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DNA Parenting Technology Answers Genetic Questions

Article-DNA Parenting Technology Answers Genetic Questions

If you ever wonder about the variation associated with the actual outcome of progeny that share the same genetic profile, just take a look around the supper table at the next family gathering. Or, match calves to their specific sires.

“We expected differences in sires, but considering the high quality of the bulls and how well they had been selected, I was surprised by the range of difference,” says Dave Daley, a professor of animal science at the Califor-nia State University (CSU)-Chico.

Daley is referring to the completion this summer of a three-year project aimed to demonstrate how commercial producers could economically and effectively utilize DNA fingerprinting as a parentage verification tool to improve selection for economically relevant traits.

The study included electronically identifying and matching more than 4,000 steers and heifers (annually) resulting from multi-sire pastures to their sires, complete with feedlot and carcass information. Pick out only calves sired by five different bulls in one year, and there's an average difference of $89.32 between calves sired by the highest value bull and the lowest value bull. And that's just looking at carcass premiums and discounts.

Understand, too, that all the bulls in the study possessed what most commercial producers would consider top-drawer expected progeny differences (EPDs).

“We had bulls that far out-produced their EPDs and others that far underachieved. We had bulls sire as many as 60 calves/year, and some that sired none,” says Mark Lacey of Lacey Livestock, Paso Robles, CA. “DNA fingerprinting allows you to measure bull productivity, so it's a tool you can use to decrease stocking rate.”

The Lacey operation and the Wood Ranch of Coalinga, CA — both participants in the Harris Ranch Partnership for Quality — were the study's producer participants. Keep in mind, the bulls Lacey refers to were all semen checked after breeding season, so that wasn't the problem.

Multiply the average carcass premium or discount/progeny across the numbers sired by each bull described earlier (Table 1), and you're talking a $3,840 difference between the most and least valuable bulls. And that's just looking at carcass value resulting from a single year.

Knock out the two least productive bulls in this example, even if you replace them with one, and you're saving bull cost and upkeep. Plus, Lacey points out, fewer bulls meant fewer bull injuries, which increases the average productive life of each bull.

Lacey has already used the fingerprinting information to change bull management. Despite claims to the contrary, and even allowing for lower stocking rates and an expected extra year of service, he says, “These yearling bulls are not nearly as productive as our two-year-olds. Some were fairly productive, but some didn't even get a cow bred. Bulls that started out productive, remained that way; the opposite was also true.”

Lacey says conventional wisdom holds that it's best to manage bulls in contemporary groups for socialization purposes. The production differences revealed by DNA fingerprinting ran counter to that, so he started mixing yearlings with older peers. There were fewer yearling injuries and their average conception rate increased.

An industry-wide effect

Bull productivity is only the tip of the proverbial iceberg, though.

“On an individual bull basis, we saw tremendous differences in the health of cattle in the feedlot, from no morbidity to 60%,” Lacey says. “We saw a trend in sire lines for feedlot morbidity.”

Between that and sire trends in feedlot performance uncovered with DNA fingerprinting, he believes the feedlot industry probably could achieve more economic gain with this technology than any other segment.

Never mind the fact that the ability to match calves to sires via DNA fingerprinting allows producers to more easily conduct their own research trials. Whether it's comparing specific animal health products, implants, management practices, etc., on their own ranches, comparisons can be made that include sire-gene interaction.

“Genes don't always behave the same way in different environments,” Daley says. “I'm not sure the absolute performance numbers for a bull are as critical in selection as being able to rank the bulls for profitability.”

Drill deeper into the possibilities and both Lacey and Daley believe DNA fingerprinting could help develop genetic selection tools for economic traits that matter most at ranch level. What if you knew a sire's daughters reached puberty sooner or at a lighter weight than those of other sires? What if you knew daughters from one sire cost a certain percentage more to develop than those from another?

For instance, Lacey explains, “We really want to identify the females that will breed within the first 45-60 days of the breeding season at a lower body condition score.”

But even before such multi-trait, profit-based selection tools and value indexes are available, the returns from DNA fingerprinting can be significant.

“After the third year of the study we were able to look at the females. We were able to track producing females back to their sires and look at fertility performance,” Lacey says. “As a cow-calf producer, I think that's probably the biggest pay-off, to not only see progeny in the feedlot and packing plant, but to be able to incorporate their siblings back into the herd.”

Short of artificial insemination (AI), Lacey believes retaining replacements out of superior bulls is the most effective way to multiply desired genetics within a herd.

As with the AI they utilize on first-calf heifers, Lacey says he looks to be able to make similar improvements through DNA fingerprinting. With AI, he explains, they increased weaning weights in calves out of first-calf heifers 25-30 lbs., along with increasing uniformity and consistency.

Moreover, even when superior sires are identified, there's no guarantee commercial producers will still be able to find sons or grandsons to use in their pastures. Lacey tackled the challenge by contracting with seedstock suppliers to produce matings with the sires he wants, even when that means he also must buy the females produced in the process.

It isn't easy or free

The notion of differences in progeny performance between bulls, even ones that share a high degree of relationship isn't new, but the degree of difference revealed by the project will likely raise eyebrows. What is new is how commercial producers may be able to identify and capitalize on these differences.

