By Lauren Hyde, Ph.D. |
Nearly a year and a half ago, on Saturday, May 5, 2018, the American Simmental Association released the first full suite of multi-breed EPDs powered by the state-of-the-art BOLT software. I have to admit that the ASA staff, with the exception of very few (maybe only Steve McGuire), was very scared as to what we would find in our email, voicemail, Facebook Messenger, and so on come Monday morning. However, it wound up being so quiet, we all heard that mythical pin drop. I’m not saying that we were perfect in our execution, but as your members started to evaluate the new EPDs, you had some well-deserved comments and questions that we were expecting. We knew that the software wasn’t “done”. It never will be. In fact, I was still revising the 30-year-old Cornell software as recently as two short years ago. As with the old Cornell software, we will continue to update, revise, and improve the EPDs produced by the new BOLT software.
Check out what we have done so far:
• Developed evaluation audit reports on incoming record counts for ASA staff and IGS partners
• Developed quality control (QC) reports for incoming genomic data
• Started clearing up erroneous and missing genotypes among all associations
• American Shorthorn Association released IGS EPDs
• Started parallel (aka beta) testing for IGS partners yet to release IGS EPDs
• Started delivering weekly QC reports to each association through the genomic pipeline, which routes genomic data from all genomic labs to the IGS partners and then the IGS database
• American Gelbvieh Association, North American Limousin Foundation, and Canadian Simmental Association released IGS EPDs
• Added embryo transfer data to the evaluation
• Discovered and corrected duplicate animal IDs
• Began collecting feed intake and heifer pregnancy data from IGS partners
• Canadian Shorthorn Association released IGS EPDs
• Initiated monthly IGS partner conference calls to discuss issues and updates with the evaluation
• Red Angus Association of America released IGS EPDs
• Developed a web-based interface for bull lookups and QC error checking for ASA staff and IGS partners
• Established a “white list” to keep animals with insignificant genomic discrepancies in the evaluation
• Adjusted the evaluation system to add genomic data on animals without carcass or ultrasound phenotypes
• Implemented a Java script to compute breed composition of all animals in the IGS database at a much faster rate
• Began a research project with CSU to develop a days-to-finish EPD
• Initiated a project known as Work Order 1 (WO1) in order to:
– Remove erroneous birth weights from the evaluation
– Separate birth contemporary groups between calves out of two-year-old dams from calves out of older ones
– Include heterogeneous variances for weaning weight based on sex of calf
– Remove the moderately negative genetic correlation between weaning weight direct and maternal and set it to zero
– Implement an updated marker subset of genomic data
• Added trio (sire + dam + calf) mating checks to the QC error reports
• Began investigating multi-breed imputation
• Started evaluating the latest version of the FImpute software package
• Began refining the Zoetis arm of the genomic pipeline
• Received preliminary results on the days- to-finish EPD research project
• Combined the heifer pregnancy (HPG) data from the IGS partners and began refining it
• Started to investigate potential improvements to the carcass weight-ribeye area (CW-REA) evaluation
• Fixed minor bugs in the online bull lookup tool
• Added birth dates and other supplemental data to the HPG dataset
• Received the first set of health data courtesy of Darr Feedlot
• Upgraded the Postgres evaluation database
• Started exploring modifications to the utilization of external EPDs
• Tested several scenarios in the investigation to potentially improve the CW-REA evaluation
• Updated carcass breed differences with new data from USMARC
• Fixed a small bug in the docility evaluation scripts
• Canadian Angus released IGS EPDs
• North American South Devon Association submitted external EPDs
• Began planning for the IGS partner meeting to be held October 23-24 in Bozeman
• Started building and developing server #5
• Developed a standard format for sharing pedigree extracts among IGS partner associations in order to catch dual-registered animals more quickly
• Released data to Colorado State University (the leaders in PAP EPD development) for development of a PAP EPD
• Implemented multi-breed imputation software
• Installed and configured FImpute
• Implemented updates to the CW-REA evaluation
• Added Australian Shorthorn Association data
• Added updated American Angus Association externals
• Re-calculated progeny equivalents for each trait computed by IGS
I am writing this article on September 18. In just a few days, I will be traveling from Denver to the Rhine River in Germany to find out where my maternal grandparents lived before they immigrated to Chicago and met in English school. After my excursion, I will be finishing up all of my outstanding projects so that I can retire on December 31 to pursue my dream of coaching and teaching swimming.
