Genetic improvement in the cattle business over the past 20-30 years has been nothing short of phenomenal. Every industry segment has benefited from the increased ability to identify superior genetics and employ them in economically important traits.

Still, there are more selection tools on the horizon in the emerging discipline of molecular genetics. With the sequencing of the bovine genome, scientists expect to discover a number of benefits to basic animal biology. Those discoveries may translate to increasingly efficient and profitable methods of meat and milk production.

“The cattle, swine and poultry industries stand to reap huge rewards from the sequencing of the human and bovine genome,” says Ronnie Green, USDA's national program leader for food animal production.

“For the cattle business, it's going to allow a convergence of the science of DNA marker-assisted selection with performance-based selection tools like EPDs,” he says. “There's a long list of scientists who have worked for decades to see us get to this point.”

Comparative genomics

Early on in the discipline, animal scientists noticed that while the arrangement varied, similarities in regions of the DNA code between some animals and humans were remarkably high. They also found large regions of the genome had been conserved throughout evolutionary time.

This provided a leg-up by allowing a linkage of genomic information from one species with another.

The international cattle research community was quick to organize itself in a manner similar to the biomedical research community, says Steven Kappes, a geneticist at the U.S. Meat Animal Research Center (MARC) in Clay Center, NE.

“Genomics has caused the integration of genetics with all types of biology — growth, muscle, reproduction, immunology, behavior, nutrition, development, biochemistry and cell biology research,” Kappes says.

To date, a handful of genes have been mapped in cattle through the “comparative mapping/fine mapping” approach. This has led to the commercialization of DNA “fingerprinting” or marking genes associated with economically important traits that seedstock and commercial cattle producers can incorporate into their genetics selection systems.

A DNA marker can be used to follow the transmission of a gene or a chromosome segment from parents to offspring. In this way, favorable and unfavorable genes can be tracked and animals can be ranked accordingly.

Commercial applications

Among the first DNA fingerprints developed was Frontier Beef System's “eating quality” test — TenderGENE. It's based on the calpain gene marker developed by MARC. Frontier (now part of Merial's IGENITY DNA testing services) also developed ParentMATCH, a parentage verification test and DoubleBLACK, a homozygous black color test.

These tests complement Merial's IGENITY L test, which identifies the leptin genotype of cattle from DNA samples. Leptin is a protein linked to energy balance, marbling score and red meat yield in beef cattle.

IGENITY DNATrace, another Frontier test acquired by Merial, provides birth-to-consumption ID on an animal. With it a certain cut of meat can be traced back to the original individual animal.

“Some day, we'll have genetic tests that show which cattle are more likely to get sick, whether it's BVD, BRSV or other diseases in beef cows,” says Jim Gibb, former general manager of Frontier Beef Systems. He now serves as Merial's senior manager in beef segment development.

Bovigen Solutions, LLC, is the American licensee for Australian-based Genetic Solutions Pty. Ltd. Its products include SureTRAK, GeneSTAR and SireTRACE.

Firms like these recognize most economically important traits are controlled by multiple genes that interact with each other as well as with environmental factors. Therefore, gene markers for complex traits will be best applied as a component of an integrated genetic improvement system, says Jay Hetzel, scientific director of Genetic Solutions.

“The maximum impact of DNA markers will be for traits difficult to breed for, either because phenotypic measurements are inaccurate, expensive, only possible on one sex, or they can't be carried out at a young age,” he says.

Hetzel adds it's important to fully evaluate new markers to determine economic value, as well as under what circumstances the markers have value.

“Both the GeneSTAR marbling and GeneSTAR Tenderness 2 tests have been independently validated which explains why the industry uptake of these tests has been rapid,” Hetzel says.

“It's been exciting to see the discovery of these few genes and how they can be used to make genetic improvement,” Green adds. “But, there are hundreds of others identified for various traits yet to be successfully mapped to the gene level.”

The first-ever marker-assisted expected progeny differences (MA-EPDs) were published in the American Simmental Association's 2004 Fall Sire Summary. Calculated by Richard Quaas of Cornell University, shear force MA-EPDs blend the outcomes from DNA marker tests with tenderness data on sires' offspring. They are used to arrive at slightly more accurate EPDs, particularly on low-accuracy animals, than with tenderness data alone.

