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Genetics

Milt Thomas, Colorado State University (CSU) professor and Rouse chair, says cattle from CSU’s Rouse Ranch are asked to perform in a variety of ways, and the operation must produce livestock that can successfully graze in the valleys of southeast Wyoming but also on the high-mountain slopes. 

“As we start up these slopes, it takes a much different critter to get out there and forage in rough rangelands,” Thomas says. 

CSU began looking at and tracking cattle performance on rangelands, eventually asking the question, “How much of that is genetic?” he continues. 

Further, Thomas says data show that improved grazing distribution comes through use of products like protein lick tubs or other minerals. Using these products, he continues, is easy in lower-elevation pastures or even mountain areas with road access, but Thomas notes, in wilderness areas, distributing supplements, adding fences or improving water to change grazing distribution isn’t always an option.

“It might be two dollars a linear foot to build fence in good country, but that jumps to five dollars in rough country sometimes,” he says. “The next thing we know, we’ve spent more money on infrastructure than the entire ranch is worth.”

Thomas notes, “Then, we got into the idea of whether we can select cattle based on genetics that distribute across the rangeland. Therefore, we get cattle that just work and distribute across the range, rather than us having to herd them.”

Research efforts

As CSU’s research team traveled the world collecting data, Thomas says, “Some cows are bottom dwellers, while some were hill climbers. That’s just where they prefer to graze.” 

Utilizing GPS data collected over the course of their study, Thomas and New Mexico State University’s Derek Bailey developed two indexes – the Rough Index and the Rolling Index. 

The Rough Index incorporated slope and elevation, while the Rolling Index included both slope and elevation, as well as distance from water. 

Cows were classified phenotypically as bottom dwellers, average or hill climbers using GPS data. 

“We got 80 cows phenotyped and genotyped,” Thomas explains, noting that the gene was very polygenic, showing many genes that were associated with the trait for both indexes. “There is no one single gene that drives how or why a cow goes out and does this, but there are high points.” 

In looking closer, the research team began looking for specific genes which might be particularly important, locating a handful of key contributors. 

“Derek started talking about GRN5, the glutamate receptor metabolic form number five expressed in a part of the brain that controls appetite,” Thomas explains. “That gene is known for being involved in locomotion, motivation and special memory. That’s one of many genes that is important and probably has something to do why some cows will go further and why some cows will climb higher.” 

However, for that particular gene, Thomas expressed it isn’t possible to tell whether the cow is actually hungry and seeking food or satiated, full and “just wants to go on a hike,” he comments.

“Now, we can start using these technologies to start to exploit grazing distribution,” Thomas says.

Next steps

After their initial study, CSU obtained funding from the Western Sustainable Agriculture Research and Education (SARE) program to continue their research through a multi-disciplinary approach.

“Derek and his team at New Mexico State are range science folks, and they are in charge of tracking cows and working with phenotype data,” explains Thomas. “Our group at CSU is working on the genetic side of it.” 

The team hopes to develop a breeding value from the data collected, in collaboration with teams from University of California, Davis and University of Arizona.

“In our second study, our goal is to get 400 cows both phenotyped and genotyped,” Thomas comments. “We will keep tracking cows as long as we have money to send collars. Our goal is to get cows tracked in every western state.” 

The team sent groups of 20 collars to ranches across the West and is working to build their database of animals with both phenotype and genotype.

“We took the five initial genes, which included GNR5, and started doing SNP discovery,” explains Thomas, noting that SNPs are regions on the genes that are significant. “We went to those genes and looked them to see whether we find a lot of markers on the gene that might tell us more about the function of the gene.”

The team found 1,090 markets in Angus cattle, 560 in Brangus and 376 that overlapped between the two. Compared to their reference inbred Hereford female, the researchers found 10 overlapping markers across the three breeds that may provide useful tools for segregating cattle based on whether they are “hill toppers or bottom movers,” says Thomas.

Analysis and validation

Analysis continues to use more powerful statistics that have less error and more power in looking at distribution. 

