When the first draft of the bovine genome sequence was made available in 2004, it unleashed a world of opportunity to better identify and promote desirable traits in cattle. One of the best and most recent examples of how far we have come is the recent identification of arthrogryposis multiplex, more commonly referred to as curly calf syndrome in Angus and Angus-influenced cattle.

“From a genetic standpoint, this is an amazing story,” says Alison Van Eenennaam, PhD and professor at the University of California, Davis.  “In an approximately two-month period beginning last September, the problem was identified, a test prototype was developed and information on the carrier status of 736 bulls was made available.

“This is a great use of DNA technology,” she adds. “Angus breeders are still able to use the lineage of a very popular AI sire because you can identify carriers and non-carriers.”

AM is a lethal genetic defect that is a recessive trait. So, in other words, a calf must inherit the recessive gene from both parents in order for it to be expressed phenotypically. Genetic profiling allowed researcher Jonathon Beever, a University of Illinois molecular geneticist, to develop a test that can accurately identify carriers. The test works by distinguishing a deletion caused by a  mutation in the DNA sequence of specific genes of an animal.

This success story shows just how powerful molecular genetics can be in a real-world application. It also demonstrates the potential that exists to identify an animal’s ability to express desirable traits.

In a paper coauthored by Van Eenennaam and Dorian Garrick, PhD and professor at Iowa State University, the researchers said that the identification of genetic markers provides two novel opportunities to influence genetic selection:

  • Parentage identification to minimize the costs associated with progeny testing.
  • Identifying specific markers for desirable traits that may eventually offer an alternative to progeny testing.

 Parentage identification has already proven itself and allowed cattle operations using multiple-sire pastures to trace calves back to their respective sires. Because the technology identifies individuals that, due to a specific combination of marker alleles, could qualify as a parent, it basically works through a process of elimination.  If the bulls in a multi-sire pasture are closely related, it can potentially make it more difficult to identify with certainty a specific calf’s sire.

James McAllen, Jr., co-owner and manager of the South Texas McAllen Ranch, made a decision last year to work with Igenity to use genetic profiling for both parentage identification in his commercial calves and to characterize carcass traits in his purebred Beefmaster bull battery. The historic ranch, which dates back to a Spanish land grant, runs approximately 1,000 head of commercial cows, plus a Beefmaster purebred herd of approximately 500 females. The ranch also runs approximately 800 to 1,000 head of stocker calves every year.

“We are really trying to push the limits of our cattle to gain more value,” McAllen says. “We wanted to expand the ability to collect meaningful data on our commercial calves and correlate that with their lineage.”

The extensive nature of the operation means that calves from the commercial herd are not tagged at birth, and the cows are run in multiple-sire pastures. By collecting DNA samples from the calves at a later time, ranchers like McAllen will be able to identify the sires that produced more desirable progeny. The ranch retains ownership on its commercial calves and will eventually have the ability to tie feedlot performance and carcass data back to the calves’ respective sires.

In addition to collecting a lot of carcass data over the years, the ranch also places a large emphasis on the maternal traits of its Brahman-influenced females. All of the commercial heifers are retained, and any that are not kept as replacements for the ranch are eventually marketed as bred females. For the time being, McAllen has made the decision to conduct parentage analysis only on his first-calf commercial heifers and use their production information to better evaluate their sires’ ability to pass on desirable maternal traits.

Marker-assisted selection

This is really the next frontier in genetic improvement in cattle, as accurate DNA profiling allows producers to gain an understanding of an animal’s genetic potential even when it is still very young. A marker is essentially a “flag” for good or bad genes. The technology works by identifying specific DNA variations that are associated with measurable effects on complex traits such as tenderness. 

“DNA testing in beef cattle for desirable traits is really going through an evolutionary process right now,” Van Eenennaam says. “Genetic profiling or marker-assisted selection may have been oversold when the technology initially hit the marketplace. Some of that was due to a lack of validation, which is partly due to a lack of available validation populations.”

That concern is being addressed by the National Beef Cattle Evaluation Consortium as part of an international partnership that includes NBCEC; the U.S. Department of Agriculture; National Cattlemen’s Beef Association; the Beef Improvement Federation; the University of Guelph, Canada; and the Australian Beef Cooperative Research Centre. Validations have already been completed on some of the leading commercial tests, which has improved their accuracy and expanded their capabilities. The validation process also allows for an independent analysis of published claims made by the gene-profiling companies.

One of the other major challenges to the current use of genotyping is that it is not being incorporated into national cattle evaluations and breed-sire summaries. “Right now there is no national structure, at the breed association or any other level, to routinely capture genotypic information in a consistent form for the purpose of national evaluation,” Van Eenennaam says.

“Genetic profiling will not be extensively used until it is merged with other available technologies,” says Ronnie Green, PhD and senior director of global technical services for Pfizer Animal Genetics. “We are actively working with breed associations to combine EPDs with molecular selections as one method of overcoming that hurdle.”

Green also adds that educating producers will be critical to effectively use DNA profiling in the future. Both Pfizer Animal Genetics and Igenity provide a multitude of technical resources to aid producers in understanding the DNA profile data. The National Beef Cattle Evaluation Consortium also provides additional third-party resources.

“DNA information is just DNA information if producers don’t know how to manage or apply it,” says Kevin DeHaan, PhD and technical services director for Igenity. “We have to make it easy for producers to use the technology, provide results that are easy to interpret and give producers the technical support they need.”

“As DNA-marker technology continues to evolve, beef producers will have a growing supply of tools to help make more precise management decisions,” Green says. “We have really just scratched the surface on the understanding and development of DNA markers that can enhance beef cattle production. Future innovations could even focus on disease susceptibility, fertility and other traits related to animal husbandry that are of critical economic importance to beef producers.”

Right now, DeHaan believes that producers who retain ownership on their calves or keep their own replacement heifers are achieving the greatest economic gain; however, as the technologies continue to expand, the opportunities will continue to grow.

McAllen has worked with Igenity to DNA-profile the ranch’s entire bull battery, including AI sires that are no longer living. “We won’t use this as a definitive selection criterion, but right now, it certainly is another tool for us to use to make selections,” McAllen says. He does express some concerns that the accuracy of the DNA-profiling tests may need to be further validated; however, he plans on giving the technology time to continue to prove itself.

The already has broader applications in the dairy industry where there is a more uniform cattle population that has contributed to greater accuracy. “In dairy cattle, we’ve already shown that a large number of markers used together can predict the breeding value of a young bull with no offspring with a 70 percent accuracy for traits such as milk protein yield,” says Australian researcher Michael Goddard, PhD and chief scientist for the Beef Cooperative Research Centre at the University of New England in Armidale. He believes it is only a matter of time before the beef industry will see similar results.

 At the same time, Goddard does urge producers to be reasonable in their expectations of what the genetic tests can offer currently. “People need to be cautious when investing their money. They need to ensure the product which is available justifies the price.”

 “As part of our overall program, our goal is to improve carcass quality and feed efficiency, so we will still continue to utilize the DNA-profiling information we have collected as we move forward,” McAllen says. The ranch is considering more direct-marketing opportunities for its fed cattle, and McAllen believes that offering prospective beef buyers more information on the genetic potential of his cattle will prove beneficial.  “Whether it’s marketing our purebred bulls, our commercial heifers or direct-marketing our beef, I believe offering as much information as possible is what will help separate us from the competition,” he adds.