It could be argued that in the second half of the 20th century, the beef industry made more progress in production efficiency than it had in its entire history up until that time. This was due to the rapid adoption of technology, which included artificial insemination, performance testing, utilization of expected progeny differences (EPDs), embryo transfer, ultrasound, genomics, and more recently with single-step calculation of genetic predictions.
Even with this record of achievement, many feel that we are on the cusp of taking a quantum leap forward like never before seen through the adoption of the next generation of genetic technology. This includes gene editing, genomic sequencing, specialized breeding systems, and genomically-enhanced predictions on new traits with an emphasis on fitness traits. This promises to reshape the beef industry, and lead to more profitable and sustainable selection and production.
New Technologies: Gene Editing
The ability to edit genes is appealing as a fast track to making progress. The technology now exists to edit genes, as has been demonstrated by Recombinetics, Inc., when they introduced the polled gene into Holstein clones at University of California-Davis. A simple single edit like this could have huge economic impact in the health and well being of the animals because they no longer need to be dehorned.
Another straightforward trait being considered is the introduction of the slick hair gene found in Senepol into other breeds. Cattle with this gene have been shown to breed back quicker and adapt better to hot environments. In addition, the gene editing technology holds the promise of correcting genetic defects like those conditions that cause early embryonic death loss.
Although gene editing is here and ready to be utilized, a major hurdle for commercial implementation in the U.S. is the regulatory process. At the end of the Obama administration, the regulation of the technology was moved to the Food and Drug Administration (FDA) to be treated like a drug in terms of the regulatory approval. Unless moved to another agency, the regulatory process the FDA requires will likely make it too expensive and burdensome to be implemented in the U.S. beef industry.
There are other hurdles to gene editing like the possible stigma among the public towards biotechnology. This will probably keep the technology within species, so there will not be introduction of genes from other species.
Dr. Tad Sonstegard of Recombinetics, Inc. is at the forefront of gene editing technology. He reports that the regulatory and potential stigma problems the U.S. faces are not a concern in most of the world. Most of the world is more interested in feeding people in an economical and efficient way. In Canada, the technology is already being prepared for the commercial market in Holsteins with the polled gene. Sonstegard also sees the technology being implemented quickly in countries like Australia and Brazil where the slick gene should have an immediate economic impact.
[inline_image file=”ff69327efbab7485db48305d2d23e346.jpg” caption=”Dr. Michael Bishop”]
Dr. Michael Bishop, former agrigenomics global market development specialist for Illumina, who is now an industry technology consultant, sees other applications for gene editing in South America. He notes that most of the world’s beef cattle are raised in tropical environments where the cost of production is low. Gene editing could affect not only cattle adaptability, but also improve beef palatability, fatty acid composition, and end-product shelf life. This would make beef raised in the tropics from Zebu-based cows more competitive on the world’s market.
Typically, the U.S. supplies genetics to the world. However, with the differences in the regulatory climate between the U.S. and other major beef producing countries, we may see edited genes being introduced back into the U.S. by importing germ plasm in the form of cattle, semen, and embryos from abroad. Sonstegard predicted that 20 years from now, the U.S. may be looking back wondering why it put itself in such a noncompetitive situation when it came to this technology if the U.S. maintains its current regulatory position.
One of the biggest questions that arises when it comes to the possibility of gene editing is, “What is the target?” Other than simple traits like horned and polled, the process becomes more complicated.
[inline_image file=”c47672a56f24b79c9ea026d14eed5983.jpg” caption=”Dr. Dan Moser”]
Dr. Dan Moser of Angus Genetics, Inc. said there is a need to discover major genes for more complicated production traits like disposition and longevity. He also points out that candidates for gene editing, like genetic conditions that cause early embryonic death loss, respond rapidly and effectively to traditional selection. In the end, there is a great need to continue to map the genome of animals where extensive phenotypic data has been collected.
New Technologies: Deep Learning
Genomics already play an important part of genetic prediction technology and this dynamic will continue to expand in the future at an ever-increasing pace. One of the keys to that expansion is the transition of the industry from chip technology for identifying genomic markers to ever more-detailed genetic sequencing. In addition, there is the need for the collection of more phenotypes on a broader range of traits.
When it comes to improving genomics, Bishop believes that site-specific DNA marker sequencing will replace the chips currently being used within the next five years. The cost of sequencing is rapidly declining, making it an ever-more-attractive alternative for purebred, composite, and hybrid seedstock producers. Site-specific sequencing has 10 to 12 times the number of markers as the chips. The cost of whole-genome sequencing of individual animals is also becoming affordable. The American Hereford Association is taking advantage of this by whole-genome sequencing its most influential sires.
[inline_image file=”782cfebe8bf922a020d79f845236572d.jpg” caption=”Dr. Dorian Garrick”]
According to Bishop, databases complete with large amounts of phenotypes on a broad range of traits combined with sequenced genotypes could be analyzed by computer programs and result in what he calls “deep learning.” This will mine more information from the data on a broader range of traits than ever considered possible.
