By Bill Zimmerman
No matter what your motivation is for being in the beef industry, your profit or success is contingent on improving phenotype. Phenotype is what we can see and measure – it’s what we sell! Think about these examples across the beef industry.
A retail meat purveyor wants appetizing appearance and eating (and social) satisfaction of increasingly diverse customers.
An AJSA member striving to stand in the winner’s circle depends on visual appraisal, sound structure, and good disposition.
Stocker/Backgrounder/Feedlot producers need efficient and rapid calf growth, good health, and resistance to disease and stress.
A cow-calf producer seeks a combination of optimal maternal performance, superior calf vigor and growth, and feeder calf market acceptability.
And, it all begins with the foundation of seedstock producers providing predictable genetics to meet the phenotypic targets of various customers.
Beef cattle production starts and ends with genetic improvement of phenotypes
In trying to improve various beef cattle phenotypes, seedstock providers can only control some of the known environmental factors through management. But today, they have increasingly sophisticated tools to identify, select, and target superior genetics.
Speaking at the World Simmental Fleckvieh Federation Congress (WSFFC) last fall, Dr. Mark Allan said the increased availability of selection information, what he calls the “genetic toolbox” of techniques, data, and information now readily accessible to virtually every seedstock provider, has driven the exponential progress in genetic evaluation over the past 20 years. Allan, current Director of Genetic Technology for Trans Ova Genetics, has been intimately involved in the development, progression, and commercialization of genomics for genetic improvement in the beef and dairy industry. He said, “Genomics have enhanced our ability to know the true genetic value of animals at a younger age.”
Using the formula for predicting genetic gain (called the key equation, see below), Allan demonstrated the four main factors affecting genetic gain. Genetic gain is accelerated by increasing any of the factors in the numerator – increased accuracy of prediction, increased selection intensity, and greater genetic variation – or by reducing the generation interval. Why is it important to speed up genetic gain? According to Allan, customers across the spectrum are increasingly asking for targeted genetic specifications or particular verifiable traits.
Genetic Gain = (Accuracy x Genetic Variation x Intensity) Generation Interval
This equation seems simple. However, it tends to become more complex when considering that accuracy, selection intensity, genetic variation, and generation interval are often different for males versus females, and for growth versus reproduction or carcass traits.
Accuracy and intensity are independent concepts. You can select intensely regardless of the accuracy of the performance data. Even if you have good indicators of what is the best animal, if the accuracy is not high there will be a slower rate of genetic change. When the product of these two factors is a small number, the rate of change will be slow.
Accuracy of selection
The more accurately you can predict breeding values, the more likely the animals you choose to be parents will actually be the best parents. Accuracy ranges from zero, when there is no performance information used, to almost one, when there is an abundance of information. Accuracy is never negative.
Accuracy of selection hinges on two main factors:
Heritability – the higher the heritability of a trait, the better each piece of performance information is as a predictor of underlying breeding value.
Genetic prediction technology – accuracy can also be increased by using more information and more sophisticated
genetic prediction technology. Selection based only on individual phenotypic record, particularly if the trait under selection is lowly heritable, is not very accurate. Alternatively, the selection of potential parents on the basis of expected progeny differences (EPDs) derived from large volumes of progeny data is very accurate. The key elements here are collecting quality data, and accumulating large amounts of it.
Mathematically, selection intensity is determined by the difference between the average performance level of selected parents and the average performance level of all potential parents. Selection intensity will be different on the sire side as compared to the dam side. While we tend to focus more selection on sires, because parents contribute equally to the genotype of the offspring, both the sire and the dam will contribute to the selection intensity involved.
Genetic variation is basic material that animal breeders work with. It is the variability in breeding values within a population for a trait under selection. With lots of variation, the range between the best animals and the worst is large and the best animals are far superior genetically to the worst. If there is little genetic variation, then even the best individuals will be only a little better than average, so will their offspring, and the rate of genetic change will be slow.
Allan told the WSFFC attendees, “The younger the parents are, that is, the shorter the generation interval, has a massive impact on genetic gain.” Since generation interval is the denominator of the equation, even if nothing in the numerator changes, the shorter the generation interval, the faster will be the rate of genetic gain. Generation interval refers to the amount of time required to replace one generation with the next. It is a function of the biology of the reproductive rate, gestation length, nursing period, and age at puberty. Because of this biological disadvantage to pigs and poultry, it is critical to use the available technologies and management for the beef industry to make competitive genetic gains.
