Holly Neibergs, PhD, and her team at Washington State University search the bovine genome for genes that influence resistance to disease.
Holly Neibergs, PhD, and her team at Washington State University search the bovine genome for genes that influence resistance to disease.

Similar cattle, same environmental conditions, same vaccine protocols, same exposure to pathogens, and yet some get sick while some do not. Veterinarians have long observed that genetic differences must account for some of the variation in disease resistance or susceptibility in cattle, but the complexity of disease and immune response make development of selection tools much more difficult than for traits such as birthweight or coat color.

The emergence of genomics technology, however, opens up possibilities for more incorporation of health into selection strategies and development of more targeted vaccines, management and treatments based on genetic backgrounds.

DNA technology in livestock production has come a long way over the past decade, and ongoing research promises continued advancements and opportunities for veterinarians to further serve their dairy and beef clients.

Healthy genesGeneticist Matt Spangler, PhD, at the University of Nebraska, says in the immediate term, marker-assisted selection has been most useful in selecting for or against simple traits such as horned versus polled, hair color and genetic defects.

Parentage is another simple, but often overlooked, application of DNA technology with a great deal of value, particularly for evaluating bull performance in beef herds where producers use multiple bulls in breeding pastures.

Next , Spangler says, the technology has advanced to the level of providing genomic predictions for more complex traits already described by phenotype-based measurements such as expected progeny difference (EPD) and predicted transmitting ability (PTA). These include traits such as growth, milk production, longevity, fertility, somatic-cell count, calving ease and carcass merit. Breed associations and milk recording agencies have collected phenotypic data for these traits on large numbers of cattle, which facilitates testing and validation of the genomic markers. By combining genomic predictions with an established EPD or PTA, breeders can offer an enhanced, more accurate prediction, particularly for young animals that lack progeny data.

The development process for genomic-enhanced predictions becomes more difficult when dealing with traits for which there are no conventional EPDs or PTAs, such as feed efficiency or susceptibility to specific diseases.

One of the challenges, Spangler notes, lies in defining the phenotypes for a trait such as bovine respiratory disease (BRD) susceptibility. These could include clinical signs of morbidity, animals pulled for treatment, body temperatures, lung lesion at harvest or others. But we know that diagnosing BRD in live animals provides inconsistent results. When researchers look at lung lesions at harvest and compare their incidence with treatment records, they often find numerous untreated cattle with lesions, and other cattle that were pulled for treatment but exhibit no lung lesions.

Jason Osterstock, DVM, PhD, director of genetics technical services at Zoetis, agrees and cites a similar challenge with developing a prediction for susceptibility to Johne’s disease, where diagnostic tests are not entirely reliable. If you can’t accurately describe the disease, he says, it’s hard to detect the proper markers.

Genomic predictions for reproduction and fertility also are challenging, with key traits relatively lowly heritable. Some breeds have collected sufficient phenotypic data to develop predictions for traits such as heifer pregnancy, allowing them to develop genomic predictors and incorporate them into existing EPDs for that trait.

Unraveling the BRD complex
Researchers at multiple institutions currently are working to compile large volumes of phenotypic data related to BRD as part of a large collaborative USDA grant program. The project involves researchers at Texas A&M University, Washington State University, University of California- Davis, New Mexico State University, Colorado State University, University of Missouri, USDA’s Agricultural  Research Service and Gene Seek Inc.James Womack, PhD, Texas A&M University, is project director for the study.

Spangler says that project will lay the groundwork by identifying specific genomic regions or mutations related to resistance or susceptibility to BRD, but the effort will need to continue within the industry, including breed associations and genomics companies, to build and refine genomic predictions tested against phenotypic data.

Washington State University animal scientist Holly Neibergs, PhD, coordinates the research portion of the project, which also includes teaching and Extension components. She describes several studies currently underway in beef and dairy cattle.

A pair of studies involves two large groups of pre-weaned Holstein calves, one in California and one in New Mexico. The California group included 2,000 male and female calves, while the New Mexico study involved 800 heifer calves. In both cases, the researchers collected blood samples from every calf for genotyping, using a panel that evaluates 780,000 markers. The team sorted the study calves from larger groups between 20 and 73 days of age, aiming for half healthy calves and half with signs of BRD, based on the BRD-scoring system developed by Sheila McGuirk, DVM, PhD, at the University of Wisconsin.

They managed the calves in outdoor hutches, with case calves and control calves located in adjacent hutches to allow opportunity for exposure to BRD pathogens. They monitored control calves for signs of BRD and used two deep-pharyngeal swabs and one mid-nasal swab to collect samples for pathogen identification at University of California and Washington State University diagnostic laboratories.

