By IGS Genetic Evaluation Team |
Change can be a scary concept to some yet sought after by others. Many ASA members and International Genetic Solution (IGS) partners wonder about the changes on the horizon once BOLT is fully implemented. That change may be nerve racking but in reality, things should change. Why invest in new and improved methods if you get the same answers? Here are key changes to expect with the new genetic evaluation:
1. Movement of EPDs and reranking. EPDs will change especially in younger, lower accuracy cattle. Members should expect movement in lower accuracy cattle, as seen in the existing evaluations, because they may have new progeny data reported. Some cattle will move in a favorable direction while others will do the opposite. Keep in mind even if the EPDs get worse, the prediction of them is more accurate. With enough calves and phenotypes, the current evaluation would eventually arrive at a similar EPD as BOLT, it just would take longer or more information in the current system. With BOLT and the new genetic evaluation methodologies, we will have more accurate EPDs earlier in an animal’s life.
2. More accurate accuracy. This idea takes a little time to sink in. The accuracy reported for each EPD will be a directly calculated and thus closer to the “real” accuracy. The methods to solve accuracy directly are extremely difficult and take a lot of computer power. In the current evaluation, it is not possible to solve for accuracy directly so an approximation method is used to estimate accuracy for each EPD. There are inherent flaws with approximating the accuracy which until BOLT were just part of the evaluation. Now with BOLT, the accuracy reported with the EPD will be more reliable.
3. Reported accuracies will tend to be lower. Again, this is a little confusing at first and sounds like the opposite of what was just explained. The EPDs will be more accurate. The accuracy reported will be more accurate. Both statements are still true. However, one of the inherent flaws in the approximation methods used to find accuracy in the current evaluation, and in all evaluations not produced through BOLT, is they tend to bias the accuracies upward, especially for younger animals. This was known for a long time, but there was no way to calculate the accuracies directly. With BOLT, having accuracy directly solved results in a more reliable accuracy but that accuracy will often be numerically lower than the current evaluation would predict. However, the new reported accuracies with BOLT should better represent the possible changes for the EPDs.
4. DNA testing will have a larger impact. With the switch to BOLT, IGS will use Single Step genomic evaluation on all EPDs (currently using Single Step for Stayability EPDs). Single Step uses the DNA markers, pedigree information, and phenotypic data simultaneously in the prediction of the EPDs. Previously molecular breeding values (MBVs) were calculated from the genomic information and those MBVs were blended separately into the EPD prediction. The Single Step method squeezes more information from the DNA markers than the previous approach allowed. Also, there are biases inherent in the blending process that aren’t a problem with the Single Step approach. Additionally, with Single Step, the genomic information will not only enhanced EPDs for the genotyped animal but also will be used in the EPD estimates of relatives.
5. More frequent genetic evaluation runs. With the horse power behind BOLT, IGS can run genetic evaluations much more frequently than the current system allows. This has many benefits. It allows members to get more immediate feedback after submitting their records. If members miss a deadline, the next deadline for data won’t be far away. It allows for more accurate EPDs throughout the year and faster incorporation of the genomics. The down side is the EPDs put in print will quickly be outdated.
Genetic evaluation is not stagnant. There will always be improvements as new research in animal breeding, genomics, and statistics advance. BOLT is revolutionary in the innate flexibility, the computational power, and the statistical methods made possible using this software. Embrace the change to a new and improved genetic evaluation, it’s coming!
Welcome to the IGS Feeder Profit CalculatorTM.
Finally, you have a powerful, no-nonsense tool to highlight the true profit potential in your calf crop. It is time to leverage the investment you’ve made in your bull battery and the expense you’ve put into your health program to receive a third-party validation of the predicted feedlot success of your feeder calves. The IGS Feeder Profit CalculatorTM incorporates the genetic knowledge of most mainstream sires, regardless of breed, by referencing their EPD profile. At the same time, the extra time and serious effort you’ve put into your preconditioning and vaccination program are also considered as a fundamental part of feeder calf value. Weaning management and a responsible health program set your calves up for success. When superior calf management combines with profit focused genetics you’ve done your job. Now it is time to make your buyers aware.
What is IGS? IGS, or International Genetic Solutions, is a collaborative effort of numerous breed associations working together to generate the largest beef genetic evaluation on the planet. The IGS evaluation has the substantial benefit of being multi-breed, thus providing a much more accurate genetic picture of crossbred and composite cattle.
The member associations of IGS, and the seedstock producers, involved are invested in the future and sustainability of commercial producers by providing profit focused solutions and tools. The IGS Feeder Profit CalculatorTM is a highlight. And as such, it is offered at no cost to you.
