributed to this research have a five-year exclusive rights period to obtain genomic evaluations for males.

However, evaluations for females are available to anyone who provides a DNA sample and purchases genotyping from a cooperating organization. At press time, those cooperating organizations have not been formally identified but could include breed organizations, A.I. companies, and other commercial entities.

Could change young sire sampling . . .

"Our genomic test should help us better identify elite genetics. It likely will become a major prescreening tool for A.I. studs," predicts Van Tassell. "A.I. studs will not only use it to prescreen potential bulls dams but to select the best littermate from a group of young bulls. However, it will not replace the information received from the traditional progeny test program."

This test has the potential to shore up one of the longtime beefs some dairy producers have when it comes to selecting future bull dams that rarely complete a lactation before they are contracted for future progeny test bulls.

"We will be able to get the equivalent of four to five lactations worth of phenotypic production data for daughters and the equivalent of 9 to 10 daughters for most traits for sires. This will be a better indicator for production and, more importantly, health traits," says Zwald. "It is important to note we are not replacing progeny testing, but instead we are making it more efficient by doing a more accurate job of sourcing the bulls we test. Genomic testing will have little impact on currently proven bulls."

When looking at the combined reliabilities for the genomic test results and the traditional parent averages, health traits like productive life (PL), somatic cell score (SCS), and daughter pregnancy rate (DPR) will look more like today's production traits. In the table, you will see that production traits will now have reliabilities ranging from 54 to 72 percent, while SCS and PL will be at 54 and 47 percent while DPR lands at 40 percent, on average.

"The improvements in reliability are conservative; we recently doubled the number of genotype bulls," says Paul Van Raden with USDA-ARS. "The additional information should theoretically further improve reliability."

Will better identify . . .

"In the past, we also had only a few tools, besides our intuition, to determine if animals received preferential treatment (which, in many cases, falsely raises indexes). Now we can test a group of females on a farm to see if they are consistently scoring at, above, or below current index levels and make a fact-based judgment," says Zwald.

While this is an exciting breakthrough, numerous questions remain, along with a big learning curve. "There likely will be enhancements made to this test," says Will. "For example, the current productive life evaluations are much better than those first released."

At the present time, the research team is asking that these new genomic evaluations not be used in advertising because they will not be considered official evaluations yet. More research and education is needed before genomic predictions can replace official PTAs. Additionally, methods are being developed to incorporate genomic information into evaluations of relatives that have not been genotyped. This embargo is expected to be short-lived. It could be less then a year before they appear in official pedigrees, sale catalogs, and advertisements.

"Labeling will be important," says Will. "All parties involved will need to know exactly what genetic evaluations are being presented."

Future plans include a public release of the information in January 2009. "We plan to make genomic bull evaluations public when a bull is enrolled with NAAB," says George Wiggans with USDA's Animal Improvement Programs Laboratory. "Female evaluations will be made public immediately after the test is run on the USDA-AIPL website. Ultimately, we are trying to develop a system that makes this new information work for everyone."

This article is posted with permission from the April 25, 2008 issue of Hoard's Dairyman. For more information on this publication, please visit their Web site: www.hoards.com