GENETICS

Cattle breeds and beef genetic testing

Angus Gene Reboot

A journey through the “dark early years” delivers producers to solid genetic ground

Genetic defects are a fact of life. We are fortunate today to have technology available that makes a defect manageable instead of potentially debilitating to business the way it was just a few decades ago. But no matter how fancy the DNA tests get, managing genetic conditions successfully takes transparency, time, and thought. Over the last several years, the American Angus Association (AAA) has updated the protocols on several genetic conditions that have been discovered, allowing their members and clients to continue to improve Angus genetics.

“All breeds of beef and dairy cattle have identified recessive genetic conditions,” explains Dr. Dan Moser, President of Angus Genetics Inc. (AGI), owned by the AAA.  “Some, dwarfism for example, were identified in the 1950s, long before genetic testing was available. In order to identify carriers the suspect pedigrees had to be strategically bred and it just took too much time and too much money to test through designed matings.”

Prior to joining AGI, Dr. Moser was an animal science professor at KSU. While he wasn’t with AGI when some of the early genetic defects were identified and protocol changes were made, he saw first hand the implications with the Kansas State cattle herd.

“Since DNA testing is now available, when recessive genetic conditions are identified in Angus and other cattle breeds we can use genomics to locate the causal mutation,” he explains.  “We test potential carrier animals and find those free of the condition that will transmit the positive aspects of their ancestors.”

The AAA policies evolved with time and information. The requirement of testing may also depend on if a defect is lethal or not. Testing is required for registration for recessive conditions that are lethal to the affected progeny, like Arthrogryposis Multiplex (AM, sometimes called Curly Calf). Arthrogryposis Multiplex was first recognized in 2008. After the AM discovery, rather than cancelling or suspending the registration of AM carrier females and bulls, the AAA required that their offspring born before December 31, 2009 be DNA-tested for the AM gene and results of the carrier status would then be noted on their registration and performance pedigree certificates.

Today, heifers have to be tested but can be registered no matter the outcome. Bulls, however, can only be registered if they test AM free. Steers don’t require testing, while calves from AI carrier bulls may be registered if they were conceived less than 60 days from the time the bull was identified as a carrier. The policy is less aggressive for a non-lethal condition like Oculocutaneous Hypopigmentation (OH, or White Eye). The AAA provides detailed information about each defect as well as guidance for breeding and management. The carrier status potential carrier status is clearly noted for every animal so they can be managed appropriately.

The testing and grace period allowed Angus breeders to identify the affected animals so that they could be strategically bred to have calves that test free of the AM gene—therefore keeping the quality genetics of their parents without passing on the problem genes.   

“The Association offers education; we clearly identify carriers and potential carriers and promote transparency so that our members and their customers can be confident,” Dr. Moser reassures. “Our customer service representatives do a great job working with members and helping them understand how to breed the next generation of Angus with better genetics than the one before.”

Breeders are vigilant

Regardless of the breed in question, finding genetic defects attached to certain bloodlines presents a challenge for many producers, despite our ability to identify them.

“The identification of genetic recessives in the Angus breed created a major negative impact on our business,” says Brian House, Vice President, Beef Program and Product Manager at Select Sires. “During the period of time when AM, NH (Neuropathic Hydrocephalus recognized in 2009) and CA were identified, we tested and identified 41 bulls who were carriers of these recessives. This included bulls of all ages—older proven bulls and young bulls that were just getting started. Due to strict policies implemented by the AAA, these bulls became unmarketable—so we ended up getting rid of both bulls and semen and our sales dropped during this time. As we learned with subsequent genes being identified and the greater use of DNA testing, genetic recessives can be managed in a breeding program. Our dairy customers do this every day.”

“Through the process of testing for various genetic conditions, breeders became more familiar with DNA, testing procedures and how genes are passed to subsequent generations. This probably helped pave the way for genomic testing, which has gained rapid acceptance across the industry, and is moving genetic progress at a much faster pace,” says House.

According to Dr. Moser, the peak year for DNA test purchases for AGI was 2014. Currently they test about one-forth as many animals.