I am fortunate to have worked with the best team in the beef cattle industry. The ASA staff is knowledgeable, hard-working, creative, and fun. This fantastic group of individuals has shown time and time again that it is more than capable of developing and implementing innovative science-based products to help you produce cattle that make a significant genetic contribution to the beef industry. I truly wish all of you — ASA members and staff alike — much success in your efforts to keep moving the breed forward and ensuring that SimGenetics continue to have a major influence in the global market.
The International Genetic Solutions (IGS) has recently welcomed its newest partner, Neogen® Corporation, to better serve seedstock and commercial beef cattle operations across a wide array of breeds. The partnership combines IGS, the world’s largest beef cattle genetic evaluation, with Neogen, the world’s largest agricultural genotyping company, to better service the beef cattle industry with better genetic decisions. “The mission of IGS is to leverage science, technology, and collaboration to improve the profitability of commercial cattle producers. Bringing Neogen in as an IGS partner is a natural extension of the mission of IGS,” says Wade Shafer, American Simmental Association (ASA) Executive Vice President. “This clearly positions serious, profit-focused beef producers to take advantage of the most credible and capable genetic awareness effort in the beef business.”
IGS is a global, unprecedented collaboration between progressive breed associations and companies across the US, Canada, and Australia that are committed to enhancing beef industry profitability. The collaboration encompasses education, technological advancement, and genetic evaluation. Through collaboration, IGS has become the largest beef cattle evaluation in the world.
Neogen Corporation develops and markets products dedicated to food and animal safety. Neogen’s Animal Safety Division is a leader in the development of animal genomics along with the manufacturing and distribution of a variety of animal healthcare products, including diagnostics, pharmaceuticals, veterinary instruments, wound care and disinfectants.
International Genetic Solutions offers free, third-party validation on feeder calves.
Using the IGS Feeder Profit Calculator, cattlemen are able to provide sire information, regardless of breed, as well as preconditioning, weaning and health data in exchange for a Total Relative Value that compares the profit potential of their calves to the industry at large. That value, indicated on a formal certificate, can be used for producer benchmarking and buyer insight.
Superior Livestock Representative Clint Berry says such technology is in line with what he sees for buyer demand.
“We sell cattle in all capacities, all formats, but the one thing we see continued pressure on is cattle that offer flexibility to the buyer, that gives the buyer a chance to have some value-added options,” Berry says. “If he can recapture from that purchase price, he can recapture a profit on his side. Whether those are export verification programs or cattle that simply grow and grade better in the feedyard on his side of the business.”
“Producers get paid to have better cattle. It’s common to see spreads of $20-$40 at market from additional information and value-added programs,” Berry says. At present, he adds, there’s no ceiling.
“As we move forward, the genetic key in that is becoming more and more prominent for producers who are wanting to sell at the top of the market,” he says. “Being able to verify those genetics and have a record of those genetics is the key difference.”
As a third-party validation tool, the IGS Feeder Profit CalculatorTM satisfies that need. Buyers who pay a premium on a set of calves will look to recoup those and add additional profit down the road at harvest.
“In our format, they might buy a calf in July, that ships to them in October, that doesn't die until April of the next year. There's a lot of time frame between the day that he made the decision to do the bid price, and the day that he recaptures his monetary value,” Berry notes.
By leveraging what is there on the front end, success is more likely to follow.
“Having flexibility and having a security blanket, you might call it, for a buyer to know this set of cattle is better than the average goes a long way when you want to demand a premium for your cattle on the market,” he says.
The IGS Feeder Profit Calculator is offered to all cattle producers at no cost and is available for mobile use through the App Store.
Staying profitable year in and year out in the farming and ranching business is not easily achieved. Perhaps there is no bigger case of this than with dairy farmers who have struggled with low fluid milk prices for years.
However, dairy farmers are realizing that their approximately 5 million breeding-age heifers and 9 million cows can generate profit from more than just milk. One of the most underdeveloped potential profit centers is the production of specialized dairy crossed steer calves and excess heifers that can be profitably fed and marketed by feedyards. With that in mind, there has been an exponential increase in the use of beef semen in dairy herds to produce more desirable feeder cattle.
Affordable genomic tests that give commercial dairy producers a look at their heifers’ genetic potential has helped make this happen. Dairy farmers can now determine if a heifer entering the herd has the genetics to produce outstanding replacement dairy females or would be better used to breed beef bulls to produce value-added feeder cattle.
