Exploring Genetic Defects in Beef Cattle

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Exploring Genetic Defects in Beef Cattle

By Lilly Platts      |      

Dr. David SteffenDr. David Steffen has dedicated his career in veterinary medicine to studying and identifying genetic conditions in beef cattle. His work has been instrumental in identifying the majority of the defects ASA tracks.

Genetic conditions emerged as an economic concern in beef cattle as the species was domesticated, and as intense selection for specific traits became prevalent. Today, the recognition and emergence of recessive genetic defects are fairly common, and with advancements in genetic technology, identification and management have become quite simple. Dr. David Steffen has been involved with the identification of the majority of emergent genetic defects in beef cattle characterized in the last three decades, including those affecting Simmental-cross cattle.

Dr. Steffen earned his Doctor of Veterinary Medicine, followed by a Ph.D. in pathology and bovine genetics under the direction of Dr. Horst Leipold at Kansas State University. Dr. Steffen started his academic career at North Dakota State University as a diagnostic pathologist and assistant professor. During this time he became board certified in anatomic pathology by the American College of Veterinary Pathologists. In 1995, he returned to the University of Nebraska, Lincoln, where he did his pre-veterinary studies. Today he is a diagnostic pathologist and professor at the Nebraska Veterinary Diagnostic Center. He examines tissues for diseases across all species and researches adverse genetic and congenital conditions in cattle. His research is focused on determining if an issue is inherited or due to environmental factors, and is an expert in determining if an issue is of concern. He works to establish phenotypic descriptions of emergent diseases and collaborates with molecular geneticists to develop tests that can offer long-term solutions for beef cattle breeders.

What Distinguishes a Genetic Defect?

One of the most important distinctions that must be made whenever phenotypic abnormality is observed is if it is inherited (genetic defect), or due to environmental factors. Dr. Steffen explains, “The big distinction we need to be aware of is a genetic defect versus a congenital defect. That’s important because a lot of reports are just about congenital defects, which just means present at birth. All congenital defects aren’t genetic, and some genetic defects aren’t congenital.”

There are a large number of environmental factors that can cause abnormalities in cattle, just like in humans. Vitamin A deficiency, viruses, fever in females during fetal development, and toxic plants are just a few common things that can cause a calf to be born exhibiting an abnormality, and Dr. Steffen estimates that at least 90% of the cases he sees end up being attributed to something other than a genetic defect. This makes it even more important for breeders to be vigilant about reporting abnormalities — an environmental issue and a genetic condition could present similar phenotypes, which may lead a producer to simply chalk the issue up to a fluke and disregard it when in fact, it could be a genetic defect. Alternatively, a producer could wrongly cull a good sire for an environmental effect noted in offspring. In commercial herds, Dr. Steffen sees a lot of cases where the producer will wait until there are multiple abnormal calves to report anything, which ends up making a diagnosis more difficult. Even in a commercial herd with few pedigree records, these reports can be extremely helpful in identifying defects and controlling disease.

By definition, a genetic defect is a mutation that results in an allele with an undesirable phenotype (disease or trait). When a mutation results in a physical or developmental issue that is deadly or causes extreme loss in function, it is classified as a genetic defect. Dr. Steffen explains that when he first started working with genetic defects, a sire was identified as a carrier if he was parent verified to two affected offspring. This could have major financial implications, as normal non-carrier offspring of the sire could not be distinguished by phenotype. Today, identifying carriers is still extremely important, but the affordability, speed, and availability of testing make it much easier to weigh the benefits and consequences of continuing to breed an animal that carries a defect. Genetic testing allows producers to retain the favorable characteristics of the pedigree, but to precisely remove the deleterious gene. Technology allows research to often determine the cause in as little as six months if breeders cooperate by reporting and sampling affected calves, sires, dams, and half-siblings for sequencing

A genetic defect is a mutation that results in an allele with an undesirable phenotype.

When Did Defects Become a Problem?

Dwarfism in Hereford cattle is a classic story of a genetic defect in beef cattle, as well as an example of how difficult it was to identify the cause and eliminate the pedigrees that were causing the issue. Dr. Steffen’s grandfather raised registered Herefords and experienced this first-hand. Dwarfism became an issue just over 70 years ago, and in one case, 25% of a California Hereford breeder’s herd showed visible signs of the defect. The only way to eliminate the issue was to remove any animal suspected of carrying the gene, purely based on observation and what was known of pedigree relations. This took years, and the breeder essentially had to start over with his purebred herd, which was a major financial hit. This happened to varying degrees with other defects, and until the technology became available to identify carrier animals within an individual animal, it was quite difficult to eliminate the issue entirely. 

