In just a few short years, the field of DNA testing in cattle has evolved from covering just a few markers for a few traits to over 50,000 markers for a suite of traits. The technology still has its limits though, with its best applications enhancing, rather than replacing, traditional selection tools such as Expected Progeny Differences.
University of Nebraska animal scientist and genetics specialist Matt Spangler, PhD, says the industry gradually is working toward integrating genomic information with phenotypic data to develop true marker-assisted EPDs. As multiple-trait selection becomes more complex, the industry needs to incorporate those EPDs into economic in-dices applied toward targeted breeding objectives.
As the tests explain more genetic variation, they will have more impact on accuracy of prediction. Currently for most traits, Spangler says, genomic information is most useful in bulls with low-accuracy EPDs. As the accuracy of EPDs increases, the genomic information has less impact.
Spangler believes inclusion of marker information into EPD calculations holds three primary benefits:
1. Increased accuracy for young animals such as yearling bulls, which is particularly beneficial when selecting on traits that are measured later in life, such as stayability.
2. Shortened generation intervals.
3. EPD values for novel traits such as efficiency, healthfulness of beef products or disease susceptibility, for which phenotype information is lacking.
Increased accuracy means less risk and faster genetic progress, he adds. Two yearling bulls might have equal EPDs for a trait, but more information and greater accuracy can show significant differences.
Spangler also points out that for some traits, using an average for the bull battery can be sufficient for moving the herd toward a genetic goal. But for other traits such as calving ease, individual data is more important, as one outlier bull could cause economic losses.
As the information available from DNA testing grows, increasing numbers of commercial producers are getting a head start, putting the new tools to work in their herds.
Barb Downey and her family own Downey Ranches, a commercial cow-calf and seedstock operation near Wamego, Kan. The ranch manages an Angus-based herd of about 550 cows, of which 150 are registered Angus managed for production of registered bulls and replacement females.
“Our focus over the years,” Downey says, “has been to produce high-quality beef while also maintaining solid, productive range cows.” Toward that goal, the Downeys have finished their calves and collected carcass data ever since the option became available around 1990. As founding members of U.S. Premium Beef, they have fed all their calves as finished cattle since its inception, except for those selected as seedstock animals.
Although they were involved in some early research with Igenity and have tested bulls for genetic defects, Downey says they did not begin using DNA profiling in their commercial herd until the past two years, when they felt the scope of the tests and supporting data made them practical at the commercial level.
Last year, the Downeys employed Igenity’s replacement heifer profile as a selection tool in their commercial herd. This test, which applies to any breed, provides ratings for fertility, maternal calving ease, average daily gain, percent Choice and tenderness in heifer calves.
While the family has selected for carcass quality for years based on progeny data, Downey believes the test will speed the rate of improvement. She also believes including beef tenderness among selection criteria will pay in the long run. Packer grids currently do not offer premiums for tenderness, but she wants to be ready when they do.
Downey sees the replacement-heifer profile as a good tool to use in conjunction with traditional selection criteria for replacement females. It provides information early on young calves, which allows early sorting. Heifers that looked good in the profile can be sorted again later, based on traditional phenotypic traits. Downey believes the genotype information will, over time, pay off for replacement heifers returned to the herd and for heifers the family sells, by giving just a little more confidence in their value as replacements.
This year, she plans to use Igenity’s Angus-specific profile on the operation’s bulls. This test uses a marker panel that covers 21 traits including dry-matter intake, birthweight, mature height, mature weight, milk, scrotal circumference, weaning weight and yearling height. Igenity has an agreement with Angus Genetics Inc. to provide Angus breeders with genomic-enhanced EPDs for multiple traits.
Profiling bulls, Downey says, should help identify outliers early and capture more value by allowing early marketing of cull animals. Conversely, the testing could also identify bulls that have good potential but don’t express certain economic traits, such as backfat or marbling, during the typical bull-test time frame.
Downey says while she is looking at genomic information on feed efficiency, she’s taking it slowly in terms of selection pressure, wanting to be sure selecting for efficient feeder steers has no negative effect on cow performance.
For now, the Downeys are focusing on maternal traits, stayability, docility and carcass traits. They’ve been selecting for the same combination of traits over the years using phenotypic measures and progeny testing, but they believe incorporating genetic profiles will speed the process.
Andrew Maupin, cattle sales manager at Spruce Mountain Ranch, a seedstock operation near Larkspur, Colo., says the operation recently began gathering and testing genomic information using the HD-50K test from Pfizer Animal Genetics, a high-density 50,000-marker panel for Angus cattle. This analysis covers 14 economically important traits, with results reported as percentile ranks associated with molecular breeding values, benchmarked against more than 5,000 HD-50K-tested Black Angus animals and reported to the nearest 1 percent. According to Pfizer, the panel provides accuracy on yearling bulls or heifers equal to that from information on up to 15 progeny.
Pfizer currently is working with other breeds to develop 50K tests and offers its GeneStar test for any breed, providing molecular breeding values for feed efficiency, marbling and tenderness, as well as a meat quality palatability index and homozygous black.
The Spruce Mountain operation manages about 450 cows, with an emphasis on embryo transfer in a donor herd. Maupin says the ranch has begun with testing sires in their breeding program, with plans to eventually include replacement heifers. He also sees the tests having application for evaluating differences between flush mates, which look the same but can vary in genetic potential.
In an eye-catching example of this concept, Spruce Mountain supplied Pfizer Animal Genetics with three yearling Angus bulls, each full-siblings flush mates produced using embryo transfer. Pfizer displayed the bulls in their trade-show exhibit at the 2011 Cattle Industry Convention in Denver, challenging attendees to guess their differences. The bulls looked identical, and as full siblings with no progeny data, their EPDs were identical. The 50K-marker panel, however, found differences. They were all good bulls but for different reasons. The test revealed one as superior for calving ease, another better for milk and reproductive traits in his heifer daughters and the third rated higher for growth and carcass traits.
Maupin sees tremendous economic potential in genomic ratings for feed efficiency, and the group intends to apply the information toward early selection decisions. Growth and carcass traits are already built into the herd’s genetic base; now the ranch wants to identify those that perform most efficiently. Or, more precisely, identify those that perform least efficiently. Maupin says early testing will focus on identifying inefficient outliers, adding they do not want to wait two years for progeny testing to determine if they are headed in the right direction.
Spangler says the greatest benefits of marker-assisted selection begin in seedstock herds at the nucleus level, creating higher-accuracy EPDs for herd sires. Those benefits trickle down to the commercial level with better information on the bulls cow-calf producers use in their herds.
Finally Spangler encourages producers to set genetic goals and apply information that already is available. “For those who have not yet adopted 30-year-old technology such as EPDs, the inherent selection mistakes that have been made in the past will only be exacerbated as the accuracy of genetic predictions of young animals is increased.”