Sexed semen is another piece of the puzzle that allows the top dairy heifers and cows to have only heifer calves, decreasing the number of females needed to supply a dairy operation with replacements. Statistics from the National Association of Animal Breeders (NAAB) show how popular it has become to breed the bottom-end dairy cows to beef bulls, with a 59 percent increase in beef semen last year alone. To be sure, the majority of this increased semen in going into dairy cows and not beef cows.
However, the use of beef semen in dairy cows has often involved little thought in terms of selecting the right bulls, so dairy producers need a better strategy to make this system sustainable.
A global collaboration of major beef breed associations seeks to empower commercial cattlemen with genetic insight and more powerful tools for better breeding decisions.
Modern-day ranching requires more information to produce better animals, and International Genetic Solutions is propelling the effort across multiple breeds. The aim is to provide more accurate selection tools that allow for head-to-head comparisons and maximum profitability — regardless of breed.
“Tying all of that information together adds a lot of value to commercial and seedstock producers because it provides a set of EPDs that are comparable across breeds without doing a bunch of extra math to figure out how they compare,” says Bob Weaber, Kansas State University Extension Specialist.
“It’s easy to make crossbreeding decisions where we’re seeking out specific genetic traits and inputs for our production system. We don’t have to spend a lot of time trying to figure out how does breed A compare to breed B? It’s all laid out and they’re on the same base and scale.”
International Genetic Solutions, or IGS, is a collaborative effort between numerous beef breed associations from the US, Canada, and Australia, resulting in the largest and only major multi-breed cattle evaluation system. With decades of data and nearly 18 million animals in the database, IGS Director of Commercial and Industry Relations Chip Kemp says IGS is helping producers make more powerful breeding decisions than ever before.
“You can directly compare a yearling weight from a Simmental to a Red Angus to a Limousin. You can directly compare the stayability or the cow longevity from a Balancer to Angus in the system to a SimAngusTM,” he says. “It empowers that commercial client to get past all of the clutter to make smarter, wiser, more profit-focused decisions.”
IGS uses a single-step genetic evaluation model that incorporates genomic and phenotypic information on purebred and composite animals. The collaboration allows participating breed associations to gather and analyze data on traits that are difficult to measure but economically important.
“We’re able to calculate EPDs on those cattle, and these cattle bring the power of heterosis and crossbreeding to the commercial cattleman as far as increased performance in their cow herds, increased growth, and productivity in their calf crop,” says Tom Strahm of the American Gelbvieh Association, one of many IGS collaborators.
IGS also helps cattle producers verify the value of feeder calves, weighing good management practices alongside genetic merit through free tools like the Feeder Profit Calculator. The goal: Better returns on genetic investments.
“The greatest thing it’s brought is just a better system for cattle evaluations and the collaborative effort of people working together through different breed associations. When you’ve got this many cattle in the evaluation, what you get is crossbred cattle evaluations that the commercial cattleman can use,” says Mark Anderson, North American Limousin Foundation executive director. “So in the race to make the better kind of cattle, the science we’re using today, I think it’s on the forefront and getting really exciting.”
- IGS Feeder Profit Calculator
- Non-breed specific, independent
- Free to all IMI Global customers
CASTLE ROCK, Colo., July 16, 2018 (GLOBE NEWSWIRE) -- Where Food Comes From, Inc. (WFCF) (OTCQB:WFCF), the most trusted resource for independent, third-party verification of food production practices in North America, today announced that its IMI Global division has established an exclusive partnership with International Genetic Solutions (IGS) to offer the IGS Feeder Profit Calculator within its suite of verification services for beef producers.
The IGS Feeder Profit Calculator utilizes the largest and most comprehensive set of management and genetic data available in the beef industry to calculate the Relative Value of feeder calves in a one-of-a-kind, breed agnostic, independent manner. The evaluation and resulting value are based on both management and genetic criteria. The Relative Value, as indicated on a formal certificate, enables producers to benchmark their work to continuously improve management and genetic decisions in their herds. For buyers of the cattle, it provides insight into projected feedlot and carcass trait performance and overall profit potential.
