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Where are we going with genomics?

Stewart Bauck for Progressive Cattleman Published on 24 October 2016
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Bottom line, beef producers are getting more for their money when it comes to genomics.

Industry pioneers who have used data from DNA tests to pick bulls and replacement heifers have fully installed genomic selection into their management and production systems and are seeing the benefits.

For those more recently interested in genomics, lower costs and greater ease of use make it less of a leap to try the practice.

The technology is getting easier, cheaper, better, and there is a larger toolbox of options.

Who’s benefiting?

The widest adoption of beef genomics is in seedstock. Many breeders enhance their expected progeny differences (EPDs) with genomic test results through their breed association, and the majority of associations currently offer that service.

As a result, accuracy of EPDs for yearling and 18-month-old sale bulls is greatly improved. Seedstock producers are lowering risk in selecting bull calves for development and are able to make marketing decisions more confidently.

Bulls with higher accuracy genomic-enhanced expected progeny differences (GE-EPDs) are worth more to customers. Consider the rancher driving away with a new heifer-bull whose traits for low birthweight have been verified by an independent third-party DNA lab.

The reliability of GE-EPDs adds value to that transaction and helps cement the relationship between the commercial customer and the seedstock supplier.

New low-cost, highly accurate genotyping chips are now making DNA testing more affordable than ever. Affordable use of genomic-assisted selection on the female side helps breeders raise cows that give birth to superior bulls.

Breed association executives see value in this and are building up more extensive herd reporting to take advantage of the new tools.

The idea is that breeds will improve faster if associations use DNA tests on more sires and females, plus collect more phenotype data. Increased prediction accuracies for traits that manifest late in life, such as fertility and stayability, are possible with genomic testing and will greatly enhance commercial production.

What’s new?

A new change coming for breeds that offer GE-EPDs is the “one-step” method of genomic predictions. These new formulas use genetic data to see which parent a bull calf favors more – the way a child may favor a father more, or a mother more.

There is more to it, but at a basic level this information is used to predict more accurately the future performance of the bull calf and can potentially be done much faster, which is always a positive.

In the big picture, value is also being created where genomics and other technology platforms overlap. An example is work combining genomics with embryo transfer. Seedstock producers can do a genomic test to find out the gender of an embryo before it is implanted. They may choose to increase the number of males implanted, or to implant embryos into fewer recipient cows and lower production costs.

It is also possible to screen embryos for common genetic problems. So a bull which is superior, but carries a defect, may still have great value because his embryos can be screened and those without the defect are used.

It is also possible to use genotyping to pick out the best and implanting them will cut 2 ½ to 3 years from generational improvement. Only recently has this become a practical alternative.

The wellspring of this new age of DNA testing is affordable, effective genomic selection. These tools will impact all phases of beef production.

  • Using genomic profiles for selection of young breeding stock, producers can make simultaneous gains on traits that drive production, performance efficiency and quality.

  • Selecting heifers with better fertility and maternal profiles – the main benefit for many cow-calf producers – improves the herd’s calving percentage and produces more cows that stay in the herd longer.

  • Profiling indexes that predict carcass composition help advance carcass quality, rather than relying solely on ultrasound or carcass data after slaughter.

  • Feedlot operators, particularly those aligned with calf production, are seeing how genomic profiles that verify feed efficiency and carcass potential fit into value-added programs.

What’s next?

Overall, the industry may only be scratching the surface on the value creation possible from using genomic profiles. For example, BRD-resistance genes could be bred into cattle that have superior gain and carcass traits.

The result would be reduced losses due to BRD, a billion-dollar problem, plus an increase in feed efficiency, another billion-dollar opportunity. This creates a lot of value to share between cattle sectors.

In addition to selection for health, major USDA-funded projects on feed efficiency are concluding and those results will lead to new tools for both cow-calf and feedlot operators. Not surprisingly, efficiency is a heritable trait.

Selection for efficient cows will not only improve the profitability of the commercial cow herd, but the calves from those females also will be more efficient replacement heifers and feeder cattle.

For commercial cattle, cow-calf producers can buy bulls and pick replacement heifers tailored to their system. Producers who wean and market calves straight off the cows can place selection pressure on fertility and gain traits. Others who retain ownership of steers can emphasize carcass quality.

The dairy industry has been leading the way in using genomic rankings to modify breeding strategies. Top-producing cows, or high-merit heifers based on genomic testing, are bred A.I. with sexed semen to produce the next crop of replacements. Moderate genetic-merit cows are bred to high-quality dairy bulls.

The bottom 25 to 30 percent of heifers and cows, ranked by genomics, are bred to beef bulls. These heifers go into milk production after having a higher value, crossbred calf that is sold for beef. Often the added value of that crossbred calf is enough to pay for the cost of genomic testing for the rest of the heifers.

Meanwhile, some scientists are studying genetic adaptation to the environment. One is Dr. Jared Decker, University of Missouri, who is leading a USDA trial on this idea. This study will look at hair shedding, DNA and tall-fescue tolerance.

“When gene-by-environment interactions exist, some genetic variants have large effects in some environments and small effects in others,” Decker writes in his blog, A Steak in Genomics.

“This leads to cattle that perform poorly in a certain environment, but well in other conditions. Cattle poorly adapted to their environment result in lost revenue and cause headaches for farmers and ranchers.

One of the goals of this research project will be to create region-specific genomic predictions, thus helping farmers and ranchers match cattle genetics to their environment.”

Producers should expect to see more demonstrations and studies that look into key questions for particular regions, whether animals graze coastal bermudagrass or semi-arid mountain rangeland. These studies favor a cooperative approach, and when Dr. Decker put out a call asking producers to participate, the study was quickly filled.

In the beef industry, genomics is going in profitable directions. The tools are giving better insight into future cattle performance, while at the same time costs of testing are declining.

As the technology becomes more affordable, it is being mainstreamed in ways that are limited only by the imagination of our nation’s innovative beef producers and the researchers who serve them.  end mark

Stewart Bauck
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