That is correct, you can receive a third-party validation of your feeder calves at NO COST to you!
So what is the process? Simple. Here is a link to the IGS Feeder Profit CalculatorTM Input form. You need to compile the requested information and fill out the form. You must know the registration numbers on your bull battery and the Association in which they are registered. Likely, your seedstock provider(s) can help fill in any gaps. Also, if you know the sires represented in your cowherd, that will add tremendous awareness. For those who don’t know maternal grandsires, you will need to provide the approximate breed composition of your cowherd. These requirements form the basis of the genetic predictions of your calves.
This provides you with an IGS Feeder Profit CalculatorTM Certificate to share with potential buyers and marketers of your feeder calves.
All producer provided information will be highlighted on the official certificate. Buyers will be able to view and evaluate all information given. This allows a transparent process whereby you highlight your efforts and the buyer has the confidence of knowing the background of your calves.
It’s that simple. Finally, a streamlined process for progressive commercial producers to validate their hard work and focus on producing a quality product.
Know. Or Guess. Choose Know.
Article by Wes Ishmael | Beef Magazine
As the art and science of genomics becomes more accurate, cow-calf producers benefit. While cow-calf producers won’t directly participate in genomic evaluation now that single-step evaluation is a reality, they’ll be able to buy bulls with more accurate and reliable EPDs from their seedstock suppliers.
“If you’re a breeder doing a lot of genotyping and phenotyping — you’re measuring all of the data in all of the traits — single-step genomic evaluation lets you leverage the accuracy from that immediately,” says Stephen Miller, director of genetic research for Angus Genetics Inc. (AGI). “I think that’s a strong component of why breeders may become even more active in genotyping than they have been so far.”
Miller is describing what he believes will be one of the results of the single-step beef cattle genetic evaluation currently being refined and tested by organizations with massive databases, including AGI and International Genetic Solutions (IGS), which is a collaboration of 12 breed associations.
For the American Angus Association (AAA), AGI conducts a single-breed genetic evaluation. AAA’s registry grows by about 300,000 annually. The AAA database for genetic evaluation includes weaning weights for 8.3 million animals and birth weights for 7.6 million, among a host of various phenotypes.
Conversely, Mahdi Saatchi, lead genomicist at IGS, explains the organization’s database includes more than 16 million animals — the largest multibreed beef cattle genetic evaluation system in the world — adding more than 400,000 each year.
Single-step genetic evaluation is meant to replace what is currently and usually a multistep process used to incorporate genomic information into the calculation of expected progeny differences (EPDs).
As Alison Van Eenennaam, University of California, Davis, Extension beef geneticist, explains in the report titled “Recent Developments in Genetic Evalua-tions and Genomic Testing” (available at ebeef.org), “Currently, the incorporation of genomic information into genetic evaluations is statistically complex, and often involves a multistep approach that requires 1) traditional genetic evaluation with an animal model, 2) estimation of the marker effects and development of the prediction equation, and 3) a blending of those two pieces of information using a variety of approaches to develop a genome-enhanced EPD [GE-EPD].”
With this multistep approach, GE-EPDs are available only for genotyped animals. Including their information in genetic evaluation requires what’s termed a “training population” used to recalibrate prediction equations periodically. Suffice it to say, this is an added step that requires lots of time.
A shortcoming of the multistep approach is that selection bias can creep into the evaluation, since animals superior in genetic merit are the most likely ones to be genotyped. Saatchi adds that weighting estimates for the information included can be a primary source of biases.
Keep in mind that EPDs were already the gold standard of genetic prediction, even before genomic data was included in genetic evaluation.
by Will Townsend and Chip Kemp
Imagine you had to find bulls for your operation but you didn’t know any breeders, nobody used EPDs, or even shared actual data. It’s obvious to anyone interested in building quality cattle and maximizing profit this would be a major blow to the bottom line.
Yet, this is how the feeder calf business exists today. Frequently, when purchasing quality feeder calves, we can receive crucial information regarding environmental factors such as management and health protocols, weights, etc. However, when it comes to genetic awareness, color and polled status are often asked to substitute for true knowledge. A common scenario, and at times the best-case scenario, is that the calf buyer has a previous relationship with the seller and has owned and experienced the performance of the seller’s calves before. In more rare cases, we may have some information on the seller’s bull purchases. Again, this is a powerful step forward. It provides at least some insight into a portion of the genetics within the program. However, in a data-driven world, this level of genetic awareness is woefully inadequate. Especially since the financial stakes for feeder calf procurement are even higher than the stakes for bull procurement. Understandably, most large cattle buyers have technology to estimate genetic and environmental performance on feeder cattle but that information is not public and, for obvious reasons, is kept to those companies. Therefore, price discovery as we know it today, most often does not take account the actual performance potential of a producer’s feeder cattle.