Dr. Steffen explains that the identification of genetic defects in beef cattle has progressed immensely since he first started in the early 90s — from the first observations of abnormalities in animals to the development of a test, it could be up to five years, if at all. In context, if a breeder used a bull carrying a recessive defect for one year and kept back replacement heifers, that genetic defect risk would spiderweb throughout half of the sire’s offspring unknowingly for some time and cause that herd to go from having no genetic defects to a large portion being at risk. For a recessive defect to be expressed, both the sire and dam have to carry and pass on that mutant allele, but this scenario sets a herd up for massive failure if the wrong pedigrees are combined.

Genetic and scientific advancements have revolutionized this process. For example, in the spring of 2020, Dr. Steffen helped identify and develop a genetic test for a facial defect in calves in around four months. “If everything goes perfect and we get good breeder reporting and cooperation it can be four to six months,” he explained. However, Dr.Steffen cautions, “There are some disorders we have been working on for years.”

Discovering a Defect

The identification of most genetic defects starts with breeders reporting abnormalities to breed associations and veterinarians. For example, ASA’s DNA department takes calls and emails from breeders who have observed an abnormality in their herd, has the breeder file a report, takes photos, and ideally, collects a DNA sample. If the animal is still-born or dies, Dr. Steffen strongly encourages breeders to take an ear sample, and if necessary, freeze it as a DNA source. From a live calf, it is usually best to collect whole blood (EDTA purple tube). “If they run across something on a weekend, or when they can’t get a hold of anyone, I’m a big believer in freezing things. You can preserve the calf for later examination that way, and even though we were told by pathologists not to freeze samples, I do that for my research routinely and we can make it work.” Dr. Steffen says.

If a calf is born with an abnormality, it is extremely important to get photo documentation as soon as possible, take at least a DNA sample, and if possible, it is best to wait to discard the animal and place it in the coolest place possible until an expert has a chance to look at the photos. Breed associations, experts like Dr. Steffen, and local veterinarians can be extremely helpful in these situations.

Even though the large majority of abnormalities end up being attributed to environmental factors, Dr. Steffen considers every case that comes across his desk with an open mind. He says, “We investigate every report to some degree as a potential new problem. How we approach it then depends on what we see in the phenotype. If someone has an abnormal calf, I do consider how useful it will be, but I will look at everything delivered to the program. I tell people that at a minimum they need to take a photo and get someone to look at it or get the calf to a veterinarian. From that, we can determine if the case is worthy of further pursuit. Our typical approach is to determine the phenotype, and get a DNA sample from the calf, and if it’s convenient, from the sire and dam. We can bank that DNA, and record what we can about the phenotype.”

Cases worthy of investigating can be coordinated through the breed association, local veterinarians, or a regional veterinary laboratory. Often an autopsy or veterinary examination is needed to establish a diagnosis, whether it is genetic or environmental. Storing DNA samples on high-impact animals can be highly beneficial if an abnormality emerges in a herd — if the sire is culled after one season, at least a DNA sample will be available for later research. If a second case comes in the next year, and the phenotype suggests that this may be a new defect, having that banked DNA on the parents becomes more important. Dr. Steffen will look at the pedigrees to identify relationships as part of the investigation when those records are available. 

If a pattern of disease and relationships are identified, the next steps involve working with the breed association. Dr. Steffen explains, “At this point, we say, ‘we have really good epidemiological evidence showing this may be a genetic defect’. Then the breed association will assist research to allow us to sequence DNA samples and to determine if a relationship between genotype and phenotype truly exists. Once that is verifiable and the mechanism of inheritance is confirmed, the disease phenotype and mode of inheritance are published to inform breeders to aid selection. Once the mutation is known, the genetic tests are typically adapted to and validated on commercial DNA tests and offered to breeders to aid selection.”

Why Do Defects Matter?

Genetic defects can have massive financial implications if they go unchecked. For example, Developmental Duplication causes the duplication of a body part, oftentimes a limb. An affected animal may end up being healthy and productive, but an extra body part can cause extra calving difficulty, which only adds to the financial losses caused by dystocia, and can be more at risk for injury. Other defects, like Neuropathic Hydrocephalus, are always lethal, and as everyone in the cattle business knows, each and every calf is important.

As science continues to advance, harder-to-detect mutations that cause loss are being identified. For example, in 2011, researchers at UC Davis and the USDA were able to identify a lethal mutation in the Holstein bull, “Chief”, which was responsible for 525,000 spontaneous abortions worldwide since the 1962-born bull went into production. Chief is also estimated to have increased profit in the dairy industry by $30 billion dollars, which exemplifies the importance of being able to identify mutations and breed selectively to avoid issues. There is an unidentified number of mutations that cause hidden losses like this that can be discovered due to advancements in genomic technology without seeing abnormal calves, but by identifying missing genotypes in adult cattle populations.





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