“The race to win – genetic improvement of young animals”
Of the four major factors affecting genetic gain, the focus of most technical, scientific, and management work today centers on improving selection accuracy and intensity through the use of genomically-enhanced predictions (GE-EPDs), and reducing the generation interval by using advanced reproductive technologies. As a result of his somewhat unique familiarity with current work in both beef and dairy genetics, Dr. Allan described the work being done in the Holstein dairy cattle industry in the US where genetic gain is far more rapid than in any sector or breed in the beef industry.
Historical selection in dairy cattle (and beef) focused on identifying superior sires from proven dams and through extensive progeny testing, and multiplying their genetics through the use of artificial insemination and retaining female offspring as the dams of the next generation. Allan explained that today’s high-density genomic technologies allow us to identify outstanding donor prospect females shortly after birth, producing IVF embryos from them well before a year of age – giving the power to
increase selection intensity on the dam side – and multiply full-sib offspring through embryo transfer. With similar reproductive technologies on the sire side, genomically superior young bulls are being managed to produce viable sperm before a year of age to be used as the sires for the IVF matings. The technologies are collapsing the historical biological generation interval. And, these procedures are not being done at the fringes of the dairy industry. Rather, they are being used every day across the industry.
The keys to success are quality data and lots of it
Allan is emphatic when he calls for more quality phenotype data tied to more DNA in the beef industry. “The dairy industry has won the race,” he says, ”because of DHIA [Dairy Herd Improvement Association] they had decades of accurate production and progeny data collected across the commercial industry.” And, they have embraced DNA testing and genomic predictions across their commercial sector.
For example, data from the Council for Dairy Cattle Breeding (CDCB) shows that 2,478,997 Holstein genotypes were included in their March 1, 2019 evaluation. This includes DNA tests across density platforms, all tied to verified pedigrees and production records. A monthly total of 44,442 Holstein genomic tests were submitted to the CDCB evaluation pipeline in February alone. This volume of genomic information tied to quality phenotypic data has literally changed everything for dairy cattle breeders. Genomics has completely changed the value of superior animals at younger ages and made outstanding females just as important in high-end breeding programs as bulls.
Dr. Allan explained at the WSFFC the power and success of the dairy industry genetic gains are based on having a powerful database – which we need to address as a beef industry.
- Data from commercial progeny – not just selected seedstock animals
- Lots of phenotypes and genotypes
- Unbiased data collected routinely for management, not just for evaluation or marketing
- Connectivity across the world
How do ASA, SimGenetics, and IGS compare?
When asked to identify the most significant milestone in beef genetic evaluation, without hesitation Allan responded, “Single-step. Most of the important breeds are using some form of single-step evaluation.” ASA initiated “Operation Quantum Leap” in January 2014 which resulted in the May 2018 release of the IGS Multi-breed Genetic Evaluation powered by BOLT,a single-step genetic evaluation. The IGS database has over 17 million records from 13 different breeds, with over 375,000 added annually. SimGenetics animals account for 5.6 million of those phenotype records. During 2018, SimGenetics breeders added 145,392 animal records with some performance data to the database and 77,341 had genomically enhanced EPDs. By January 2019, the total number of IGS genotypes grew to 201,406 (74,908 from the ASA). While this pales when compared to Holstein data, these numbers show exponential growth in genomic testing!
Possible barriers and pitfalls
Adoption of new technology or methods almost always comes with some concerns about barriers to success, or pitfalls of success that comes too quickly. Addressing this question, Dr.Allan said that the number one barrier to more rapid genetic gain in beef cattle is the lack of quality phenotypes. Repeating his earlier statement, “We need lots of phenotypes,” he continued, “I get concerned about the quality of our (beef) data. It may be difficult to get breed associations to allow the broad collection, analysis, and publication of truly unbiased data. And, we need to tie into large sets of commercial data to allow us to predict the most important economically-relevant traits, especially efficiency and carcass data. And, health data is rapidly becoming very important in the dairy evaluation. We need that, too.” Allan complemented the ASA on the recent Cow Herd DNA Roundup and the Carcass Expansion Project as important steps by a breed association.
See Dr. Mark Allan deliver a keynote address
at the annual Beef Improvement Federation conference
being held June 18-21, 2019, at South Dakota State University in Brookings.