“The rules did a really good job of eliminating carriers from the population,” Dr. Moser says. “At the time of discovery of some of the traits, some carriers were no longer used and the pace of genetic improvement slowed. Genetic improvement has rebounded since 2010 for a wide variety of traits. There was a short-term cost in genetic improvement but we have been able to make it up while eliminating the worry and economic impact for commercial cattlemen.”

Gathering information is the first step in management of genetic conditions. The policies and protocols adopted by the AAA have helped to inform and guide producers, but the success of those rules depends on producers that identify issues and report them.

“Our breeders are vigilant,” shares Dr. Moser.  “I give them a lot of credit for their willingness to report calves when things aren’t right. Abnormal calves are sometimes born as a result of the environment and are not necessarily a result of genetics. Working with Dr. David Steffen at University of Nebraska, we confirm parentage, collect DNA, sometimes are able to get pictures and x-rays and we store that information in a very detailed database should there be similar issues in Angus or other breeds. The information is gathered and tracked. We also store our own DNA. We have over 900,000 DNA samples here at the office.”

Data collection saves the day

Dr. Moser noted a situation in which an older AI sire in their archives was identified as a potential carrier of Osteopetrosis (OS).

“We were able to go to our archives and retrieve a semen sample for testing. He turned out to be free of the condition, and we were able to clear over 100,000 of his descendants in the database as well. It saved a tremendous amount of cost, not having to test every descendant,” reports Dr. Moser.

With information, education, and strategic policies in place the AAA has been able to reduce the number of cattle carrying genetic defects and continue to improve Angus genetics. But the last few years have been a DNA crash course.

“Today’s customers are very well informed, but it hasn’t been that way very long,” says House. “We, along with our customers, learned ‘on-the-fly’ about genetic conditions and their ramifications. I believe today’s level of understanding regarding DNA/genomics was kick-started in part due to genetic recessives. Are we better off today than we were before these things were identified? I would say yes.”  

Strategic DNA testing and management allows Angus breeders to produce great cattle that are desirable to the commercial customer. Making intelligent rules to handle the reality of genetic defects has allowed the AAA to stay on top and serve as a model for other breeds when they confront their own genetic defect challenges.

 

The Ways We Graze

Not All Cows Dine The Same

If left on their own, cattle and wild ungulates like to hang around the water hole and graze the dickens out of riparian areas. This fact has caused more than a few cowboys to scratch their heads and wonder if they can breed a critter that'll head for the high country when the grass greens up.

If left on their own, cattle and wild ungulates like to hang around the water hole and graze the dickens out of riparian areas. This fact has caused more than a few cowboys to scratch their heads and wonder if they can breed a critter that’ll head for the high country when the grass greens up.

By: Jaime Pullman

What makes cattle good at grazing? Is one breed better designed for grazing than another?

Recently a reader asked WR if cattle bred to live off western grasses could survive easily on the grasses of the east, and vice versa. The answer depends on a multitude of factors, but the key is adaptation. When cattle evolved as grazing animals, their job was simply to survive and reproduce. Domestication asked them to produce within the limits of their environment and climate. Today, cattle genetics from across the world can be easily exchanged, and animals are moved thousands of miles within a day. This provides unique opportunities for introducing heterosis and improving various traits. But this type of movement comes with problems, as well.

According to geneticists and producers from a 2004 National Beef Cattle Evaluation Consortium meeting report,“A gene pool conferring adaptation to past and distant environments confers less than optimum adaptation to current and, indeed, to future conditions.” The report continues, “In many instances, management systems and environments are changing more rapidly than animal populations can adapt to such changes through natural selection… While providing many benefits to efficient livestock production, movement of genes into new environments also can reduce adaptation of a resident herd to its unique conditions and challenges.” As a result, the report suggests “Rapidly increased genetic potential for production may be achieved at the expense of decreased genetic merit for adaptation” (fertility and survival). 

Breeds of cattle don’t exhibit remarkably different grazing habits in general, but they are each best adapted to graze under the conditions in which the breed developed. During the early 1990s, researchers from the Northern Agricultural Research Center in Havre, Montana, found that different biological cattle types do not significantly differ in the amount of time or distance they traveled when grazing rangeland.