“There are some real challenges in that we have many, many more markers than we do phenotypes,” Thomas explains. “That is a real problem. We’ve had to do interesting things to validate markers.” 

With initial evaluation of several markers, including a marker on chromosome 15, Thomas says, “With analysis, markers have validated, but it’s a challenge that we need more data to really work with the analysis that we’re doing today.”

Ultimately, Thomas says the research team hopes to develop a breeding value by coupling genotypic and phenotypic information. 

“There is no doubt the genetics of grazing distribution is a complex trait,” Thomas summarizes. “I predict we’ll probably do research with the data set we’re developing over the rest of our careers.” 

Despite the complexity of the work, Thomas says some markers have been found, but the trait is highly polygenic.

“There’s not one single magic gene or magic marker that tells us why a cow walks up the hill or stays at the bottom,” Thomas comments. “There is a lot of work we have to do to translate this to the industry, but we’ve got to start on it.”

Thomas spoke during the 2018 Beef Improvement Federation Conference, held in mid-June 2018 in Loveland, Colo. 

Saige Albert is managing editor of the Wyoming Livestock Roundup and can be reached at This email address is being protected from spambots. You need JavaScript enabled to view it..

The added value of genomic information to expected progeny differences (EPDs) in beef cattle might produce more accurate EPDs, especially in young, unproven bulls.

The evolution of genomic information isn’t designed to replace EPDs but to make the information more accurate, according to Matt Spangler, University of Nebraska beef geneticist.

Commercial implications

The use of genomic information can be particularly helpful for commercial cattlemen. If a commercial producer is evaluating two yearling bulls with identical EPDs, which should he choose?

If additional genomic information is available that shows one bull has a calving ease of +11, while the other is -2, that producer could have made a serious mistake without this additional information, Spangler said.

This technology can really be useful in younger animals that don’t have a lot of EPD data available.

Parentage

Genomic testing has also been used as parent testing to ensure animals have the correct pedigree but it has now evolved into collecting data for complex traits, which are traits influenced by numerous genes that have EPDs.

“When genomics first came into the marketplace, bull sale catalogs were filled with a plethora of information,” Spangler said. “A lot of that information was useless because the ratios, EPDs and accuracy were too low.”

Nucleus breeders who produce seedstock for other seedstock operators need to be the first to implement genomic information into their programs.

“Within each breed, the nucleus population is what drives genetic change,” Spangler explained. 

“Seedstock producers can utilize this information to make genetic change quicker. They can use fewer animals because they have more accurate data and more confidence in the animals they use,” he explained.

Using tools

Spangler discussed the current application of genomic tools, including testing for genetic defects, paternity, genomic-enhanced EPDs and the potential for marker-assisted management. His take-home message to seedstock producers is to continue to collect and routinely record phenotypic information, even if they collect genomic data.

“As a seedstock producer, we still need to weigh our calves at birth,” he said. “Genomic technology only makes these tools stronger. It does not replace them.”

Spangler sees genomic predictions being particularly valuable to seedstock producers with young, unproven bulls. Before genomics were available, producers used EPDs to select a sire and then had to test the bull by producing many offspring to improve accuracy for the traits carried by that bull.

“Genomics and the corresponding marker-assisted or genomic-enhanced EPD, have become a reality,” Spangler explained.

“Within a breed, genomic predictions have proven to add accuracy for several traits, particularly to young bulls,” he added.

Breed specificity

The problem with genomic testing, Spangler continued, is it tends to be breed specific.

“If a test was developed for Angus, it will work best for Angus cattle. The test will not be as accurate if it is used in other breeds. An Angus test used on Charolais will not work as well, and we will be really disappointed if we use it in Bos indicus cattle,” he explained.

In fact, Spangler discussed a study where the application of a genomic prediction test developed for Angus was used on the closely related Red Angus. The results showed a substantial amount of variation and were deemed inaccurate, he said.

Better bulls?

Many producers question whether a genotyped bull is better.

“His EPDs should be more accurate, but it does not make him a better bull,” Spangler explained. “As accuracy increases, some bull’s EPDs will go up, and some will go down. We don’t need to understand genomic test results. They are supposed to be incorporated into the EPDs to make them more accurate. Just look at the EPD.”