“The IGS Feeder Profit Calculator is the perfect addition to our suite of value-added services for our beef producers,” said Leann Saunders, President of IMI Global, a division of Where Food Comes From. “We have been searching for this kind of solution for years, and feel that the IGS tool is far and away the most inclusive and sophisticated calculator available in the industry today. By enabling beef producers to see the value their management and genetic decisions are providing to their operation, it enables them to have a benchmark from which they can make confident, knowledgeable choices about how to continuously improve their operations. As my dad has always said, ‘If you buy unknown genetics you never know if they are going to finish like an elephant or an ant.’ Knowledge matters and the IGS Calculator provides producers with one more tool in their toolbox to make transparent, informed management decisions.”
The IGS Feeder Profit Calculator will be offered to all of IMI Global’s customers at no added cost to their existing verification programs.
“Deciding to establish a partnership with a company like IMI Global was an easy decision for us,” said Chip Kemp, Director of IGS Commercial and Industry Operations. “Even in today’s data-driven world, this level of genetic awareness in the commercial cattle sector is woefully inadequate. Price discovery as we know it today most often does not take into account the actual performance potential of a producer’s cattle. The IGS Feeder Profit Calculator is unique in that it offers a level of genetic awareness of feeder calves that have not been previously possible in the beef business. This, combined with the progressive, market-driven programs IMI Global provides, will enable their producers to market calves with the ultimate value-added package.”
To learn more, visit http://www.internationalgeneticsolutions.com/index.php/feeder-profit-calc.
About International Genetic Solutions
International Genetic Solutions (IGS) delivers objectively described, user-friendly and science-based genetic predictions to enhance the profitability of beef cattle producers. To learn more, visit http://www.internationalgeneticsolutions.com.
About Where Food Comes From, Inc.
Where Food Comes From, Inc. is America’s trusted resource for third-party verification of food production practices. The Company supports more than 15,000 farmers, ranchers, vineyards, wineries, processors, retailers, distributors, trade associations, consumer brands and restaurants with a wide variety of value-added services through its IMI Global, International Certification Services, Validus Verification Services, SureHarvest, A Bee Organic and Sterling Solutions units. In addition, the Company’s Where Food Comes From® retail and restaurant labeling program utilizes the verification of product attributes to connect consumers to the sources of the food they purchase through product labeling and web-based information sharing and education. Visit www.wherefoodcomesfrom.com for additional information.
This news release contains "forward-looking statements" within the meaning of the U.S. Private Securities Litigation Reform Act of 1995, based on current expectations, estimates, and projections that are subject to risk. Forward-looking statements are inherently uncertain, and actual events could differ materially from the Company’s predictions. Important factors that could cause actual events to vary from predictions include those discussed in our SEC filings. Specifically, statements in this news release about industry leadership and demand for, and impact and efficacy of, the Company’s products and services on the marketplace, are forward-looking statements that are subject to a variety of factors, including availability of capital, personnel, and other resources; competition; governmental regulation of the agricultural industry; the market for beef and other commodities; and other factors. Readers should not place undue reliance on these forward-looking statements. The Company assumes no obligation to update its forward-looking statements to reflect new information or developments. For a more extensive discussion of the Company’s business, please refer to the Company’s SEC filings at www.sec.gov.
Chief Executive Officer
Pfeiffer High Investor Relations, Inc.
Or go to: http://www.agnews890.com/episode/10-31-16-farm-talk-segment-5
Dr. Bob Hough, WLJ correspondent
As EPDs and other breeding tools get more complicated, some ranchers have returned to the “tradition” of just looking at animals to determine their genetic worth. DON’T. EPDs work.
Due to objective genetic predictions such as EPDs (expected progeny differences) and indexes, the cattle industry has made tremendous progress in production and efficiency. However, as the models that produce the predictions become more sophisticated and producers understand less of the mathematics behind them, some people are turning off from the technology.
This is a problem because, although calculation of modern genetic predictions has become complicated, the precision and reliability of the EPDs have likewise improved.
An EPD is defined as the difference in expected performance of future progeny of an individual, compared with expected performance at some base point for the population. EPDs are estimated from phenotypic and genomic merit of an individual and all its relatives. They are generally reported in units of measurement for the trait (e.g., lb., cm., etc.). EPDs are best used for comparing the relative genetic transmission differences to progeny between individuals.
What it boils down to is EPDs let a producer sort out genetic differences between animals, eliminating the “noise” of the environment. Some producers think they can do this better with their eyes or just a simple set of scales. This has been soundly proven wrong. The most glaring example of this occurred in Red Angus.