However, the bite rate did differ among breed groups (a bite is defined as that tearing sound heard as the forage is pulled from the stems – bite rate is the number of bites in a given period of time). The larger, higher-producing biological types had a higher bite rate. The researchers proposed that the increased bite rate might be a response that, essentially, allowed each breed to get the right amount of intake for their breed-specific needs.

Introduction to a new environment would require the individual microflora to adjust to new forage, but that adjustment would occur over time to improve feed efficiency. Other stressors, including changes in terrain, heat, humidity, and altitude require longerterm adaptation.

The genetic grazing ability of an animal, while an important consideration, is less important than climate, forage conditions, available labor and management skill. Choosing the best cattle type for a climate is most successful if you consider the climate in which the breed developed, and the ability of the cattle to adapt to the environment. Cattle native to temperate regions do well in cooler conditions, for example. Which brings us back to adaptation. There are about 75 different cattle breeds in the US and most can be grouped according to their place of origin (Bos taurus, Bos indicus, etc), and some assumptions about their ability to adapt to different climates can be made from that information.

According to Dr. William Pinchak, a professor at Texas A&M AgriLife Research who has more than 30 years experience as a grazing beef cattle nutritionist, every genotype and environment exists across wide regions. If you break up the country by region, some sections will have different forages than others. For example, in some sections there may be greater amounts of tall fescue and perennial ryegrass. Humidity, temperatures, and precipitation can vary significantly across small distances. Even small changes can impact cattle that are adapted to one environment when they are moved to another.

Dr. Pinchak says, “Generally, cattle highly adapted to hot humid environments do not fare well in colder, dry environments. Similarly, cattle from the Northern third to half of the West take a year or two to adapt to the Southern Great Plains region. Northern latitude western cattle are usually selected for higher growth potential and body size than southern cattle and are fed hay, silage, etc. for up to six months per year to meet genetic potential for performance.”

Sparse forage suits cattle of small to moderate size best, while abundant forage can maintain larger cattle or a greater number of smaller cattle. When forage is low quality, lower milking cattle are best, since those that have high milking ability can lose body condition which may result in a drop in reproductive ability, unlike in a high quality forage situation. Inconsistent forage situations are most adapted by easy fleshing cattle types with low to moderate milk production.

Body size is also important because smaller cows tend to do less damage to grass paddocks, particularly during wet weather. There is also some evidence that smaller cattle are more mobile and are less impacted by heat stress than larger cattle.

Many of the traits improved through heterosis are especially important in grazing systems, including productivity, longevity, and fertility. This can be achieved by using high quality sires and breeding to large-gene-pool breeds. Genetics of cows is very important, but in terminal breeding situations, sire choice will have the broadest genetic impact on a herd.

Though research has shown some differences among breeds in the way grazing occurs, there is no evidence that one breed is generally more adept at grazing than another, except that some excel under certain conditions. But even under those particular conditions, the genetics of one group of animals within the breed may be significantly different to others. Research completed in the 1990s by New Mexico State University researchers found significant among breed and within-breed genetic variation in diet selection, which changes how range is utilized and managed.

This is why many experts recommend using large population breeds because sire selection options will typically provide the most genetic progress. Beef cattle diets are primarily pasture and stored forages, but pasture is the most economical feed program. It is also very sustainable when grazing cattle numbers align with the right amount of forage, the right type forage, and all at the right time. For this to happen, management is key.

STAY-AWAY-FROM-STREAM GENE
According to the 2004 National Beef Cattle Evaluation Consortium report, because cattle and wild ungulates prefer grazing near streams, preventing the over-utilization of riparian zones before adequate grazing of upland terrain is highly important. Research suggests that this type of problem can, at least in part, be solved through genetic selection.

A Montana State University study published in 2004 found that Tarentaise cattle, which are native to the alpine region of France, spent a higher proportion of time grazing on slopes distant from water sources than Hereford cattle, which are native to the British Isles. In addition, the researchers observed heritable variation within the Hereford breed to graze steeper, drier range areas.

Dr. Pinchak says, “We risk a lot in the beef cattle industry when broad generalizations are made.” He says the West versus East question can only be answered precisely if geographic location, forage/pasture type, winter feeding program and, most importantly, ownership and management objectives are identified. With our knowledge of genetics constantly developing, producers now have an opportunity to use both management techniques and genetic selection to improve forage utilization.