Originally, genomics was developed to help researchers pinpoint genetic defects like marble bone. Before this testing was available, Spangler said animals were purged based on their pedigree.

“We can now use genetic testing to pick out the carriers and determine what to do with them,” he explained. “Without this testing, some breeds would have been decimated in the past few years.”

Genomic testing will also continue to be developed and used to identify genetic defects in cattle.

“There are many more genetic defects out there,” he said. “We just haven’t identified them all yet.”

Gayle Smith is a correspondent for the Wyoming Livestock Roundup. Send comments on this article to This email address is being protected from spambots. You need JavaScript enabled to view it..

 

 

 

Douglas – “This is a good time in the cattle business to AI heifers,” says Willie Altenberg of Genex Beef. “We are turning the corner.”

Because the beef industry is poised to expand, Altenberg mentions that heifer development and breeding considerations will become more important moving into the future.

“We have 29.8 million beef cows,” he says. “We have stayed flat at 4.2 million beef replacement heifers, and the last five years, it’s been going down.”

Because of drought and high feed costs, heifers are worth a lot, so producers have sold their heifers in the past few years. However, weather is turning around, the cattle business is good and cow numbers are down.

“We want to rebuild, and how do we do that? We retain heifers,” Altenberg notes. “Heifers will be worth a lot of money.”

AI breeding

With 29.8 million beef cows in the herd, Altenberg estimates that of the cows bred by artificial insemination, 15 to 20 percent of those are heifers.

“Why do we breed more heifers on the percentage basis? We want to make sure we get the right bull for birth weight and calving ease,” he explains. 

By utilizing low birth weight, high calving ease bulls, Altenberg notes that heifers don’t need to be grown in a feedlot, they are easier to breed, calves don’t have to be sorted and there is no post-partum interval.

“When we AI heifers, we synchronize them, and they cycle and settle well,” he says. “They are easy to breed, and we generally get good results.”

Profitability

“What I found interesting is that the spread between the unprofitable producers and profitable producers is bigger than it was five years ago,” Altenberg comments. “Profitable producers have high conception rates and more pounds per female exposed.”

Altenberg notes that conception rates are important for profitability.

“At the end of the day, if we can get females pregnant and if we have more pounds of calf to sell, we can be more profitable,” he says. 

AI breeding, he adds can result in higher conception rates.

With a synchronization program, Altenberg says approximately 60 percent of heifers bred in a single afternoon will get pregnant, and genetics companies who specialize in AI are skilled at achieving those rates.

When compared to using a bull to breed heifers, Altenberg figured that the cost is approximately $56.55 per pregnancy.

However, with an AI program, the cost per calf is $60 for the first 60 calves that are born, which is very similar to traditional breeding. 

Picking a bull

In choosing the right bull to breed, Altenberg notes that it is important to look for double-digit calving ease EPDs.

“The first thing we want when we are breeding our heifers is live calves, which means we want calving ease bulls,” Altenberg explains. “Red Angus and Herefords public calving ease numbers.”

While most Angus breeders don’t publish calving ease numbers, they do publish birth weights.

“Buy semen from a proven bull,” he adds. “My contention is that calving ease EPDs are more important, but producers should look at birth weights and ratios as well.”

Because the calving ease direct EPD incorporates birth weight, Altenberg notes that considering that number isn’t as important.

Saving replacements

Altenberg also notes that if producers set a threshold and stick to it, they can gauge their progress. 

“If ranchers pick a bull that has a 15 calving ease EPD, and it is easy, then the rancher can go to a lower calving ease bull or stay there,” he says. “I would rather have easier calving.”

After putting two years of investments into replacement heifers, Altenberg comments that it is important to make sure heifers calve easily in their first year.

“Don’t be a little afraid to give the heifers a little break,” he adds.
“We don’t have to throw our heifer calves away,” Altenberg comments. “Ranchers might be surprised. If they are able to give their heifers a little care, they can be the best cows in the herd.”