International implications

Thanks to a new gene profiling technique, Canadian researchers are one step closer to describing the potential productivity and profitability of cattle with regard to feed intake.

“We've identified a collection of candidate genes that have a role in regulating hunger and fullness in cattle,” says David Glimm, University of Alberta.

The Canadians hope to further characterize candidate genes in more cattle and relevant breeds. The aim is to develop molecular genetic markers that allow selection of cattle for superior feed intake ability.

“This is just a part of leading-edge functional genomics strategies that promise to deliver a wealth of new information,” Glimm says.

Breeding cattle that produce more-tender beef is the primary aim of Brazil's Cattle Functional Genome Project. Project coordinator Luiz Lehmann Coutinho, a University of Sao Paulo ag professor, says if the project is successful, it would mean higher productivity and improved quality of Brazilian beef.

The research will focus on the tropically adapted Nelore breed, which represents 80% of the genetics in Brazil's 170-million-head cattle herd. Nelore beef is not as tender as beef from breeds originating in more temperate climates.

Nelore cows generally aren't sexually mature until 2-3 years of age. Identifying the genes of early sexual maturity is of great interest to firms like Sete Estrelas Embriões and Central Bela Vista, Brazil's leading suppliers of cattle semen and embryos.

The Brazilians, like others, are careful to point out this project, like similar genomics projects around the globe, won't include the processes associated with transgenesis.

“That is, there will be no introduction of genes from other species,” Coutinho says.

Len Stephens, livestock production innovation manager for Meat and Livestock Australia, says the potential advantages of genomics are enormous. He says gene markers will allow producers one day to even identify the more productive and sustainable pasture plants, allowing them to produce more meat from less pasture.

Concerns and considerations

The challenge is to integrate DNA mapping with quantitative genetic procedures in genetic evaluation of beef cattle. But, while recognizing the potential of functional genomics, John Pollak, professor of animal genetics at Cornell University, has some concerns.

“My first concern right now is that there are no checks and balances, Pollak says. “DNA testing will be subject to the same problems as any field data recording process — including misidentified animals, misidentified samples, etc.”

Under the current system, there's no random retesting of animals to confirm their genotype by a breed association or any other organization, as is done with parentage.

“Quite simply this means to me that there will be a significant proportion — 5-10% — of animals for which the genotype is wrong or not consistent with that animal's pedigree,” Pollak says.

Another of Pollak's concerns has to do with testing at the ranch level.

“At the current pricing of DNA tests, there's no question in my mind testing will be done selectively,” he says. “I would like to see us develop a decision-aid program that helps producers decide which animals to test.”

A major factor influencing cattle genomic research is the vertical integration and consolidation in other food animal industries. Vertically integrated companies are more likely to implement new and more efficient technologies because they can spread the costs and benefits across several company-owned segments.

“The cattle industry is less likely to be vertically integrated,” he says. “Therefore it is slower to implement new technologies. That's because in a commodity-based industry, the segment that needs to make the initial investment has a difficult time getting compensated.”

Most geneticists agree enthusiasm for this emerging technology is best tempered with caution. The Beef Improvement Federation has convened a committee charged with addressing these concerns and addressing mechanisms for getting the DNA test information into breed association databases.

Virginia Tech's David Notter cautions that individual gene markers often account for a small percentage of genetic variation for specific traits. He suggests genetic markers will be most valuable not as re-placements for existing methods of cattle evaluation but as refinements of the already proven tools.

“More specifically, gene marker information can be used to augment development of EPD values with improved accuracy,” Notter says.

“Most of the work to date has been in product quality,” Green says. “Future genomics will focus more on factors like feed efficiency and disease resistance — the cost side of the production equation.”

Finally, Gibb emphasizes that genomics is still a very immature discipline.

“Management by genotype through discovery of markers for critical traits such as fertility, feed efficiency, disease resistance and adaptability holds great promise,” Gibb concludes. “This is just the beginning.”