They found that pathogen loads varied considerably between the test groups in California and New Mexico, and susceptibility appears specific to individual pathogens, with relative susceptibility profiled by different genomic markers. Research reports on the dairy studies are in development now, Neibergs says.

In another trial at the University of California-Davis, researchers have challenged 700-pound Angus calves with single BRD-related pathogens to evaluate gene expressions and began to identify which specific genes are associated with susceptibility to specific pathogens.

Several studies also are underway in beef cattle. In one 1,000-head Colorado study, researchers commingled calves in feedyard pens, with half of the cattle in each pen diagnosed with BRD and the other half healthy controls. Again, they collected samples for genomic profiling of each animal. The team collected treatment data and lung scores at harvest, and will conduct an economic analysis of treatment and control groups.

The research intends to find regions of the genome related to BRD susceptibility and use those markers as proxies for the actual genes involved. Analysis  based on genomic markers is imprecise, though, Neibergs points out, and accuracy varies between breeds and over time as cattle are exposed to different pathogen populations. The next step is to find the actual causative mutations or genes relating to susceptibility to individual pathogens. Current research at that level is taking place primarily in dairy cattle, but Neibergs says, researchers believe the locations of those genes and their expressions will likely have some overlap between breeds within the same species.

Neibergs says findings indicating different pathogen loads in cattle at different locations lead to questions regarding regional or seasonal differences in causative pathogens in BRD outbreaks, and implications for genetic selection, vaccination and treatment.

Once geneticists identify the specific loci influencing susceptibility to individual pathogen species, they likely will need to combine them into an index for selection purposes. As those genes are identified, Neibergs says today’s technology makes it relatively easy and inexpensive to add 50 to 100 markers to a panel used for DNA tests.

Results in the BRD research have been encouraging, Neibergs says. The researchers estimate heritability of susceptibility to individual pathogens within a region at around 20 percent. Heritability drops, however, when measured for all BRD pathogens across regions. “Complex diseases are tough,” she says, “involving lots of interactions, but we can make some improvement.” Genomic-enhanced selection can’t do it all, but it can serve as another tool, along with vaccines, animal husbandry and treatment, to reduce the cost of disease in cattle operations.

Inheritance of fertility
Neibergs and the team at WSU, University of Idaho, USDABeltsville, USDA-Fort Keogh and the University of Florida are also conducting two genomic studies relating to fertility, one in dairy and the other in beef cattle. Tom Spencer is the project director for these two studies. The trials compare pregnancy rates in dairy heifers and primiparous lactating cows and then collect genomic profiles on fertile, sub-fertile and infertile females. In beef cattle, the maintenance of pregnancy is also being studied by monitoring heifers that are repeatably pregnant or not pregnant after transfer of in vitroproduced embryos. Similarly, the investigators can identify fertile, sub-fertile and infertile heifers that can be profiled to potentially identify genetic markers of heifer and cow fertility.

Hidden genetic defects
Healthy genesSpangler says researchers are using whole-genome sequencing to unravel the mystery of “missing homozygotes” in cattle populations. At some loci (individual locations along the genome), he explains, geneticists find some individuals that are homozygous for the dominant gene or heterozygous, but they cannot find homozygousrecessive individuals. Researchers suspect these missing homozygotes actually represent genetic defects that result in embryonic death or early abortions. Spangler theorizes that presence of these hidden defects could help explain the increase in fertility in crossbred cattle, as crossbreeding reduces the probability of homozygous-recessive traits in offspring. Whole-genome sequencing could reveal hundreds of these defects, Spangler says, allowing testing and potentially the application of advanced breeding strategies to reduce the incidence of those defects and improve fertility.

Some of these genes affecting fertility, or the blocks of DNA that contain them, which are called haplotypes, have been identified in several dairy cattle breeds. Genotyping chips from GeneSeek and Zoetis now include markers for them and can be used to detect animals that are heterozygous carriers. Mating programs from AI companies can then reject or penalize matings between animals that are likely to carry the same genes or haplotypes. More defects impacting fertility are likely to be identified and included in tests over time.

Practical applications
Stewart Bauck, DVM, is general manager at GeneSeek, the company that now administers and markets the Igenity profiles for cattle.

“We’re seeing a growing perception that the technology has moved into the mainstream,” he says. “We increasingly engage veterinarians who work in consulting relationships with progressive beef and dairy operations, integrating genomics into their routine management.”

Dairies increasingly use genomic tests to help in replacement heifer selection. Using sexed semen, dairies produce more heifers than they need and can select the best. And they integrate genomics with sexed semen to speed genetic progress by producing replacement heifers from their best heifers.