The breed was founded based on performance principles in 1954 with performance reporting as a requirement for registration from the very beginning. Although all Red Angus breeders had weights and measures from the beginning, the breed made no genetic progress for over 20 years. That all changed when it began converting this data into information in the form of EPDs. Since the breed started calculating EPDs, the genetic trend for traits measured has improved linearly.
Red Angus also studied the phenotypes for various traits and how they compared to the genetic predictions of the population. An example is weaning weight EPDs, which have been increasing linearly. This lines up perfectly with the breed’s adjusted weaning weights, which have improved at the same rate as the EPDs. EPDs have also allowed the breed to beat genetic antagonisms like increasing weaning weights without increasing birth weight.
Indexes are an even more powerful tool for genetic improvement. Certified Angus Beef studied when cows were flushed to either low or high $B ($Beef terminal index) bulls and all progeny were fed out and harvested. The progeny out of the high $B bulls were significantly better for all input traits into the index including weight per day of age, age at harvest, carcass weight, quality grade, and yield grade. The progeny of the high $B sires had $48.65 lower feedlot production costs and produced carcasses with $166.82 more value for a total financial benefit of $215.47.
The prediction models have also been proven to be unbiased. Cornell University did a retrospective study of the American Simmental Association’s cattle by going back and adding two years of data at a time. They then observed the differences in how cattle’s genetic predictions changed as they went from pedigree estimates through being proven sires. Animals changed up and down as the possible change chart indicated they would, as more information was added to the genetic predictions. They equally moved either up or down demonstrating no bias in the model producing the genetic predictions. If the model was biased, the predictions would tend to move in only one direction.
The basic input into genetic predictions is contemporary group deviations, and the models assume there is no environment by genotype interaction. Cornell also studied this in the Simmental population, and the assumption was validated as true.
That the models have been improving over time only makes the genetic predictions and indexes even that much more valuable.
Genetic predictions using field data were first introduced to the industry with the 1971 Simmental Sire Summary, but those early models were fraught with problems. The early models were based on sires and all dams were assumed to have equal genetic merit, which of course is not correct.
Early models also didn’t account for mating bias. The most common case of mating bias occurs when high-priced artificial insemination sires are only mated to producers’ top cows, so accounting for this bias is important. Over time, these and many more problems have been eliminated. However, with these improvements, the models have become ever more complicated and more of a challenge for the layperson to understand how they work.
This brings us to today’s modern genomic models, which are light years better than the old models, but the complicated statistics that go into the genetic predictions are admittedly hard to understand. The goal of the genetic predictions has always been to sort out what is genetic—thus will be transmitted to progeny—from what is due to environment. Marker-assisted selection is the ultimate way to determine genetic value because, by definition, genomics are not influenced by environment.
Adding genomics to traditional information that goes into genetic predictions—like contemporary group deviations, heritability, and trait correlations—all adds up to predictions that are more precise and reliable. They do a much better job of establishing genetic relationship between animals, as well as identifying markers associated with causative genes, all to improve the accuracy of genetic predictions.
The whole goal of animal breeding is to improve cattle genetically. This means different things to different people—some are looking to optimize genetics to their environments while others are looking to maximize the genetic potential for traits.
Whatever a producer’s goal, EPDs, and indexes are the best way to achieve it. Today’s prediction models do an unprecedented job of removing all the noise from EPDs and indexes, allowing producers to make the most informed genetic selection decisions possible.
It has been demonstrated time and again that visual evaluation and simple weights and measures are inferior substitutes for modern genetic prediction. Those who ignore objective genetic predictions do so at the long-term peril of their business’ ability to compete.
Performance pioneer Don Vaniman summed it up nicely in 1978 when he wrote, “Is it those who feel cattle that look good must perform, or those who accept that animals that perform look good?” — Dr. Bob Hough, WLJ correspondent
Dr. Bob Hough is the retired executive vice president of the Red Angus Association of America and a freelance writer.
International Genetic Solutions (IGS) is an unprecedented collaboration between progressive breed associations fervently committed to enhancing commercial profitability. The collaboration has yielded the world’s largest genetic evaluation of beef cattle with over 17 million animals and 120,000+ genotypes.
In keeping with our commitment to the cattle industry, IGS is pleased to announce the IGS Multi-breed Genetic Evaluation powered by BOLT. The new genetic evaluation provides more predictive EPDs, better use of genomics, more accurate accuracy reported with EPDs, all with weekly evaluations. The announcement ushers in a new era in genetic evaluation — an era made possible by a genetic evaluation system dubbed BOLT (Biometric Open Language Tools, owned by Theta Solutions, LLC).
