Stayability EPD. Does it Work?

Tuesday, 28 July 2020 11:40

By Drs. Randie Culbertson, ASA and IGS Lead Geneticist and Jackie Atkins, Director of Science and Education        |       

Daughters sired by bulls in the top 25 percent for stayability were over twice as likely to remain in the herd as six-year-old cows and averaged almost two more calves in their lifetime compared to daughters sired by bulls in the bottom 25 percent for stayability EPDs.

The financial success of cow-calf operations depend on a cow’s ability to remain in the herd long enough to recoup the cost of heifer development and cow maintenance. In order to achieve this, a heifer needs to calve as a 2-year-old and produce a calf each subsequent year. Stayability EPD was developed to predict this reproductive success (or failure) and is defined as a cow’s ability to remain in the herd to a specific endpoint, with the assumption that open cows are culled. The typical endpoint is defined at six years of age. Stayability has an economic influence on a cow herd through female reproduction, increased calves per cow, and increased calf performance given mature cows on average wean heavier calves.

As with most reproductive traits, the heritability of stayability is low (less than 0.20) indicating a large non-genetic influence on stayability. These non-genetic influences can range from ranch conditions to ranch management and are not inherited by future progeny. On the flip side, if you provide the optimal environment for your herd but lack the genetics for cow longevity, you will still find yourself with cows falling out of the herd prematurely. Although a low heritability for stayability illustrates the importance and significance of management, it also tells us that there is an underlying genetic aspect to a cow’s ability to remain in the herd. Furthermore, since cow longevity is largely determined by the environment, making genetic selections to improve longevity is far more accurate with a stayability EPD compared to a phenotype heavily influenced by the environment. In the context of genetic improvement, ignoring stayability EPDs will slow or reverse the genetic progress for this highly relevant trait.

Since its development, the stayability EPD is currently being published by multiple breed associations but how reliable is this EPD for predicting cow longevity? To examine this question, over 140,000 daughters from high-accuracy bulls for stayability from the IGS database were analyzed. These sires were ranked by their stayability EPD and divided into four percentile groups (or quartiles; 1-25 [top or best], 26-50, 51-74, 75-99 [bottom or worst] percentile). Within each quartile, the percentage of daughters remaining in the herd to six years-of-age and the average number of calves from daughters in their lifetime was compared.

As you can see in the graph, as Stayability EPD increased, the percentage of daughters reaching the age of six also increased. When comparing the lowest quartile to the highest quartile, the percentage of daughters remaining in the herd to age six more than doubled.

Only 22% of the daughters reached the age of six for the lowest quartile compared to 49% of daughters for sires in the highest quartile.   

But how does this translate to calves on the ground? The second graph illustrates the average number of calves from daughters of sires within each Stayability EPD quartile group. There is a clear increase in the average number of calves per cow as we move towards the top percentile. Daughters from sires in the top Stayability quartile averaged nearly two more calves in their lifetime compared to daughters out of sires in the lowest Stayability quartile.   

Female longevity is one of the most economically impactful traits of commercial cow-calf operations. When choosing genetics for replacement females, emphasizing stayability will optimize the genetic potential for longevity in the herd. 

An industry-wide collaboration is improving breeding tools.

International Genetic Solutions (IGS), a group of more than 17 cattle associations and organizations, is working across the breed spectrum to provide resources and technologies that ensure cattlemen and women along the industry chain are set up for success. 

“We’ve put together a massive collaborative effort with approaching 20 million head of cattle to provide the most scientifically-credible, the most cost-effective, the quickest, multi-breed, directly-comparable genetic evaluation on the planet,” says Chip Kemp, IGS Commercial & Industry Operations.

IGS partners and leaders across the beef industry meet virtually this week during the Beef Improvement Federation (BIF) virtual symposium, beginning June 8. 

“If you think about IGS, from a big-picture standpoint, it’s the value of collaboration,” says Tom Brink, Red Angus Association of America CEO. “Beef breeds, historically, haven’t always worked together so well, or so much, but IGS broke the mold on that. Being able to combine these data sets, more analytical power, better EPD predictions to use for all the breeds involved, IGS just really facilitates that in an unprecedented way.”

The collective effort is intended to help individuals make more informed decisions – from seedstock to commercial producers.

“The collaboration that we have with IGS will do two things: not only will it help their members sell seedstock bulls and replacement heifers but it will also help their customers, commercial producers make an informed decision in their operations. And those two things together will contribute to accelerating genetic improvements,” says Stewart Bauck, vice president of agrigenomics for Neogen Genomics. “It’s going to have a significant, important, and long-term beneficial impact on the beef industry.

Bob Weaber of Kansas State University agrees.

“Getting everybody pulling the wagon together allows the IGS team and the leading scientists in the world, working in beef cattle genetics, to accelerate the process of genetic improvement,” Weaber says. “Tools like the IGS Feeder Profit Calculator puts increased profit potential in the hands of cattlemen and women as they assign and assess the value of their stock.”

IGS, and the tools it provides, is unique, Brink adds.

 “We’re a lot stronger working together than we are individually,” he says. “We’re getting a lot better genetic predictions by doing what we’re doing, working together, so that’s really the power of IGS.” 