Attempts to determine relative value of feeder cattle have been made for a long-time; however, certain issues have made it difficult. The foremost limitation has been accurately gauging the profit potential in the largest genetic group within the beef industry — the crossbred calf. It is a known scientific fact that commercial beef producers wishing to maximize cowherd fertility and longevity must crossbreed. This not only provides them a sustainable and profitable cow base, but fortunately generates an end product that is known to be the best combination of growth potential and carcass merit — the crossbred calf. The history of the Feeder Profit Calculator (FPC) has its roots in ASA’s Terminal Index ($TI). The $TI was developed over a decade ago by ASA in collaboration with Dr. Michael MacNeil, who was a USDA research geneticist at the time. The $TI is an economic selection index designed for selecting terminal sires. Though $TI could do a reasonable job valuing feeder calves, it was determined that evolving $TI into a tool that could account for such things as a current accounting of prices/costs, heterosis, and non-genetic factors (e.g., vaccination status), would improve the accuracy of predicting feeder calf values. Dr. MacNeil, now with Delta G Genetics, was tapped to evolve $TI into that tool — the FPC. Many of the FPC’s non-genetic components were sourced by Dr. David Lalman of Oklahoma State University. Providing the most robust genetic awareness of crossbred calves requires the most robust multi-breed genetic evaluation. Fortunately, International Genetic Solutions (IGS) provides the ideal platform to generate unparalleled information on crossbred and composite feeder calves. IGS, along with its’ member associations, the science team at Theta Solutions, and scientific contributions by Dr. Matt Spangler of the University of Nebraska is ideally suited to provide the industry’s benchmark in gauging feeder calf value. The IGS Feeder Profit Calculator empowers producers to market with confidence and allows feeders to maximize their purchasing dollars.
Capitalizing on novel technology usually requires a tremendous learning curve and a major outlay of dollars. Not this time! The IGS Feeder Profit Calculator is unique. It will offer a level of genetic awareness of crossbred feeder calves that has not been previously possible in the beef business. The IGS science team, the IGS partner associations, and the world’s largest beef genetic evaluation database allows the IGS FPC to be delivered at no cost to producers. That is correct. No Cost!
Beef producers looking for a transparent and straightforward assessment of their calves will harness the power of IGS by simply making a call, sending an email, or visiting the IGS website. IGS and/or breed association personnel will request information on herd health, basic management protocols, the bull battery used in previous years, and insight into the makeup of the cowherd. The more thorough the inputs from the producer, the better the predictive ability of the FPC. While individual sire identification isn’t required, identification of the bulls used in the operation is required. Producers will be asked to share preconditioning information and the health program in place. The IGS FPC will be demonstrated at the 2017 NCBA Convention in Nashville, TN, and be made available to the public shortly thereafter. Three short demos will be held at the IGS booth each day of the convention. For producers who have interest in having their calves evaluated through the IGS FPC please contact one of the IGS breed partners or contact beef@internationalgeneticsolutions. com. Cattle feeders who are interested in integrating the capabilities of the IGS FPC into their purchasing decisions please use the same email. Additional information and highlights will be provided in the coming months.
Over the last 50 years we have had evolution of the statistical methods used to calculate genetic predictions, EPDs, for livestock. What drove the evolution of these methods? Knowledge of statistical models? New methods? Data? Enabling computer technology? Golden states that he believes the drive for better models has been a desire to increase the accuracy of prediction.
Golden and Garrick had written grants to write genetic prediction software in the past. This avenue appears to have dried up, so they decided to start a company, Theta Solutions, in order to fund the development of genetic prediction. The latest genetic prediction runs contained 46,000 animals with genomic data.
Theta Solutions uses graphical processing units, originally built for video gaming, to have a high performance computer at a relatively low cost. The BOLT software focuses on custom turnkey analyses, once the system is set up all one needs to do is feed it data.
Using non-GPU computing, Golden can solve 51 million equations in 1649 seconds. The fastest GPU implementation took 78 seconds.
Why do we use a Bayesian sampler for solving mixed models?