There is no one perfect breed, even under perfect conditions, but genetics can be selected to improve on the situation you have. Understanding the demands of your environment and climate on your cattle, and the ability of the cattle to adapt to those conditions, can make the best salable product within the challenges you face, regardless of your grazing situation.

Cattleman’s Crystal Ball

Genomic Testing May Be Complex, But Is Finally A Reliable Window Into The Future?

By: Jaime Pullman

Depending on your perspective, the world of cattle breeding has gotten more complicated in the last twenty years just as it has become more transparent. Genetic testing, genetic tools, and the unfurling of the bovine genome have given us the opportunity for more information than you ever dreamed of in years past. But knowing when exactly you need that information, when it will work for you, and when it will make sense for your bottom line and breeding decisions depends on some key considerations.

“DNA testing can be a very valuable resource but it still incurs a significant cost,” says Robert Weaber, Cow-calf Extension Specialist and Associate Professor at Kansas State University. “Producers should understand that they need a comprehensive plan to utilize the information in selection of animals to realize a return on their investment. The realized gain is typically easier for seedstock producers as the genomic information for many breeds is incorporated into the animal’s EPDs.”

Genetic testing can identify carriers of undesirable genetic mutations, enhance EPD accuracy earlier in an animal’s life with genomically enhanced-EPDs, and improve the ability of producers to make informed, thoughtful decisions for breeding and management.

“This is especially helpful for traits like stayability or maternal calving ease where evaluation of an animal using progeny data will take 4 to 8 years,” says Weaber. “With genomic data incorporated into a genomically enhanced genetic evaluation system animals that may be less than a year old can have EPD accuracies similar to those of an animal with 5 to 20 progeny depending on the trait.”

Improved accuracy for young animals doesn’t apply to testing proven sires, however, because most of his genetic potential has already been shown. In either case, it’s clear that genetic testing is not a one-size-fits-all proposition. Perhaps one of the best things producers can do to make the most of genetic tools is simply to refresh their understanding of genetics.

“Unfortunately my experience tells me that there is a disappointingly large fraction of producers, both commercial and seedstock, that do not adequately understand EPD or the accuracy value associated with EPD,” says University of Nebraska Associate Professor and Extension Beef Genetics Specialist Matt Spangler. “It is impossible to understand genomics and the benefit of this information if the fundamentals (EPD and accuracy) are not understood first.”

WHAT DOES IT MEAN?

Most major beef breed associations now incorporate genomic information into EPDs—they aren’t two separate pieces of information.

“The DNA and EPD information represent a part-whole relationship. The DNA test describes a portion of the genetic merit for a trait. The EPD describes the net merit (or sum of the value across all genomic regions and their interactions). Using both pieces separately is confusing as they may point different directions,” cautions Weaber.

“For instance a bull might have a great DNA marker result and rank in the bottom 5% of the breed for Weaning Weight EPD. What does this mean? It means that the net merit is not very good. However, at the regions of the genome included in the DNA test he appears to have very favorable merit. Then by difference, the remaining genetic merit for all other areas in genome, he must be very bad to pull his rank very low.”

Ahh… back when things were simple. Just roll out a couple bales for the cows, chop a water hole, fill the mineral feeder and choreup the big team. Then all this genetic jargon shows up and complicates things. Here at WR, we were pretty sure a locus was big flying grasshopper

Ahh… back when things were simple. Just roll out a couple bales for the cows, chop a water hole, fill the mineral feeder and choreup the big team. Then all this genetic jargon shows up and complicates things. Here at WR, we were pretty sure a locus was big flying grasshopper

Typically breed associations today will handle the genomic testing developed for the particular breed, resulting in the GE-EPD, or genomically enhanced EPD. If you don’t belong to a breed association, genomic testing might be best relegated to parentage and defect testing because one test isn’t accurate across all breed types. High density (HD) testing is now offered by many organizations, which looks at a large number of single nucleotide polymorphisms (SNPs) – the variations in DNA makeup. But that’s not always your only option.

“For seedstock producers they should use the test that their breed organization includes into EPD. Historically this has been the 50K. The density (number of SNP) of these tests has continually grown (e.g. 80K),” informs Spangler.

