The tale of the missing homozygotes

USDA NIFA grant enables national project aimed at improving reproductive rates in the U.S. beef cattle herd by identifying genetic variations in genes that cause embryonic mortality.

From the February issue of Drovers CattleNetwork.

It is known and widely accepted that reproductive traits and fertility are among the most, if not the most, economically-valuable traits when it comes to selection strategies in the beef industry. In fact, it has been suggested that U.S. cow-calf producers should have relative economic emphases of about 47 percent on reproduction, 24 percent on growth and 30 percent on carcass traits. While reproductive traits are of the most economic value, they are lowly heritable. Further, the use of artificial insemination (AI) has allowed for rapid genetic improvement in many herds, but it also has resulted in a narrowed genetic base in many breeds, which may be resulting in fertility losses due to the early loss of embryos that inherited two broken copies of genes that are essential for life. Combined, these two factors have presented challenges to fertility in the U.S. beef cowherd. Fortunately for the U.S. cattle industry, a team of animal scientists across the country are in the middle of a five-year effort to improve reproductive rates in beef cattle using genomics technology to identify the variations in genes that cause embryonic or early development mortality and develop selection tools to manage these so-called "lethal recessives."

The discovery

The project, "Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle," is being led by Dr. David Patterson from the University of Missouri. While it began as an Angus-focused project, it has since expanded to include multiple breeds in the United States with additional funding coming from the specific breed associations and other industry partners. Dr. Jerry Taylor, University of Missouri's Wurdack Chair of Animal Genomics and Curators" Professor of Genetics and Animal Sciences, is leading the research components of the project, or what he calls the "discovery" process. Dr. Alison Van Eenennaam, Animal Genomics and Biotechnology Extension Specialist from the University of California, Davis, is focused on the translation of that research, a role she describes as taking the research and determining how to use it in the industry.

The basis of the project, Taylor says, is simple. "Our concept is that there are loss of function alleles (alternative DNA sequences or forms of a gene that differ between individuals) floating around that you don't actually ever get to see because when they get together in two copies, which occurs at fertilization, these embryos either fail to implant or they fail to develop and we get relatively early stage embryonic loss, and for the most part, we don't even notice it. We don't see a fetus on the ground. We don't know that an abortion occurred."

Thus, the team hypothesizes that if they can identify these loss of function alleles, sensible, inexpensive reproduction selection technologies can be developed to manage these genetic conditions along with other economically important traits.

The first step of the project was to sequence the entire 3 billion nucleotide base pair genome of more than 250 Angus, Hereford, Simmental, Charolais, Gelbvieh, Red Angus, Maine Anjou, Beefmaster and Limousin bulls to identify loss of function alleles. Taylor says in all, they have found about 10,000 loss of function alleles, but he notes that at least 60 percent of them are not lethal because at least one of the sequenced bulls carries them in two copies. "The ones that are potential problems are the ones we find that never turn up in two copies, which means one of two things. Either we didn't sequence enough bulls to find one that had two copies, or they're lethal." Next, was a step called "variant culling," which entails determining if the genetic variations physically change the amino acid structure of the protein in a damaging way.

Once that's done, which Taylor says should be within the next couple of months, a genotyping assay will be designed to be used on 10,000 commercial Angus heifers in Missouri's Show-Me-Select heifer development program that will ask one simple question – of all the variants that were genotyped, which ones never show up in two copies in living animals? These are the so called "missing homozygotes‘ because the "aa" genotype is missing from the population. "Those are the ones doing bad things, and we don't want them in the population," Taylor says.

The translation

Then comes the translation portion of the project that, among other things, will incorporate the identified variants into commercially utilized genotyping chips. Taylor says genotyping animals will allow EPDs to be computed for direct fertility effects and will help producers not only select bulls to breed their cows to but also helping them decide which bulls to use with which cows to avoid embryonic loss. "If they carry any of the same loss of function alleles, we don't want to breed them together because we stand to lose embryos, lose fertility and end up with open cows."

In comes Van Eenennaam and her team to determine how to take Taylor's research and apply it to day-to-day use in the industry. "We are aware that breeders already have some genetic disorders that they have to manage. We're trying to develop tools to help them deal with the embryonic lethal conditions. Let's assume there are a lot of the missing homozygotes in the population – maybe at eight or ten or even 20 different genes – it becomes difficult to manage multiple genetic conditions simultaneously. We are working on approaches to manage these recessive alleles in a sensible way."

She says avoiding the use of carriers isn't sensible because all animals carry some recessive alleles and these need to be weighed against the genetic merit that a carrier bull may possess. A better approach is to avoid carrier-carrier matings that may result in the lethal "aa" genotype. Simple as it may sound, Van Eenennaam says if you think about all the permutations and combinations with multiple genes involved it becomes a big computational task to develop the best mating strategy.

With the help of Dr. Brian Kinghorn, professor at the University of New England in Australia, a computerized program called MateSel is being adapted to optimize mating decisions in the beef industry. This software, which Van Eenennaam says is still in the developmental stage will help producers minimize the incidence of affected offspring and the frequency of lethal recessive alleles while optimizing genetic gain from mating the very best cow with the very best sire. Producers will be able to create a mating list based on factors including semen costs, trait merit, genetic diversity (inbreeding), genetic conditions and recessive lethals, logistical constraints, and more. 

Once MateSel is finalized, it will then be up to the breed associations to decide whether they wish to use the software. Comparing it to software like Microsoft Word, Van Eenennaam says you will need a license to use it. She says because some of the lethal recessives may be  breed specific, the program will have to be optimized for particular breeds, which will also entail developing an assay and a test population similar to the 10,000 Angus heifers that will be genotyped initially. The developed genotyping assay will include all loss of function variants discovered in all of the sequenced breeds and will be publicly available to all breeders.

Another easy way to avoid problems associated with recessive lethals is crossbreeding, Van Eenennaam says. "Crossbreeding doesn't require computerized mating strategies, but if you've got a breed specific mutation, one way to make sure you get a functional copy of an essential gene is to outcross with another breed. Although the computerized mating strategy is a fairly sophisticated approach, there are also some pretty simple things producers can do to avoid matings with reduced fertility outcomes from a practical standpoint."

Another tool in the works is an educational resource,, which will be launched in June at the annual Beef Improvement Federation conference. Van Eenennaam says the site will house educational resources related to breeding and genetics. She says as additional information related to this and other USDA NIFA-funded genomics projects, including research related to feed efficiency and Bovine Respiratory Disease Complex (BRD), will be available on the site.

The timeline

Taylor says by the end of 2015 the list of variants that cause embryonic loss will be developed. It may be another year, however, before enough animals are genotyped for the breed associations to all have enough data to begin constructing specific EPDs. "Instead of publishing an EPD on six animals, which doesn't help anybody, we've got to have hundreds of animals that are genotyped and are being used in the industry before breeders can adopt the technology. Within two years, I think the information will start to roll out in the breed associations so that breeders can start to use it to improve fertility."

Overall, Taylor says this project will result in another tool producers can use to estimate genetic merit among animals for fertility. If you don't have a calf but do have an open cow, particularly with today's prices, the difference of one more calf on the ground is enormous. "If we can increase the calving rate of the national herd by even one percent – that is an enormous amount of money. Any technology that we can bring to improve the accuracy of identifying individuals that have fertility issues is going to help the industry be more efficient with the cowherd we've got and get more calves out of the cows we have, and that increases the efficiency of production and increases value of production very significantly."

For more from the February issue of Drovers CattleNetwork, click here.