- No accuracy approximation bias
- Can get PE covariance
- Can apply marker selection methods
- Can include prior information
With traditional methods, it took 23 seconds per sample, with new implementation can do a sample in 2 seconds. (Gibbs sampling is kind of like turning a statistical crank over and over to solve very complex equations, each sample is one turn of the crank.) They also parallelized the sampling, further speeding up the process. This parallelized processing is like working cattle with 100s of chutes rather than a single cute.
There are three ways to combine genomics with traditional EPDs,
- blending Genomic BLUP (combine pedigree prediction with genomic prediction, two separate analyses)
- single-step Genomic BLUP (combine pedigree relationships and genomic relationships, one analysis)
- hybrid model (single step with marker effects)
Single-step genomic models outperform traditional EPDs. But, the hybrid model outperforms both models, especially for unproven animals. The purpose of the hybrid model is to squeeze more information out of the data.
Currently looking at a data set with 6 million pedigree records, 4.8 million birth weight records, and 1.9 million post weaning gain records, 46,402 genotyped animals and used 44,414 SNP markers.
Less risk in genetic selection via higher-accuracy expected progeny differences (EPDs).
That’s the bottom line promise of BOLT, new software adopted by International Genetic Solutions (IGS) to conduct its National Cattle Evaluation (NCE).
IGS is the unique collaboration of 12 breed associations in the U.S. and Canada to conduct a common, multi-breed NCE with a combined database representing almost 17 million animals.
Many at the recent annual meeting of the Beef Improvement Federation heralded BOLT as a revolutionary step in NCE.
“It's a game-changer,” believes Wade Shafer, executive vice president of the American Simmental Association (ASA).
BOLT is an acronym for Biometric Open Language Tools. Bruce Golden and Dorian Garrick — noted animal breeders familiar to those in the seedstock business — developed the new software and license its use through their company, Theta Solutions LLC.
Increased prediction accuracy with BOLT comes through the software’s ability to directly incorporate genomic data into the EPD calculation.
“Until now, we’ve had to incorporate DNA information through a post-evaluation blending process that combines the independent genomic data and traditional EPD into one published EPD value,” says Larry Keenan, director of breed improvement for the Red Angus Association of America (RAAA). “BOLT gives us the capability to incorporate genomic information directly into EPDs.”
Even though systems before BOLT meant DNA data were blended post-evaluation, its inclusion in recent years significantly increased the EPD accuracy for young animals. “This absolutely will allow us to maximize use of information in the database for pedigree, phenotypic and genotypic data,” Keenan says.
“There is so much information, but because of the limitation of the models and technology that have been available to us previously, we couldn’t squeeze out all of the value from that information. We’ll be able to get more out of it with BOLT,” he says.
Another powerful feature is BOLT’s capacity to calculate actual (true) accuracy, says Shafer.
“Prior to BOLT, the calculation of accuracy in NCE has been limited to what has been dubbed ‘approximation methods,’â” Shafer says. “These methods take an indirect approach to the calculation of accuracy and routinely result in estimates of accuracy that can be quite different than an animal's actual accuracy.”
Because BOLT can calculate accuracy directly, it is capable of producing true accuracy. “Prior to BOLT, it was thought that the calculation of true accuracy was not feasible on large databases due to the computational requirements being untenable,” Shafer says.
Keep in mind that EPDs are already the gold standard of genetic prediction. Given available technology, they’re as reliable as possible.
The massive size of the IGS database also lends itself to increased prediction accuracy.
“Accuracy is critical to making genetic progress,” Shafer emphasizes. “There are almost 17 million animals in the IGS database. The accuracy of prediction generally increases with the volume of data.”
Depending on your leanings, a multi-breed NCE also offers sturdier predictions than a single-breed analysis.
Think of it like this — a registered Red Angus bull has an EPD within that breed, built upon the pedigree, phenotypic data, and now, genotypic data — submitted to that breed’s database. But the bull may also sire or be a relative to lots of other cattle accounted for in other breed databases. Being able to account for more progeny and relatives across more of the cattle population makes for a more accurate snapshot of the bull's genetic potential.
ASA began working with Cornell University in 1995, funding research and development for multi-breed NCE. Unlike in the traditional model, where universities developed NCE models and performed NCE for breed association clients, ASA shared the development costs and ownership.
At the time, Simmental breeders — like those of other Continental breeds — were primarily focused on breeding up cattle to purebred levels.
“We had lots of halfblood, three-quarter-blood and seven-eighths-blood Simmental, but we were using a single-breed model for genetic evaluation,” Shafer explains. A single-breed model couldn’t fully account for breed differences or heterosis.
These days, of course, another advantage of multi-breed analysis is that hybrid and composite seedstock are commonplace.