The major genetic analysis companies often measure the quality of their genetic analyses by the size of their databases. Industry thought leaders like Dr. Dorian Garrick, however, emphasize data quality over quantity. At the recent Beef Improvement Federation (BIF) conference, Garrick foresaw the need for elite nucleus seedstock herds that will collect complete unbiased phenotypes on more traits. Included in this expanded data collection will be novel traits such as those related to soundness as well as adaptability; for instance, hair-shedding scores.
[inline_image file=”11236475a85d52274e60d2af353362c3.jpg” caption=”A painting of Dave Nichols, commissioned by WLJ for our 2014 Bull Buyers Guide cover.”]
Dave Nichols of Nichols Farms in Bridgewater, IA, agrees that data quality will rule and that there is a need for a “huge amount of phenotypes” to be collected on a wide array of traits by selected producers and feedlots that have the ability to collect them. Combining these phenotypes with genomic sequencing will allow for the discovery of causative genes for economically-relevant traits.
Bishop foresees that between genomic and phenotypic information gathered from elite seedstock herds, as well as the interactions between traits and the resulting deep learning, will build the next generation of models used for selection. He envisions these models to be more three-dimensional, taking into account not only the phenotypes and genotypes, but also the environment the cattle will be expected to perform within. This will lead to optimum levels of production potential to suit each unique situation.
In the elite seedstock operations, they will need to be run much as an experimental herd would be in collecting high quality, complete data on a vast array of traits. Also, the sequenced genomics combined with the expanded phenotypes will allow for the discovery of favorable and non-favorable mutations, which can be exploited for future genetic gain or to avoid increasing deleterious defects.
This will result in genomic information that can be applied more effectively to the next tier of seedstock herds, referred to as multipliers. These multiplier seedstock operations will be the ones that build the majority of the bulls used in the commercial industry.
[inline_image file=”397a6bf2703d0d1b3f0365fa6befd08e.jpg” caption=”Dr. Wade Shafer”]
Dr. Wade Shafer of the American Simmental Association (ASA) emphasizes the need to have both phenotypes and genotypes collected for genetic evaluation. They found a weakness of their IGS (International Genetic Solutions) evaluation was the shortage of genotypes on females when evaluating maternal traits like maternal calving ease. To address this weakness, ASA started the Cow Herd Roundup to collect DNA samples on females. Producer participation is incentivized; tests are half price if a producer agrees to do genomics on their whole cow herd, as well as send in mature weights and body condition scores.
Bishop also highlights the importance of collecting data from abroad if the U.S. is to remain the dominate force it is today as the world’s leading genetic supplier. He notes that the U.S. is especially sending Angus genetics to a variety of environments, including the tropics where most of the world’s cattle are located. Without access to the data from these regions, U.S. seedstock suppliers will not be able to fine-tune genetics for these customers. This will lead to entrepreneurs in these countries taking the base U.S. genetics, and then custom designing them to their environment, management, and market. The improved beef quality from the countries that successfully adapt U.S. genetics could then become a bigger competitive force with U.S. beef in the world’s market.
New Perspectives: The Right Target?
We can have all the technological tools in the world, but without the right target—and tools that properly measure our progression to that target—we will not make progress. How we build our indexes, what traits we look at (or not) for selection, and the overarching selection strategy all deserve scrutiny.
At this year’s BIF conference, it was pointed out by Garrick that, although Angus has improved the average $Beef by $103 since 1980, it has lost $57 in $Energy, which represents cow herd maintenance costs. Death loss and medicine costs have also doubled in feedlots in recent years, and to add insult to injury, much of this increase was due to sudden death of market-ready cattle at the end of the feeding phase. Much of this is thought to be due to pulmonary hypertension. Altogether, it is legitimate to ask if we have made genetic progress or just genetic change.
Shafer says part of the problem is that too much information is provided to producers on indicator traits as opposed to economically-relevant traits. He worries that a shotgun approach of bombarding producers with information that is not directly pertinent to profit can end up with producers making poorer decisions. He warned that there should be a lot of thought before adding a new genetic prediction, because once published, it is hard to ever take it back out of the EPDs and indexes available to producers.
A clear case of this is calving ease and birth weight genetic predictions. Birth weight was published first as an indicator of calving ease, but when calving ease EPDs started to be calculated, all the information from birth weight was added to the calving ease prediction as a correlated trait. The sensible thing would have been to drop the birth weight EPD, but producers had become accustomed to it and would not hear of its removal.
Reproduction is clearly the most economically-important group of traits, but it lags in terms of genetic predictions. This is due in part to breed associations’ reluctance to move to full total-herd reporting systems that follow BIF guidelines.
Nichols sees the industry going backwards on some fronts in terms of productive longevity. This is a composite trait largely influenced by reproduction, but other factors such as soundness also play a role. Additionally, genetic conditions that cause early embryonic death loss have become a problem in some breeds. Nichols feels the industry needs to turn this around with a goal of cows having 15 or more calves. He points out that F1 Brahman/Hereford cows can already achieve this in the U.S. Gulf Coast region, and similarly productive crosses must be designed for our country’s mid-South and Northern regions.
