The Coming Genomic Revolution

The Coming Genomic Revolution

We asked five experts in beef cattle genetics to look into the future. The changes they see coming would harness the power of genomics for increased precision, specialization and open doors of opportunity for cattle producers — even smaller ranchers — previously unimaginable. 

By Sharla Ishmael

You better get used to change if you plan on being in the cattle business in the next 20 years. The good news is the type of change coming on the genetic side of the business is pretty exciting as more producers will have access to and implement technology to improve their cattle, enhance decision-making and tap into more sophisticated systems of marketing.

We asked our panel to answer two questions. Here’s the first:

What do you see happening in the next five to 10 years on the genetics/genomics side that commercial and seedstock producers can look forward to – be it in evaluation, research or application?

Jamie Courter, beef product manager/genomics, NEOGEN

“As long as genetic technology has been available, it’s been a constant cycle where the technology is one step ahead of its ability to be implemented at a seedstock level. As the cycle continues to shorten, we are going to begin to reach this next realm very rapidly. As the technology progresses, as we get better and the cost goes down, the ability to whole genome sequence animals is going to be readily available. This provides animal breeders the ability to research important areas of the genome yet to be discovered, resulting in things like fertility haplotypes [a group of alleles in an organism that are inherited together from a single parent] and new EPDs for traits of interest.

“Then on the commercial side, we will continue to see increased adoption of genomic technology for replacement heifer selection. Yet we will enter into a new era of precision agriculture where genomics has a part to play in individual animal management at the feedlot level. We know a lot about an animal’s genetic potential to grade and finish as they enter the feedlot to help impact and drive profitability for that feedlot operator.

“There is something else I would hope to see as we move through the next five or 10 years. The beauty of the beef industry is that it exists in multiple segments. However, to date, the flow and sharing of information between segments has proven difficult. Genomics provides the opportunity to track an animal from the time it is born until the time becomes a part of someone’s meal. The overall buzzword around that is blockchain. Transparency is desired by the consumer and an increase in the implementation of blockchain technology can help facilitate that.”

Kent Andersen, director of genetics technical services, Zoetis

“As the future unfolds, I believe an important element of beef production will involve ‘farming all sorts of data’ to help make more profitable and less risky decisions. Thanks in part to genomics, the stage is set for commercial cow-calf producers — and other beef supply-chain segments — to affordably access complete genetic information that’s historically only been available for seedstock. 

“During the next decade, virtually all heritable traits of economic significance are likely to be genetically evaluated and included more powerfully in economic indexes and new decision support tools. Increasingly, the capture and use of all types of performance data from sources beyond seedstock are likely to become more automated, to continuously increase the accuracy of genetic predictions. 

“Sophisticated genomic-enhanced evaluations are anticipated to yield predictions that enable comparisons of merit across seedstock as well as commercial straightbred cattle, crossbreds that include blends of most all major Bos taurus and Bos indicus beef breeds, as well as beef-dairy crosses. Ideally, all segments of the beef supply-chain will be economically incentivized to strategically collaborate in the sharing of information — including phenotypes and genetic predictions — to continuously improve system-wide production efficiency and global beef demand.”

Mark Allan, owner, Allan Genetic Solutions

“If I am consulting with an individual on buying a commercial bull, and the animal doesn’t have genomic enhanced EPDs, I recommend finding a producer that does use genomic enhanced genetic evaluation technology. Genomic enhanced increases the probability of making the best decision. It’s not perfect, but it’s getting better all the time. In the near future, I think producers that aren’t utilizing genomic enhanced information are going to fall behind.

“For the commercial cattlemen buying bulls, the greatest chance for a successful outcome is to use genomic enhanced genetic information when purchasing a young sire. Additionally, sire parentage/traceback genotypes have already been collected and stored in a database. These will be part of the future for branded/elite marketed programs that require genetic proof to document quality of product.

“We’re starting to see some programs being built on some really good data that are allowing the commercial cattlemen in the U.S. to start capturing genetic information with genomics. An example is genomic data to be used to make commercial heifer replacement selection decisions.

“Likewise, that genetic information will also then overlap into the feedlot sector and start becoming part of the added value chain. It equates to the value-added vaccination programs 30 years ago – today that is the set standard for most markets if you want to meet the average or hit a premium. It’s just a must. I believe a lot of the genomic impacts on genetics are just going to become part of what you have to do to survive.

“Also, there’s been breakthroughs in advanced reproductive technologies. I won’t be surprised if we see more application of that eventually, even in the commercial beef sector, especially in making customized replacement females. The commercial producer could buy embryos to produce replacement heifers, which then allows him/her to breed the rest of the cow herd terminal. The advantage is in addition to being able to get that customized elite replacement female – whether it’s an F1 baldie or a composite-based pedigree female – and then being able to raise it in your own environment.”

Sally Northcutt, owner, Method Genetics

“Research continues to focus on refining the genomic tools available to the industry. The application side of genomic enhanced EPDs used in the seedstock industry will continue to expand. More products will be made available for commercial producers to efficiently make individual animal selections for genetic progress at a more rapid pace. I think we will also see superior advancements made with mating systems for specific traits using haplotypes and specific genes to fuel more accurate selection tools.

“Genomic data is allowing more rapid positive selection in the commercial seedstock industry, as we see the ability to accurately evaluate potential parents at a younger age. The aggressive propagation of the most current genetics in a program will continue to expand across the industry.”