Altenberg presented at the 2013 Heifer Development Symposium held mid-September. Saige Albert is managing editor of the Wyoming Livestock Roundup and can be reached at This email address is being protected from spambots. You need JavaScript enabled to view it..

On July 7, the American Angus Association (AAA) implemented a transition from a multi-step process for genetic evaluation to a new process called Single-Step Genetic Evaluation.

Angus Genetics, Inc. (AGI) Director of Genetic Service Kelli Retallick explains that the changes ultimately simplify the evaluation process and make it more current for producers.

Changes

“Basically, we’re moving from a two-step method. In that method, we had to create a training population. This population was used to train DNA markers from animals who had genotypes and phenotypes, or performance data,” explains Retallick. “AGI then used that information to calculate molecular breeding values (MBVs) for individual animals to be incorporated as correlated traits into our models.”

Now, the single-step process takes the genomic results and includes them directly into the genetic evaluation in a single step.

“What we’re doing is we’re allowing ourselves to find those animals who are more genetically related and who these animals are more genetically related to, in their pedigree,” she comments, noting that DNA is passed down in “chunks” called haplotypes.

Retallick continues, “When DNA gets passed down in that manner, individuals can be more related to some animals in their pedigree than others, and their expected progeny differences (EPDs) are going to more closely follow the performance data we have on those types of pedigrees.”

Benefits

According to Retallick, the change to a single-step system will streamline the genetic evaluation process.

“The biggest benefit of this change is we can continuously use all of the data every single week, eliminating the need for calibration,” says Retallick.

In 2010, she notes AAA changed to weekly genetic evaluations using a two-step model to incorporate genomic data. However, every 14 months, a calibration had to be performed to incorporate the new data.

“Basically, this calibration updated the prediction equations used to predict MBVs, based on new data,” Retallick comments.

She continues, “Instead of having recalibrate every year, now, genomic data will continuously flow into the evaluation, so every week, all of the new information – pedigree, performance data, progeny data and genotypes – will be used, and genomically enhanced EPDs are going to fluctuate accordingly.”

Re-ranking

“Right now, we don’t see any disadvantages to the single step method,” comments Retallick. “This is the best technology we have available to work with to work with the information we have.”

She notes, however, that producers have seen some re-rankings of individual animals.

“Our members have seen some re-rankings in individual animals due to the fact the evaluation has moved to this new system,” Retallick says. “Because several other updates have taken place to our genetic evaluation besides just moving to the single step methodology, some of these changes are due to the way the genomic results are handled in evaluation and others are due to updates made to both our growth and carcass models.”

She continues, “These concerns are something we’re working through with our membership – both membership wide and on an individual basis – to help them to understand what changes are taking place and why. While there may be a lot of movement now, the hope is that by moving to this methodology less change will be experienced in the future.”

Seedstock producers

For seedstock producers, Retallick explains the July 7 change will improve their ability to predict future progeny performance.

“I think the greatest impact for seedstock producers is they are going to have a better and more accurate prediction of their EPDs to predict future progeny performance a little bit earlier,” she says.

Retallick explains the information is more real-time based since all sources are incorporated on a weekly basis. Individual producers who take a more active role in data recording will benefit more from genomic information.

“From a seedstock producer standpoint, breeders should really be able to weed apart who is excelling and coming up toward the top a bit quicker and make those selection decisions with a higher degree of faith in what the EPDs are telling us,” she comments.

Commercial impacts

According to Retallick, commercial producers should be aware of some changes when making decisions.

“For some of our traits, the scale has changed a little bit, so what was once thought of as a target for a particular trait has changed,” says Retallick. “It is important for commercial producers to use EPDs to compare two animals when making selection decisions and talk to their seedstock provider about what the values of those EPDs represent.”

She continues, “We want both seedstock and commercial producers to pay attention to the percent rankings and how animals rank within the population,” noting that just because EPD numbers have changed does not necessarily mean the animals have shifted down in the population rank.