What you can expect
“From what we have seen thus far, it appears BOLT has the capacity to improve the accuracy of prediction well beyond any currently existing technology,” Shafer says. “As is typically the case with new genetic evaluation technology, the biggest gains will be on younger, lower-accuracy animals — which, fortuitously, is the vast majority of animals being considered as breeding stock.”
When IGS begins conducting its NCE with BOLT, seedstock producers will likely see some reranking of bulls, which always causes discomfort. The EPD accuracies for some bulls will likely decline, too. Rather than an indication that the new method is less robust, declining accuracy with the initial BOLT NCE would mean that the previous accuracy, calculated via the approximation method, was too high.
Already, EPDs can be compared directly among IGS breeds for growth and carcass traits. Ultimately, plans call for making that possible with heifer pregnancy and stayability, too.
“BOLT is a software package that is very dynamic and flexible, with the ability to accommodate most any type of statistical model,” Shafer explains. “Its flexibility makes upgrading models or developing EPDs for new traits highly feasible.”
BOLT is lightning-fast, too, compared to current NCE models and technology. Running the current IGS NCE without BOLT takes a couple of days. Running the NCE on the same computer with BOLT only takes a few minutes.
“The remarkable increase in speed is due to the software being written in a manner that utilizes the hardware to its fullest capacity — an approach that takes a world-class understanding of the interaction between computer programming and hardware,” Shafer explains. “BOLT’s dramatic speed allows for computational feats that were previously considered untenable, such as the calculation of true accuracy on a massive database.”
IGS is in the process of readying its massive database for BOLT. There is no launch date, but indications are that it should be this year or the first part of next year.
“Eventually, I believe all genetic evaluation providers, regardless of species, will go to it [BOLT] because of the power it brings to the table,” Keenan says.
Read the full article here.http://www.beefmagazine.com/cattle-genetics/bolt-software-brings-more-reliability-epds
In 2010, the American Simmental Association and the Red Angus Association of America coalesced around the goal of better serving International Genetic Solutions (IGS).
Today, IGS is a collaboration of 12 progressive breed associations that have put self-interest aside to focus on the needs of the commercial cattle producer.
With over 16,000,000 total animals and 400,000+ new animals added annually, IGS has the largest multi-breed genetic evaluation system in the world — a system that provides commercial producers with the most powerful and user-friendly selection tools that have ever existed.
International Genetic Solutions (IGS) delivers the best objectively described, user-friendly and science-based genetic predictions to enhance the profitability of beef cattle producers.
Your Success is Our Job
Let us know how we can help you be more successful. Contact any of the members of IGS for assistance, questions or comments regarding our products and the science of more profitable genetics. IGS
American Chianina Association: 816-431-2808; chicattle.org
American Gelbvieh Association: 303-465-2333; gelbvieh.org
American Maine-Anjou Association: 816-431-9950; maine-anjou.org
American Shorthorn Association: 402-393-7200; shorthorn.org
American Simmental Association: 406-587-4531; simmental.org
Canadian Angus Association: 403-571-3580; cdnangus.ca
Canadian Gelbvieh Association: 303-465-2333; gelbvieh.org
Canadian Limousin Association: 403-253-7309; limousin.com
Canadian Shorthorn Association: 306-757-2212; canadianshorthorn.com
Canadian Simmental Association: 403-250-7979; simmental.com
North American Limousin Foundation: 303-220-1693; nalf.org
Red Angus Association of America: 940-387–3502; redangus.org
Alison Van Eenennaam | University of California, Davis
The application of genomics to improve the accuracy of EPDs is a rapidly developing field. There are ongoing improvements in genotyping and sequencing technologies, statistical methods to increase the correlation between genomic predictions and true genetic merit, and the computing systems to handle the large datasets associated with animal breeding. One thing still remains true in the genomic age and that is the need to collect accurate phenotypic records. It is essential to ensure performance data, pedigree, and DNA information are recorded and reported accurately. Genomic predictions will only be as reliable as the data upon which they are based. Although it might seem like the genomics era could signal the end of performance recording, the opposite is true. Now more than ever, it is important that producers accurately report data, and ensure that animals which are genotyped are correctly identified so that their information can contribute towards improving the accuracy of the genomic predictions of the future.
"Brown Bagger" electronic presentation a couple weeks ago. Bob's focus was on the changing landscape in the area of genetic evaluation and Larry talked about MARC's involvement in multi-breed and across breed comparisons. This is a highly recommended presentation for those interested in genetic evaluation. Click here.