Moser also thinks what information goes into building indexes needs to be revisited. For example, current economic models can look at actual death loss and increased days open that calving difficulty causes, but they do not account for things like the increased labor, quality of life consideration, etc., that calving problems cause. The same goes for docility where cattle can be dangerous and can even affect employee retention. This is why Angus is going to use survey technology to get a better handle on the total economic impact of certain traits, which will serve to build better indexes to move the industry into the future.
New Perspectives: Fitness Traits
To enhance profitability, the industry must prioritize improving fitness traits such as health and adaptability. However, such a goal will take every tool available to the industry, including traditional genetic predictions, indexes, genomic sequencing, and gene editing.
Pulmonary arterial pressure (PAP) has long been an indicator of altitude-related pulmonary hypertension (brisket disease). This can be a major problem, especially for breeds that were developed to thrive at lower elevations. Angus is actively working on PAP genetic predictions, and they have found heritabilities that are better than most growth traits. They have also found a high correlation between PAP scores taken at moderate altitude with those taken at high altitude.
Feedlot death loss from pulmonary hypertension has been known since the 1970s, however, the incidence of it has been rising rapidly in recent years. With young cattle being kept on feed to higher weights, there has been an alarming increase in sudden death in cattle that are near market ready. Nichols relates that these cattle are still just juveniles that are very obese—the combination of which is likely leading to this sudden death from pulmonary hypertension. This problem must be tackled from both management and genetic technology angles.
BRD (bovine respiratory disease), which causes $1 billion in losses annually, is another area where focusing the collective power of genetic technology on this fitness trait could help the industry. The collection of sire-identified BRD data, as well as immune challenge data, could result in BRD and immune response genetic predictions. Immune challenges will be things like measuring injection site response.
Other economically-important fitness traits include early embryonic death loss, hair shedding, and soundness. Two to five genetic conditions exist in beef cattle that cause early embryonic death loss, and the industry must address the problem either through selection, gene editing, or simple technologies such as crossbreeding.
Environmental adaptability can be improved through indicator traits like shedding, and overall, cattle must be fine-tuned to their environments for production traits. Technologies such as decision support software will help design cattle that are best suited to be profitable in various situations. As opposed to static indexes, decision support software is more elastic, allowing for genetics to be custom designed for each producer’s unique environment, management and market.
Sound cattle are critical to productive longevity, which is paramount to profitability. Things like foot, leg and udder structure can be quantified in scoring systems and the traits are repeatable, meaning progress can be made through selection. One must ask then whether to display them separately or just within the economically-relevant trait of Stayability.
New Perspectives: Specialization and Mass Production
Nichols uses the metaphor that we are taking single breeds and “trying to get them to run like a Greyhound and fight like a Pit Bull but ending up with a dog that can neither run nor fight.” We are doing the same with beef breeds, trying to make single breeds be all things to all people and all market segments. Instead, he sees the best answer for the future is implementing specialized maternal and paternal lines that make full use of heterosis and breed complementarity.
Nichols thinks commercial producers of the future will be using specialized hybrid and composite cattle and will rely heavily on the technology of sexed semen. To maintain maximum heterosis and breed complementarity, these hybrids and composites will need to be constantly remade. This means elite seedstock producers will need to keep purebred cattle that are linebred for a specific purpose much as is seen in the swine and poultry industries today.
From these linebred cattle, multiplier herds will produce specialized maternal and paternal seedstock to be used by commercial producers. Multiplier seedstock herds may be the same operation as those with elite herds or separate operations that can build the cattle in quantity for the commercial industry.
Nichols believes that, depending on environmental adaptability concerns, more commercial herds will buy replacement heifers than ever before. There will also be the use of more sexed semen to produce specialized commercial replacement heifers, as well as those cattle destined to directly enter the food system.
This type of tiered system envisioned by Nichols will improve efficiency and shield commercial producers from genetic conditions found in certain breeds. The crossing of these specialized lines and breeds will give commercial producers animals that will both “run and fight,” and should also produce a consumer product that is high quality and extremely uniform. When combined with the power of branded beef, traits like tenderness can be improved, which should result in per capita beef consumption increasing.
A Decision-Making Challenge
Thought leaders envision the industry using genetic technology as never before. Technology will sort out producers and production systems, and in many ways determine profitability. The question is whether our breed association structure will keep up with private industry in adopting technology. Private industry has the advantage of having a more streamline decision-making process and does not have to worry about servicing the diverse membership that breed associations have.
A respected producer who has served on boards of multiple major breed associations said that what the people on most breed association boards tend to have in common is they are old, successful and lack diversity. This often leads them to employ a philosophy of “prevent defense” rather than innovation. This must change or our industry model will change, because the industry will be led by those who best adopt new technology.
[inline_image file=”18f5c0dcda98710fef03b90e68d403e0.png” caption=”Crow Logo”]