The concept for BOLT started in 2014 as a research endeavor between the American Simmental Association and Drs. Bruce Golden and Dorian Garrick. BOLT is, quite simply, the most revolutionary and powerful genetic evaluation system in existence. Its power allows IGS to leverage genetic evaluation methodology that was once thought to be untenable on large databases — methodology that significantly improves genetic prediction.
In December 2016, IGS published a multi-breed stayability, the industry’s first EPD using BOLT and the first single-step methodology applied to a large beef cattle database. Since that time, the IGS genetic evaluation team has worked toward fully implementing BOLT with an automated system that enables weekly evaluations for an entire suite of EPDs. As of May 5th, 2018, ASA is the first of the IGS partners to publish a full suite of EPDs generated by the IGS Multi-breed Genetic Evaluation powered by BOLT. Each IGS partner has complete autonomy to determine the release date that best fits their organization. As such, the release of EPDs by the other IGS partners is likely to be staggered over the next several weeks. As always, we look forward to your questions and comments about what you see.
Here are the notable changes in the evaluation:
Movement of EPDs and reranking. EPDs and indexes will change. These changes will be more dramatic for younger, lower accuracy cattle. The IGS team has tested the changes and proven the new EPDs result in superior predictions of genetic merit.
Shrinking of EPD range. You will notice a reduction in the range of EPDs for most traits. The IGS evaluation team tested the statistical veracity of the reduction and it has proven to be in line with expectations based on the genetic variation in the population.
Improved use of genomics. With the switch to the BOLT software, IGS will use single-step genomic evaluation on all EPDs. Single-step uses DNA markers, pedigree information, and phenotypic data simultaneously in the prediction of EPDs. Previously, molecular breeding values (MBVs) were calculated from the genomic information and those MBVs were blended in a separate procedure into the EPD predictions. The single-step method squeezes more information from the DNA markers than the previous approach allowed. Additionally, with single-step, the genomic information will not only enhance each EPD for the genotyped animals but also will be used in the EPD estimates of relatives.
The table below shows how many progeny records it takes for an animal without genomics to have the same BIF accuracy as the young animal with genomics (but no progeny). In other words, EPD on a genotyped 1-month-old calf will be as accurate as an animal with birth weights on 21 calves, weaning weights on 22 calves, etc. The carcass traits represent actual carcass records, not ultrasound records. You may notice the maternal calving ease gets the least boost from genomics. This is due in part to such few females being genotyped.
It is important to note, continued collection of phenotypic records remains a vital part of genetic predictions. DNA testing will never replace the need to record and submit phenotypes.
It is well established that DNA markers vary greatly in their effect on traits — ranging from large to virtually no impact. To leverage this biological fact in a statistically advantageous manner, the BOLT single-step method only uses markers that have a meaningful impact on the traits of interest, while ignoring those that have little to no effect. Research has shown that by using this approach, BOLT reduces statistical “noise” and thereby increases the accuracy of the EPD prediction compared to other single-step methods.
More accurate accuracy. In the previous IGS evaluation platform and all others in existence other than BOLT, the calculation of the accuracy associated with each EPD is achieved through “approximation” methods. It has long been known these methods are a less than optimal approach to the calculation of accuracy — tending to overestimate accuracy. By employing unique computing strategies that leverage both software and hardware efficiencies, BOLT performs what was previously unthinkable — utilizing a sampling methodology to calculate what is essentially true accuracy. Unlike approximated accuracies, BOLT-derived accuracies will result in predicted movements associated with possible change holding true over time. This is not the case with the previous IGS software or any other system currently in existence.
While the IGS evaluation team and partners are excited to release this new chapter in genetic evaluation, the new genetic evaluation system will only realize its true potential if the selection is made using its EPD and index values. Hands down, there is no better (more accurate) way to select for quantitative traits than an EPD. Economic indexes predict net profit by weighing the EPD for economically relevant traits coupled with economic estimates. To compete with other protein sources, it is imperative that the beef industry adopts the best science and technology to make better breeding selection decisions.
Please note, each IGS breed association has the latitude to publish the BOLT generated EPDs when the timing is right for their association.