“While the size of the larger tests has continued to grow there have been some breeds that have offered a lowdensity (ex. 10-30K) test that is less expensive than the larger alternatives. Through a process called imputation (essentially filling in the missing SNP based on information from relatives), the same amount of information can be garnered by a low-density test as can be achieved by a high-density test.”

Commercial producers are typically looking at a narrower scope of testing, usually for parentage, but have to be careful how the testing is used.

“While there are tests marketed for use in commercial cattle for traits like growth, carcass and fertility, commercial producers should use caution and understand the limitations of genomics,” says Spangler. “This technology is not robust across breeds. For example, a test designed for Angus cattle will not work in Red Angus cattle. Consequently the science suggests that using this technology in non-pedigreed crossbred cattle will not yield predictable results. There are some tests that have been developed for straightbred commercial cattle (like Angus) and cost/benefit analysis should be considered before using such a test to ensure that the cost of testing is offset by gains in performance and/or improved management decisions.”

CONSIDER PROFESSIONAL HELP TO MAKE BREEDING DECISIONS

Genetic information allows producers to make more reliable management and breeding decisions. Testing earlier in an animal’s life provides value for both the seedstock producers and the commercial producer that ends up buying those genetics. And as the cost of bulls increases, commercial producers will be looking to seedstock producers to help them find that value in the form of more complete genetic documentation and increased confidence in purchase decisions.

Balancing your knowledge of EPDs and the limitations of DNA tools is key to benefiting your herd. Weaber warns producers to align the traits they select for with the marketing end point. Don’t focus all your selection on carcass traits if you sell calves at weaning in a conventional sale barn. Don’t select replacements based on a terminal or carcass index when you need maternal traits. Remember where your value is coming from. “The genomic tools are useful, but are not a silver bullet,” says Weaber.

“Also, producers don’t always seek out the advice they need to maximize the impact of their testing program. Although producers have historically each made their own genetic selection decisions, many would benefit from seeking professional help in designing and implementing a selection/breeding system. Many don’t do their own tax accounting; selection can be just as complex.”

From identifying genetic mutations to increasing EPD accuracy it’s clear that current DNA technologies provide opportunities for us to better understand cattle genetics. Identifying where your knowledge needs a boost in applying those technologies, or in using the resulting information, and then seeking help from an extension agent, breed association, or veterinarian, will allow your business to benefit the most.

Slick Pick For Sicks

nose

Are We Closing In On A Genetic Clue For BRDC Heritability

By: Jaime Pullman

One of the most costly scourges to the beef business, bovine respiratory disease complex (BRDC), is currently under the microscope. BRDC is the leading cause of death in beef and dairy calves. Respiratory diseases cost over $250 per affected feedlot steer when treatment, reduced carcass quality, and death loss are considered. Two research studies nearing completion right now hope to recognize the best management practices both in the pasture and the feedlot, and to identify those animals that are genetically more susceptible to BRDC. In combination, that could reduce disease incidence, thereby saving money, using fewer antibiotics and improving animal health.

Dr. Russ Daly, the state public health veterinarian and extension veterinarian and professor at South Dakota State University, is part of a three-year summer pneumonia research project now entering its final year. The study aims to examine and identify risk factors significantly associated with summer pneumonia in calves.

“All of us on the research team, as well as most cow-calf veterinarians you talk to, would indicate that we can see problems with summer pneumonia in very well-vaccinated, well-managed herds as well as in herds that do not employ extensive vaccination programs,” Dr. Daly shares.

“It is frustrating for us, as well as the producers, to know that one year can present problems and the next year no problems will be present at all. A fact that is very apparent so far is that there is no one single ‘silver bullet’ that ranchers can implement to prevent summer calf pneumonia. If it was an easy question to answer, we likely would have found the answer by now!”

Dr. Daly recommends identifying management practices that ‘make sense’ first by working with their local veterinarian. What vaccines might be helpful? What issues are other producers in the area dealing with?

“We also want to look at potential sources for different strains of respiratory viruses or bacteria to come into a group of calves,” Dr. Daly continues. “Separation of young calves from feedlot animals, for example, would make sense. Knowing your herd’s risk for or status concerning BVD persistent infections also makes sense. A cow or calf persistently infected with BVD virus will spread a great amount of virus to their herd mates; BVD virus greatly suppresses the immune system.”