International Genetic Solutions (IGS) is an unprecedented collaboration between progressive organizations 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. 

More information about BIF’s virtual symposium, June 8-12, is available at

As recently as the 1960s, the Hereford breed registered more cattle than all of today’s breeds combined. Many other Continental breeds’ growth peaked in the 1980s with numerous breeds registering over 50,000 head. However, today the only breeds that reach the 50,000-head plateau are Angus, Red Angus and Hereford. Additionally, Simmental is not far behind in terms of critical mass, however, most breeds have experienced a significant decline in registrations and the revenue associated with it.

Traditionally, the services desired by breeders from their associations have included: herdbook; performance database; information technology and programming; breed improvement; research; breed marketing; promotion; commercial marketing; magazine; field staff; registry; junior program; physical plant; and comptroller.

However, the number of breeds that can maintain this full list of services is few, so associations must learn to cooperate in order to survive and remain relevant. This cooperation includes taking advantage of services offered by the National Center for Beef Excellence (NCBE) and International Genetic Solutions (IGS). Another example is the breeds Salers, South Devon and Aberdeen moving under one roof.

Read the full article here.

LINCOLN, Neb., May 18, 2020 — NEOGEN Corporation (NASDAQ: NEOG) announced today that is has launched an enhanced version of its Igenity® Beef profile, a genomic test for commercial cattle.

Last fall, NEOGEN announced a partnership with International Genetic Solutions (IGS) to put even more power behind Igenity Beef by leveraging IGS’s platform that ranks as the largest multi-breed beef genetic evaluation in the world. Those updates are now live and available to cattle producers.

“Together, IGS and NEOGEN are dedicated to ensuring commercial beef producers are armed with the best technology and information possible,” said Dr. Jamie Courter, NEOGEN’s genomics beef product manager. “Continuing to make updates to this solution with more and more data helps producers manage risk through confident selection.”

Since 2003, Igenity has been leading the advancements in commercial genomic testing for beef. With a single DNA sample, Igenity delivers an estimate of genetic merit for 16 economically relevant traits, summarized into three indexes. Now powered by genomic knowledge from the same genetic evaluation that represents the genomic-enhanced expected progeny differences (GE-EPDs) from many of NEOGEN’s partner breed associations, Igenity Beef is stronger and better than ever. Combined with Envigor and the Igenity Dashboard, commercial cattle producers have a complete package for heifer selection.

Continue reading

by Tom Brink, CEO     |    Red Angus Association of America      

Accomplishing more together than we could individually is the reason 16 beef breeds, including Red Angus, are part of the genetic evaluation partnership operated by International Genetic Solutions (IGS). What started as a collaboration between Red Angus and Simmental in 2010, with the goal of creating the industry’s first multi-breed EPDs, has now grown to become the world’s largest genetic evaluation for beef cattle. Breed associations from the United States, Canada, Australia, and New Zealand are working together to create a huge database of cattle performance records and genotypic information, and to share the cost of using cutting-edge software and technology to calculate the most accurate EPDs possible. What IGS is doing today is so large and sophisticated, it was little more than a dream five years ago.

To offer just one example of how working with multiple breeds directly benefits Red Angus, Ryan Boldt, RAAA Director of Breed Improvement, recently calculated that available data on Red Angus-sired calving events (and their associated calving-ease scores) is 20% larger through IGS than if Red Angus was conducting its genetic evaluation as a single breed.

Continue reading.

Updates to Growth Trait Predictions

Friday, 28 February 2020 09:31

Jackie Atkins Ph.D., Matt Spangler Ph.D., Bruce Golden Ph.D., and Wade Shafer Ph.D.

The genetic evaluation is constantly evolving with updates to models as new science is discovered and new technologies are available. One area under recent scrutiny is the prediction of growth traits (birth, weaning, and yearling weights, and milk). The IGS Genetic Evaluation Science Team is investigating the following five areas of potential improvement in the prediction of growth traits.

The goal of each of these changes is to improve the prediction of growth traits. Breeders and IGS partners should expect to see the implementation of improvements to growth trait prediction in the approaching months. 

 1. A new definition of contemporary groups based on the age of the dam.

Regardless of how users designate contemporary groups, the science team is considering placing all calves born from first-calf dams into separate contemporary groups (CG) from calves out of mature cows. Given the vast majority of producers actually manage this age group separately, it is reasonable to define their calves as their own CG. Handling these as separate CG is a valid way to reduce the environmental noise caused by different management strategies for this age group. 

2. Setting the genetic correlation between weaning weight maternal (milk) and weaning weight direct to 0 (compared to - 0.3).

The magnitude, and even direction, of the correlation between weaning weight direct and milk, has been long debated in scientific circles. In fact, there is a wide range of estimates that exist in the scientific literature. Given that, the science team feels the appropriate way to model these traits is to assume they are independent (i.e., genetic correlation of 0). We expect the impact of this change to be greatest for low accuracy animals.

3. Different variances for different sexes (heterogeneous variance).

Males usually have a higher growth potential than females simply due to gender. As a consequence, the variation associated with their weights also tend to be greater. This difference in the amount of variation between the sexes should be accounted for in genetic predictions. The IGS team is testing the validity of setting the variance of growth EPDs on a male base.