For more information about the IGS Multi-breed Genetic Evaluation powered by BOLT, go to www.internationalgeneticsolutions.com.
The new genetic evaluation, Multi-breed Genetic Evaluation powered by BOLT, offers groundbreaking advances in the prediction of EPDs for the IGS group. Here are some frequently asked questions and answers to help you better understand Multi-breed Single-step.
1. What are the key features of the Multi-breed Genetic Evaluation powered by BOLT?
• Faster and more automated system allowing for frequent genetic evaluations.
• Improved use of genomic data.
• Improved methodology for predictions of all traits.
• More accurate accuracy.
• More flexibility to add additional traits or change methods for future improvements.
2. How is ASA’s single-step approach different from blending for genomic evaluation?
The blending approach uses separate steps to calculate genomically enhanced EPDs. This approach requires two steps. The first step is to estimate the effects of DNA markers through a process called “training” or “calibration”. These effects are then used to calculate molecular breeding values (MBVs) on genotyped animals. The MBVs are then combined with traditionally calculated EPDs to enhance the accuracy of the traditionally calculated EPDs. The blending process is only performed on genotyped animals.
Befitting its name, the single-step approach calculates genomically enhanced EPDs in one step — using DNA, pedigree information, and phenotypes simultaneously. As a result, the DNA information not only improves the accuracy of prediction on genotyped animals, but also on the relatives and contemporaries of the genotyped animals. In a sense, all animals are genomically enhanced under the single-step approach.
There are also issues inherent in the blending process that are solved with single-step. Similar to the fact that only reporting phenotypes on a selected group of animals in your herd can lead to less informative (and more biased) EPDs with traditional evaluation, problems can exist with blending as it only involves genotyped animals — and genotyped animals tend to be highly selected. However, because single-step includes information from non-genotyped as well as genotyped animals, the issues are corrected.
3. How is the Multi-breed Genetic Evaluation powered by BOLT different than other single-step models used in other genetic evaluations?
It is well established that DNA markers vary greatly in their effect on traits — ranging from a large to no impact. To leverage this biological fact in a statistically advantageous manner, the BOLT single-step method only utilizes markers that have a meaningful impact on the traits of interest, while ignoring those that have little to no effect. By using this approach, BOLT reduces the statistical “noise” and thereby increases the accuracy of prediction. By circumventing the “noise,” BOLT-generated EPDs tend to be more accurate than EPDs generated by organizations that are relegated to using all markers in their single-step evaluation.
4. How many DNA markers are being used?
The Multi-breed Genetic Evaluation powered by BOLT uses a subset of weighted markers based on a research study performed by Drs. Mahdi Saatchi and Dorian Garrick, while they were scientists at Iowa State University. Drs. Saatchi and Garrick first used the 50,000 markers to determine a subset of weighted markers that are highly associated with economically relevant traits in beef cattle with consistent effects across breeds. Because the IGS evaluation is for multiple breeds, it is important to remove markers with inconsistent effects or no effects in different breeds.
The Saatchi and Garrick research also found that utilizing genotypes on animals of multiple breeds consistently increased the accuracy of prediction within a particular breed when compared to limiting DNA utilization to only animals of a particular breed.
5. Why are some traits influenced by markers and others are not?
The genetic architectures of various traits are different. Some are controlled by few genes with large effects and some are controlled by many small effects genes. In the current DNA profilers, there are some markers with high correlations with corresponding genes for some traits and low correlations with others. That’s why we see the different DNA added values for different traits. It is hard to change the genetic architecture of a trait. But, new DNA profilers or future technologies may help to improve the value of DNA information for such traits. Furthermore, some maternal traits, like Maternal Calving Ease and Milk, are difficult to predict with genomics because there are so few females genotyped. Increasing the number of cows and heifers genotyped will improve the ability to use genomics to predict maternal traits.
6. Will genomic testing replace the need to submit phenotype records?
No, reporting actual records is critical. The value of genomic predictions increases as the amount of phenotypic information increases. Furthermore, at this point, animals cannot achieve high accuracy with genomic data alone. High accuracy EPDs are only achievable by collecting many phenotypic records on offspring.