Bauck says tests for polled genetics, particularly in dairy cattle, offer excellent potential for improvements in animal welfare and safety and reductions in labor. In the past, he says, a smaller genetic base of polled sires created a perception that dairies had to sacrifice production traits to use polled genetics. Today, breeders can test calves at birth, or even as embryos used in embryo transfer, and use genomic profiles to identify homozygous polled individuals with EPDs or PTAs equal to those in top horned sires. This shortens the generational interval, and producers increasingly can use polled genetics without sacrificing performance.

Neibergs says WSU researchers have studied genomic associations for bovine paratuberculosis (Johne’s disease) in Holstein and Jersey cattle, and she says the team is close to publishing the putative causative mutation for susceptibility to that disease.

In beef production, genomic-enhanced selection has moved from the seedstock sector into commercial operations, with ranchers testing heifers and using the profiles for selection and strategic matings to complementary sires. Osterstock notes that in classical selection it is difficult to make progress on traits with low heritability such as pregnancy rates or somatic-cell counts in dairy cattle. Genomics can help but might still only explain a small percentage of the variation in traits such as disease susceptibility, where other factors such as nutrition and environment play important roles. Moving forward, he says, once genomic predictions for health traits become more robust, the next question will be how to use those predictions and how to prioritize them among other selection criteria. Other production traits will remain economically important, and the industry will need to learn how to integrate predictions for additional traits into selection indexes.

The veterinarian’s role
Osterstock sees opportunities for veterinarians to become more involved with their clients’ genetic-selection programs, especially as genomics moves more into the arena of animal health and well-being.

He says veterinarians can help determine current genetic limitations within a herd, or what parts of the system are not working and whether genetic selection could help solve problems. Then they can help determine whether genomic technologies complement other technologies such as using in-vitro fertilization, sexed semen or embryo transfer.

Comprehensive herd-health strategies are not easy to execute, he says. Health programs in beef or dairy operations include a lot of moving parts, involving vaccines, nutrition, reproduction, recordkeeping and analysis, and other factors. Adding another technology increases complexity, offering the veterinarian an opportunity to provide valuable service. If a dairy has an excellent program in place, optimizing health and production with effective input from their veterinarian and nutritionist, the operation could legitimately look for the next process or technology that offers incremental improvements. On the other hand, if an operation has a poor nutritional program or inadequate environmental conditions, genomic selection for health probably won’t help significantly.

Bauck also points out that veterinarians are trusted advisors involved in the total management in many cattle operations, so it makes sense for them to work with their clients in genetic selection, especially where it influences animal health and well-being. He says the company regularly hears from veterinarians who are submitting samples and helping their clients with genomic-enhanced selection decisions. He also says veterinarians can play an important role in monitoring genetic defects as they emerge, helping clients test their herds, interpret the data and plan breeding strategies. And over time, Bauk says, we’ll see exciting progress as low-cost genomic tests explain increasing amounts of variation in disease susceptibility, and many producers will rely on veterinarians to help them apply the technology.


Sidebar: Selecting for immune response
While genomics research can identify individual genes or markers that influence specific traits, genetics company Semex has introduced a new approach, evaluating phenotypes for overall immune response and using the measurement as a selection tool. Semex senior geneticist Jacques Chesnais, PhD, says the company’s “Immunity+” technology provides an indexed rating of immune response to common bacterial and viral pathogens in dairy cattle.

Bonnie Mallard, PhD, at the University of Guelph, developed and tested the technology, which is licensed to Semex.

Chesnais says the test provides a quantitative rating for immune response for each animal, unlike the “binary” record of sick or not sick, which is often used in the genetic analysis of disease-incidence data. Only bulls that score in the top 10 percent for immune response receive the Immunity+ rating. The heritability of immune response, as measured with Mallard’s technology, is about 25 percent, which is significantly higher than the 2 to 10 percent heritability for the incidence of diseases measured in the field.

Mallard’s research shows that high immune-response cows have lower disease incidence, respond better to vaccines and produce higher-quality colostrum, he says.

The patented testing process requires three visits involving antigen injections, blood tests and skinfold measures to evaluate antibody-mediated and cell-mediated immune response.

Research trials in the United States and Canada have shown that cows with high immune response have lower incidence of mastitis, metritis and retained placenta compared to average cows in the same herds.

Chesnais says the University of Guelph and the company are doing some preliminary work toward developing a genomic test for immune response. Phenotypic testing would remain important, but a DNA-based test could reduce the cost of testing, particularly for commercial producers evaluating replacement heifers. Early results are encouraging, he says, as they indicate many of the genes associated with immune response appear to be located within the BoLA Complex on chromosome 23, a region known to be associated with health traits.