Alison Van Eenennaam, cooperative Extension specialist, University of California-Davis 

“I think we’ll see better evaluation and an uptake in genomics – particularly at the seedstock level.

“We could see the utilization of single sex offspring. For example, in dairy, they only need one-third of their animals to develop replacements. The rest ideally would create a male beef animal. That can be done with sex-sorted semen, but it may also be possible through gene editing.

“Perhaps the introduction of gene editing with single genetic traits – like horns, hair coat, etc. You can’t address complex traits like marbling with gene editing as these traits are multigenic.

“A lot will depend on the government’s regulations. Right now, genome edited plants and animals are treated differently from a regulatory perspective – they shouldn’t be. The FDA has authority over genetically modified animals, because the FDA has determined intentional genetic alterations to be ‘drugs.’ This means animals carrying a DNA alteration are considered unapproved animal drugs and are not allowed to enter the food supply. So, all my research animals have to be incinerated instead of harvested. It’s crazy!

“The enabling legislation for this regulatory approach, the 1938 Food, Drug and Cosmetic Act, has been twisted into a pretzel to declare genetic alterations to be a drug. DNA wasn’t even discovered when this act was written, that didn’t happen until 1953. It makes no sense for a SNP [single nucleotide polymorphism] in an animal to be a drug, when that same SNP in a crop triggers no additional regulatory burden under the USDA. The oversight of editing for agriculture really belongs under USDA, not FDA.”

What might be possible 20 years from now?

Jamie Courter, beef product manager/genomics, NEOGEN

“If you think back to when genomics was first implemented at the seedstock level into a genetic evaluation for the beef customer, that was in September 2009. And 11 years later, we are on the cusp of being able to do so much more than that – things animal breeders and producers never would have never guessed possible in such a short amount of time.

“I think anything is possible in 20 years. As with any technology, it kind of grows exponentially. It’s just all a matter of how the producers choose to implement it. My hope would be that genomic technology is more fully seen as a tool for cattle producers to utilize for their benefit.”

Kent Andersen, director of genetics technical services, Zoetis

“An ancient Chinese philosopher named Laozi once said, ‘Those who have knowledge don’t predict, and those who predict don’t have knowledge.’

“That said, as someone who works in the genetic prediction business, it’s admittedly foolish of me to predict what might be possible in the year 2040 and beyond. If history is the teacher, it’s probable that innovations across technologies in items such as whole genome sequencing; imputation; gene editing; computational, genetic evaluation, sensor and imaging technologies; machine learning and artificial intelligence [i.e. to predict various phenotypes at any given stage of an animal’s life]; as well as new and enhanced animal health and reproductive management technologies, may be affordably available that are difficult to imagine today. 

“Let’s hope that evolving social and regulatory policies won’t inhibit the judicious development and use of these innovations.”

Mark Allan, owner, Allan Genetic Solutions

“There is some excellent work being done with STEM cells to enhance genetic gain. This type of technology will likely be 10-20 years from now when it impacts the commercial beef industry. 

“I think the biggest thing in 20 years, maybe much sooner, is going to be the impact of these technologies in value-added programs. These programs will be telling the story of conception to consumption, which the consumer wants when making purchasing decisions. 

“It also means change. Some people will be excited about the future, and some will not. But the magnitude of change is going to be as much as they’ve ever seen. I think we’re at a crossroads where we have to adapt to change or beef gets left behind. Everybody doesn’t necessarily want to hear that, but that’s just the reality, I do believe.”

Sally Northcutt, owner, Method Genetics

“From a genetic evaluation standpoint, additional traits developed from novel phenotypes will drive the ability to evaluate and select genetics that best fit the environment and production systems for greater profitability.

“Data will still be a driving force in the development and refinement of genomic selection tools. The progression of systems using new technologies will stimulate economically relevant data collection, allowing the data in commercial herds to actually feed the genetic evaluation systems to make better decisions in seedstock selection.

“A whole array of traits previously not considered on animal health, disease resistance and production ability in specific environments will surface. Sustainability of production systems and continuous improvement of the environmental footprint for the industry will evolve. Consumer acceptance of the end product not only for consistent product quality, but to also in producing more specific nutrition profiles in beef will be key.”

Alison Van Eenennaam, cooperative Extension specialist, University of California-Davis

“We could see introduction of surrogate sire technology to deliver superior genetics via natural service.

“Maybe cattle breeding in a petri dish. Currently, beef cattle producers are constrained by the generation interval. It takes about three years from birth to producing offspring. A lot of time is spent waiting for animals to mature. Something that’s been achieved in mice is they have been able to undergo meiosis in a petri dish. They can take stem cells from mouse embryos and make gametes – sperm and eggs – and combine them to produce viable zygotes. If this could be achieved with bovine embryonic stem cells, this could take the generation interval from three years to three months. This could increase the rate of genetic improvement more than tenfold.

“All of this assumes you can obtain an accurate estimate of the genetic merit from genomic testing of the embryos, and that your breeding objective is really where you want to be going. Remember, in the past, breeding objectives have not always been economically optimal; cattle breeders went from dwarfs to giants in 30 years.”

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This story originally appeared in the January 2021 issue of The Cattleman magazine, Texas & Southwestern Cattle Raisers Association’s flagship publication. Join today to start your subscription.