7. How do we know predictions via BOLT are better than the previous system (Cornell software)?
The IGS evaluation team has conducted a series of validations to compare the BOLT system to the Cornell system. BOLT-derived EPDs had higher correlations to birth, weaning and yearling weights (0.34, 0.29, and 0.26, respectively) than the Cornell derived EPDs (0.27, 0.19, and 0.20, respectively). Furthermore, there was a larger difference in average progeny performance (birth, weaning, and yearling) of the top 1% compared to the bottom 1% animals in the BOLT derived EPDs compared to the Cornell calculated EPDs. Both validations suggest the BOLT EPDs align better with the actual phenotypes than the Cornell EPDs.
8. Why do some animals have substantial changes in their indexes?
Though the correlations between the previous (Cornell derived) EPDs/indexes and the BOLT derived EPDs/indexes are relatively strong, there will be some animals that happen to move in a consistently favorable or unfavorable direction in a number of EPDs. Because indexes are comprised of several EPDs, even though movement in individual EPDs may be considered small, movement in the same direction across EPDs may yield sizable movements in the index value. This is particularly true for animals that have consistent movement in traits that are drivers of a particular index. Though in a large population like ours we would expect to see several animals with substantial index movement, these animals will be the exception to the rule.
9. How does BOLT improve our calculation of accuracy?
“True” accuracy can be thought of as the gold standard of accuracy. It is statistically unbiased, and therefore the ultimate measure of accuracy. True accuracy is the accuracy resulting from direct calculation. Unfortunately, even with the massively powerful computing capacity now in existence, the direct calculation of accuracy is not possible on datasets the size of ours. Because we cannot calculate accuracy directly, other approaches to accuracy calculation have been developed.
In our Cornell evaluation platform and all others in existence other than BOLT, the calculation of the accuracy associated with each EPD is achieved through “approximation” methods. It has long been known these methods are a very crude approach to the calculation of accuracy — tending to overestimate accuracy.
Another approach to the calculation of accuracy is via “sampling” methodology. Sampling is shown to be a more accurate predictor of accuracy. In fact, the results of this method were reported to be virtually identical to true accuracy. Unfortunately, due to its computationally intense nature, sampling has long been thought an infeasible approach to the calculation of accuracy on large databases.
BOLT, however, has changed the landscape in this area. By employing unique computing strategies that leverage both software and hardware efficiencies, BOLT performs what was previously unthinkable — utilizing a sampling methodology to calculate what is essentially true accuracy.
Because BOLT can calculate true accuracy, we can put more confidence in our accuracy metrics. Put another way, unlike with approximation, we can count on the predicted movements associated with possible change holding true over time. This was not the case with our Cornell system nor any other system in existence.
10. Why do the carcass EPDs generally have an increase in accuracy with BOLT while this is not a case for other traits?
You will notice that while the Multi-breed Genetic Evaluation powered by BOLT will generally produce lower accuracies than the Cornell system for growth and calving ease traits, the opposite is true for carcass traits.
One reason behind the differing accuracy outcomes is several years ago ASA staff developed a way to temper inflated accuracies in the Cornell carcass evaluation. Unfortunately, this was not possible for growth traits.
Another reason is that the Cornell system only used the carcass and its corresponding ultrasound trait (e.g., marbling score and IMF) to predict carcass EPDs, while records on several additional correlated traits are leveraged with the BOLT system.
A new feature of the BOLT evaluation is a new approach to the calculation of Carcass Weight EPDs. Due to limitations, our previous Carcass Weight EPDs did not incorporate actual carcass weights. They were predicted through an index of birth, weaning, and yearling weights. Besides using prior growth records (weaning, post weaning), the new approach also includes actual carcass weights. This feature will undoubtedly lead to a more accurate prediction of carcass weight.
11. What can I do to improve the predictions on my herd?
Whole Herd Reporting — If you haven’t already, you should consider enrolling your entire herd with a breed association total herd reporting program as it offers the most complete picture of the genetics involved in your herd.
Proper contemporary groups — It is important for the genetic evaluation that you group, to the best of your ability, animals that were treated uniformly. Proper reporting of contemporary groups ensures better predictions for all.
Take data collection and reporting seriously — Phenotypes are the fuel that drives the genetic evaluation. Take pride in collecting accurate data. If possible, try to collect additional phenotypes like mature cow weight, cow body condition score, feed intake, and carcass data.
Use genomics — DNA testing adds more information to what we know about an animal. The more genotypes we collect, the better we can predict DNA-tested animals in the future. Also, the more relatives genotyped, the better we can predict their relatives in future generations. Therefore, to ensure your bloodlines are well represented in the predictions, genotype your animals.
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