“The dairy industry at least knows which bulls sired which calves. In the beef industry, we don't have a clue about which calves are sired by which bulls,” Daley says. The project demonstrates it's possible to collect and track a volume of data and manage cattle individually in sprawling Western ranching operations, he adds.

But that doesn't mean incorporating the management tool at ranch level, and at the speed of commerce, is easy.

“Try running a computer in Bridgeport, CA, when it's snowing and you've got 500 head to preg-check and collect DNA samples on in five hours,” Daley says. “The first concern we always had to address was not slowing down processing speeds.”

For that matter, gathering the necessary information early enough in a bull's production life can be as logistically tough as it is critical.

“If we can ID the calves and get their DNA sample at branding (2-4 months of age) and get turnaround time on the parentage analysis to three weeks or less, we'll already know how productive the calves' sires have been. That will speed up culling non-productive bulls and identifying female offspring out of superior productivity bulls for replacement selection,” Lacey says.

But there's currently no single, simple method to allow tagging and retrieving of a DNA sample in one step. In the project, blood was drawn for DNA samples, which added to labor intensiveness. Some DNA service providers also accept hair and tissue for the DNA sample.

“Can it be done easily today at ranch level? No,” Lacey says. “Is the technology there to accomplish it? Yes.”

Cost is also an issue. In the CSU-Chico study, the cost per head, including electronic ID and data collection, was $11-$20/head, depending on the data collected.

Looking at just the cost of DNA fingerprinting, Tom Corah, director of sales for Bovigen Solutions, explains his firm's fingerprinting starts at $25/head. It declines as volume increases.

Currently, Daley believes larger, progressive commercial operations are most likely to utilize DNA fingerprints. That's especially true for those already involved in systems that pay premiums for building value into their cattle.

“Initially, I think it's too expensive for many operations, but there are ways to decrease costs,” Daley explains. “One model would be to get a genetic snapshot of all your steers. In today's calf market, that would be relatively inexpensive.”

As an example, say you had 100 calves. Presumably about 50 of them will be steers. Fingerprinting the steers and sires would, in effect, provide a snapshot of the heifers, too.

Corah suggests folks retrieving feedlot and carcass data could collect DNA samples on the top and bottom carcasses. Say you had 100 calves and five sires. Fingerprinting the bulls and the 10 most profitable and 10 least profitable carcasses, would cost about $625 based on Bovigen Solution's rates.

In each case, producers have an opportunity to exploit the top end while reducing the bottom end.

Even though the CSU-Chico project has ended, Lacey says his operation continues to DNA fingerprint all new bulls and females.

“The cattle business isn't getting easier, it's getting tougher. You don't look for the dollars you can make anymore; you look for the pennies,” Lacey says.

Table 1. Sample of carcass value difference between sires
Bull value No. of calves sired in year Carcass premium/discount (average $/carcass) Total carcass (total $/bull)*
A 26 -$38.16 -$922.16
B 65 $43.82 $2,848.40
C 53 -$4.66 -$246.98
D 5 -$28.32 -$141.60
E 1 -$45.40 -$45.50
*Number of progeny x Average carcass premium/discount Source: California State University-Chico

How fingerprinting works

DNA fingerprinting is fairly straightforward. Basically, you collect a sample of blood, hair or tissue that serves as the fingerprint, possessing DNA unique to that animal. Matching common DNA between a prospective parent and potential progeny is how DNA service providers determine the probability that a particular bull sired a particular calf.

More specifically, says Tom Corah, director of sales for Bovigen Solutions, his company and most others in the U.S. utilize nine common genetic markers recommended by the International Society of Animal Genetics (ISAG) in determining bovine parentage. Each company may also match additional DNA markers. In the case of Bovigen for example, their SireTrace program employs the nine ISAG markers plus five others.

Arguably, any of the tests from reputable companies today will share similar high accuracies for determining parentage, though different companies may report results differently. As an example, Bovigen reports the probability of an animal matching a parent in the form of odds that a bull is in fact the sire. Others may report probability as a percentage, but the concept is the same.

Given that, Corah says producers need to understand that since different companies use different panels of DNA markers, a DNA analysis for Company A can't be used to compare to one from Company B.

Beyond that, much of the difference between companies revolves around service, products offered and cost. Bovigen, for instance, offers parentage analysis, along with DNA diagnostics for marbling, tenderness and coat color.

Producers also should keep in mind that, with statistical probability, there is no such thing as 100%.

“The more markers you match the higher the validity of the probability,” Corah says. Most unrelated bulls can be matched to calves in multi-sire pastures with a great deal of certainty. Related bulls can be matched, too, but less accurately because they share common genes.

For perspective, in the California State University (CSU)-Chico study, researchers matched 70% of the calves to a single sire. Sean Earley, CSU research assistant, expects a much higher percentage in pastures with unrelated bulls.

In fact, while he realizes it's not always practical, Corah says, “In multi-sire pastures where DNA fingerprinting will be utilized, we recommend placing bulls with genetic differences.”