Disease shedding is no stranger to the feedlot, which is where another research project on the BRDC hunt is taking place. The Integrated Program for Reducing Bovine Respiratory Disease Complex in Beef and Dairy Cattle Coordinated Agricultural Project (BRDC CAP) is a 5-year USDAfunded project being conducted by six different universities led by Texas A&M University’s Dr. James Womack and USDA ARS.

The research examined both pre-weaned dairy heifers (Holstein) and beef feedlot steers (Bos Taurus). Using a health scoring system, the researchers identified BRDC cases and then applied genomic technology that allowed them to estimate heritability for BRDC susceptibility. The resulting susceptibility ranged from 19 to 21 percent in the dairy animals and up to 29.2 percent in the beef.

IT ALL ADDS UP OVER TIME

Researchers believe genetic change could reduce the BRDC incidence by one to two percent per year, which might not sound like much but would be substantial over time.

“When an economic analysis was conducted based on the differences in harvested value of BRDC affected steers, their treatment costs, and death losses,” explains Dr. Holly Neibergs, “it was estimated that the feedlot industry was losing over $1 billion annually from this disease.

Based on our heritability estimates, if feedlot cattle were selected based on susceptibility to BRDC, significant economic gains ($13-21 million annually) could be realized by the feedlot industry.”

Dr. Neibergs is a geneticist, an associate professor at Washington State University, and a member of the BRDC CAP team. She first became interested in researching the possibility of reducing BRDC via genetics eight years ago.

Like Dr. Daly, she recognized that good management wasn’t everything. “I was struck with how the dairy and beef industries have identified best management practices, have routinely vaccinated their cattle and have had access to improved treatments to reduce bovine respiratory disease, but yet the prevalence, morbidity and mortality is similar to what was experienced twenty years ago,” Dr. Neibergs recalls.

More than 20 different researchers of different disciplines are involved with the BRDC CAP. The program, now in its final year, followed 500 healthy and 500 BRDC beef cattle in two feedlot locations (Colorado and Washington). Scientists sampled cattle and followed them to harvest, tracked diagnostic data on found pathogens, treatment costs, yield and quality grades, weights and genetic information.

Preliminary results are based on data from the Colorado facility, since the Washington cattle weren’t complete at the time of this article. Those results show that both BRDC susceptibility loci and BRDC estimated heritability were similar in beef feedlot steers and the pre-weaned dairy calves. Dr. Neibergs says that the markers that have been identified with BRDC will be supplied to commercial genotyping companies once the research is complete.

The researchers will soon be providing the markers for dairy, since that part of the project was completed first and the incorporation of markers into genetic panels for beef cattle will follow soon.

HOPES TO MAKE SIGNIFICANT GAINS

By making the research available to breed associations and commercial genotyping companies, BRDC resistance could be incorporated into EPDs and selection indexes for producers to use.

“The heritability estimates for BRDC were better than we had predicted and improved further as we more narrowly defined BRDC,” Dr. Neibergs shares. “This provides strong evidence that by selecting for animals that are not susceptible to BRDC, we will be able to make significant gains in reducing the morbidity, mortality and economic losses associated with the disease.”

The BRDC CAP research suggests that regional differences might be in play with higher frequency of BRDC pathogens in some areas than in others, but Dr. Neibergs explains, “It isn’t clear if these frequencies change over time, or are the result of different vaccination programs, or different genetics of the cattle being exposed to the disease pathogens.

Therefore, it seems important to use a multi-pronged approach where best management practices, vaccination, careful observation to identify and pull sick animals, and the addition of selection for cattle that are less predisposed to disease will result in both short term and long term reduction in BRDC.” Saving time and money, and improving the life of beef cattle is a long-term goal for scientists and producers alike.

Advancements in management and genetic selection could make BRDC more of a nuisance than a curse. And the willingness to work with researchers helps make those advancements possible. “We would really like to recognize and thank all of those in the cattle industry that have made these studies possible,” concludes Dr. Neibergs. “Without the cooperation and collaboration of the beef feedlot and dairy calf facilities, we would not have been able to conduct these studies.”