4. New DNA Marker subset.

As the number of genotyped animals has increased, so has our ability to estimate marker effects and identify subsets that are more predictive. Relative to growth traits, a new (and larger) subset of markers has been identified to add more accuracy to EPD.

5. Accounting for different birth weight collection methods.

When the IGS Science Team began looking into growth trait data, we discovered that not all birth weight CG followed expected amounts of variation in the weights. In some cases, weights are rounded to the nearest 2 lb increment or 5 lb increment. In other cases, the amount of variation was substantially reduced due to the use of hoof tapes (see the December 2019/January 2020 issue of the Register for more information on hoof tapes). There were also cases where the reported weights were clearly fabricated (for instance, all calves weighed 75 lb). Some of these data are useful, but they are clearly on a different scale and need to be treated appropriately. Dr. Bruce Golden developed a way to use machine learning to recognize unique features of each class of birth weight observation and predict how it was generated (e.g., scale weights, hoof tape, rounding, fabricated). By accounting for the various categories, the genetic evaluation is still able to use the records submitted that fall out of biological expectations for most scenarios, while more accurately accounting for different practices of collecting the weights. 


Wednesday, 04 March 2020 08:05
The world's largest multi-breed beef cattle evaluation partners with the industry's leading genomics company. Here's what it means for ranchers.IGS Feeder Profit CalculatorTM - Marketing Backed by Genetics.
"We're extremely proud of the collaboration we have with IGS. It really is the first of its kind in the world," says Stewart Bauck, vice president of Agrigenomics for Neogen Genomics. "We will, along with IGS, be developing and refining a set of tools that we can make available to commercial producers so they can select superior females in a multi-breed or crossbreeding operation."
Jackie Atkins, Ph.D., Director of Science and Education says, "The IGS database is the largest on the planet for multi-breed beef cattle, and not only do we have a lot of data, but we also have a lot of genotypes in that evaluation. Because of that critical mass, we can do a better job developing DNA markers and what those markers mean for a commercial test."
During the past decade, seedstock breeders have adopted genomics to strengthen genetic prediction tools and resulting selection decisions. The IGS-Neogen partnership accelerates the effort for commercial ranchers.
"Historically, all of these types of genetic profiles have been for a single breed. If we look at geneticists and the knowledge that we've gained from their research across the years, we know that crossbreeding leads to hybrid vigor, and so being able to have crossbred commercial cows should really be the goal for any commercial cattleman because, at the end of the day, they sell pounds," says Jamie Courter, Neogen Genomics Beef Product Manager.
"We'll be able to pull from all of the information that seedstock and commercial producers report back to IGS and fully support the Igenity® Beef Profile to make it stronger and better than it is today," she says. "So it'll be a two-way street. The sales reps at Neogen will be able to drive people toward reporting information and data back to IGS while Neogen is able to pull from that data and strengthen our own products."
In the end, more data on crossbred commercial cattle reduces risk.
"That puts a proactive management tool in the hands of the commercial producer," Bauck says. "For $30 and in three weeks, I can get the same information as I could by spending $2,000 in two years to develop a replacement heifer."
Kenny Stauffer, Neogen Genomics Director of Beef Genomic Sales, says, "If you're able to tag a calf, you're able to take a tissue sample. Put the capsule in the box and mail the box to us. You send your sample to us and in 21 to 28 days, you're going to have your results."
As producers make decisions on where to spend their time and money, DNA testing offers a valuable option in finding genetic answers.
"DNA testing is a valuable tool that can get to answers faster for commercial and for seedstock producers," Atkins says. "It will never replace data recording, that will always be important, but the fact that we can squeeze more out of any single DNA test in the future, that just gives commercial producers a more informed decision to make better, more profitable choices for them." 
International Genetic Solutions (IGS) is an unprecedented collaboration between progressive organizations 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. 
I G S    S T A N D    T O G E T H E R



Data Sharing for the Good of an Industry


Matt Spangler of the University of Nebraska says the future of the beef business will depend on information sharing.


IGS and the Pursuit of Better Cattle

IGS Feeder Profit Calculator ™ Highlights Profit, Reduces Risk

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.  Continue reading.

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.  Continue reading.

Check Out What We Have Done So Far

Wednesday, 04 December 2019 17:51

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:

June 2018

• 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

July 2018

• 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

August 2018

• 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

September 2018

• Canadian Shorthorn Association released IGS EPDs

• Initiated monthly IGS partner conference calls to discuss issues and updates with the evaluation

October 2018

• 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 

November 2018

• 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 

December 2018

• Added trio (sire + dam + calf) mating checks to the QC error reports

January 2019

• Began investigating multi-breed imputation

• Started evaluating the latest version of the FImpute software package

February 2019

• 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

March 2019

• 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

April 2019

• 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

May 2019

• 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

June 2019

• 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

July 2019

• Implemented multi-breed imputation software

• Installed and configured FImpute

• Implemented updates to the CW-REA evaluation

August 2019

• 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.

Continue reading.

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. 



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