“We have several different articles, fact sheets and frequently asked questions guides written up for producers, and we have three videos up now that go over frequently asked questions about the changes that took place on July 7,” she concludes.

Emilee Gibb is editor of Wyoming Livestock Roundup and can be reached at This email address is being protected from spambots. You need JavaScript enabled to view it..

“The industry is moving forward with superior genetic selection tools,” says Jerry Bohn, National Cattleman’s Beef Association vice president. 

NCBA sponsored a webinar, titled “Moving Forward with Superior Genetic Selection Tools,” explaining how commercial and seedstock producers could utilize genetic tools to improve their herds. 

Speakers ranged from scientists to breed association representatives. The webinar aired Feb. 25 on the association’s “Cattleman to Cattleman” channel on YouTube. 

Progeny expectations

“To be put simply, the expected progeny difference (EPD) tells producers how we can expect one animal to differ from another,” says Mahidu Saatchi, International Genetic Solutions lead genomicist. 

“For example, we could have bull A scored at 10, and bull B scored at zero for yearling weight EPD,” he said. “Bull A will likely produce progeny that are an average of 10 pounds heavier than bull B. This doesn’t mean they will all be heavier but is simply an average.”

Saatchi explained the technology used to calculate EPDs has evolved a lot since its inception. EPDs are calculated using phenotypes, performance and contemporary groups, pedigrees and more recently genetics. 

Advanced EPDs

“We can now use DNA technology like never before,” he said. “We know DNA is the basis of inheritance, and we can use this technology to understand the basic genes that cause differences.” 

He explained despite the complicated nature of DNA technology, running tests is relatively inexpensive to producers and can provide more accurate EPDs. 

“Producers can choose how many data points they want in their reports,” Saatchi said. “The more data points, the more expensive the test will be.” 

“There are two types of single-step models used to calculate EPDs,” Saatchi explained. “The SS-GBLUP uses all markers, adjusts for relationships and assumes all markers have equal impacts. The SS-SHM is a marker effect model that is able to squeeze more information out of DNA by weighing markers based on their impact and leveraging biological facts.” 

He explained, even with the popularity of these tests and models, a very strong computer is required to complete the analyses. Advancing computer sciences have allowed for improvements in the software used to build these models. 

“I have found the BOLT software to be more accurate than the older Cornell system,” he noted. “The need for improving accuracy drives innovation.” 

Seedstock utilization 

“The value of purchasing genomically enhanced, parent-verified bulls is confidence,” said American Hereford Association President Shane Bedwell. 

He explained when it comes to purchasing bulls, verified parentage is extremely important to have accurate EPDs. Advanced DNA technologies used in EPDs has made this process more efficient than ever. 

“When we have better, more accurate EPDs, we can verify young bulls that haven’t performed yet,” he noted. 

“As a whole, we are making a better product from one end of the chain to the other by having genomically enhanced, parent verified animals,” said Bedwell. 

Index selection 

Bedwell explained the index selection was developed in 1943 as a means to simplify sire selection. Ideally, it utilized economically relevant traits to formulate the index and increases commercial line profit.

“To determine economically relevant traits, we have to ask ourselves some questions,” he said. “Ranchers need to determine what their breeding and marketing goals are, what traits directly impact the profitability of their specific enterprise and whether there are environmental constraints.” 

He listed some of the more commonly cited traits including, calving ease direct, weaning weigh direct, yearling weight, mature weight and carcass weight. 

“Some of the indicators for these traits include birthweight, yearling height, mature height and scrotal circumference,” he noted.

“When we utilize the index selection tool, we are simplifying the process of choosing sires,” Bedwell said. “We are able to look at traits weighted based on impact for specific production scenarios.” 

“We have to remember high index values in one trait don’t mean all traits will have high values,” Bedwell said. “A bull could be in the 100th percentile for one trait and the 70th for another, and that’s just how it goes.” 

He also stated, “Breed improvement and advancement of a breed is not always going to match the profit index goals.”

Callie Hanson is the assistant editor of the Wyoming Livestock Roundup. Send comments on this article to This email address is being protected from spambots. You need JavaScript enabled to view it..