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The Random Shuffle of Genes: Putting the E in EPD

Jared Decker
Associate Professor / State Beef Extension Specialist
Animal Sciences, University of Missouri

Summary: Why are EPDs imprecise for young animals? How can genomics be used to track the random shuffle of genes?

Even though expected progeny differences (EPDs) have been used by the beef industry for more than 40 years, many misconceptions still exist. Occasionally we will hear a producer say something like, “I bred my cows to a low birth weight bull, but I had a couple of large calves.” What the producer does not realize is that this is to be expected based on the inheritance of complex or continuous traits. Let’s look at this more closely.

A calf inherits about 50 percent of its DNA from its sire, with the other 50 percent coming from its dam. Each sperm that is produced by a sire is a random sample of that sire’s chromosomes and genes. Cattle have 30 pairs of chromosomes. So, when a sperm is produced, it is similar to flipping 30 coins. If we label the chromosomes the sire inherited from his father as blue/paternal and the chromosomes inherited from his mother as pink/maternal, there are 1,073,741,824 possible combinations of the sire’s paternal and maternal chromosomes. (See Figure 1.) And, this number ignores the swapping of parts between paternal and maternal chromosomes in a biological process called recombination. So, the number of possible chromosome combinations is in the billions! We often state this as progeny receive a random sample of the sire’s genes, and with billions of possible combinations no two sperm are exactly alike (the same is true for eggs produced by the dam).

Illustration of the shuffling of chromosomes occuring during sperm formation; select image to view enlargement(opens in new window)Figure 1. Illustration of the shuffling of chromosomes that occurs during sperm formation. The first column represents the bull’s two sets of chromosomes. Chromosomes inherited from the bull’s sire are in blue. Chromosomes from the bull’s dam are in pink. The other columns depict possible combinations of paternal and maternal chromosomes in individual sperm cells. There are more than 1 billion possible combinations.

Think for a moment about your favorite set of full siblings (brothers or sisters with the same parents). Perhaps this is the celebrity family with a reality television show, your brothers and sisters, your children, or your favorite set of embryo flush mate calves. The dissimilarity between these siblings may be striking, for example, one may be short and the other tall, one may have light hair and the other dark hair, or one may be laid-back and the other excitable. The similarities between siblings are due to shared environment and shared genes. The dissimilarities between siblings are due to differences in environment and genes which are not shared. Siblings share 50 percent of their DNA on average, but in humans this can vary from about 40 percent to 60 percent (See figure 1 in PLOS Genetics article(opens in new window)). Because their genomes are similar in size, we can expect a similar distribution of shared genes in cattle. The sharing of genes between siblings (except identical twins) is due to the random segregation and shuffling of genes during the formation of sperm and eggs.

If we assume random mating and that the parents are unrelated, we can show mathematically that the breeding value variation (i.e. EPD variation) observed between a set of full siblings (calves with the same parents) will be half of the breeding value variation observed in the population. Even if our assumptions about random mating and unrelated parents do not hold up in real populations of cattle, the variation between full siblings will still be quite substantial. Research in Brown Swiss, Holstein and Jersey dairy cattle provides evidence that the variation between full siblings is very close to, if not greater than, one half of the population’s genetic variance (the variation in EPDs or breeding values, see article in Journal of Animal Breeding and Genetics(opens in new window)). The EPDs reported by breed associations can be thought of as one half of the sire’s breeding value plus one half of the dam’s breeding value plus the Mendelian sampling term (EPD_calf=1/2 EPD_sire+1/2 EPD_dam+Mendelian Sampling). The Mendelian sampling term represents a calf’s difference from the average of the parent’s breeding values. This difference is due to the random sample of genes and chromosomes that the calf inherited. When a calf is born, we have no data, so we assume this Mendelian sampling term is zero and the EPD is reported as the parent average. As we gain more data about the calf and the calf’s eventual progeny, we are better able to estimate this Mendelian sampling term and the EPD accuracy increases and the EPD estimate either increases or decreases.

Unfortunately, in the past embryo transfer flush mates have been marketed by some seedstock producers as containing identical genetics. The only cattle that share identical genetics are identical twins and clones (but even clones do not share short segments of DNA, i.e. mitochondrial DNA). Because birth weight and weaning weight data from embryo transfer calves are not typically used in national cattle evaluation (as the calves are reared by recipient dams not the biological dam), the flush mates have identical EPD profiles early in life. These EPD predictions remain identical until data on the flush mates’ progeny is recorded. These identical EPD profiles are simply the parent average EPDs. Like all parent average EPDs, these EPDs are not precise (reported as EPD accuracy) because the EPD estimation equations do not have data to predict the gene variants inherited from the sire and dam. In other words, without data the EPD equations are not able to predict the Mendelian sampling term, the random set of genes inherited as a result of gene segregation and shuffle. Traditionally, EPDs for flush mates have not changed until data about the progeny of the flush mates were recorded.

With new genomic technology the Mendelian sampling term can now be estimated for flush mates and other progeny. Genetic tests that provide genotypes on thousands of DNA variants enable an estimation of which set of genes an animal actually inherited. Genomic testing provides an estimate of the Mendelian sampling term and the genetic merit associated with the inherited variants. This information is then combined with the traditional pedigree EPDs to produce more reliable genomic-enhanced EPDs. In a roundabout way, this technology is tracking which bits of the sire’s and dam’s chromosomes were inherited. In a slightly different approach used by the dairy breeds and by the Santa Gertrudis beef breed, the pedigree relationship information used to calculate EPDs is supplemented with genomic relationship information. Shared DNA variants are used to estimate how closely related two animals are, in other words their genomic relationship. This procedure can tell whether a calf is more closely related to its paternal grandsire or its paternal granddam, thus tracking the inheritance of the sire’s chromosomes and identifying the Mendelian sampling term. See Figure 2 for an example based on real world data. Based on averages, we would expect a calf to share 25 Pedigree-based versus genomic-based relationships of its genes with any of its grandparents. But, due to the random shuffle of genes and chromosomes, this percent can vary greatly. Whether genomic data is used to produce a genomic prediction or supplement the relationship estimates, both of these approaches increase the accuracy of the EPD as they provide data that allows the Mendelian sampling term to be estimated.

Pedigree-based versus genomic-based relationships; select image to view enlargement(opens in new window)Figure 2. Pedigree-based versus genomic-based relationships. Based on the pedigree, we would expect the bull at the bottom of the figure to share 25 percent of his genes with his paternal grandsire (orange chromosome pair) and his maternal grandsire (green chromosome pair). But, when we calculate the actual percentage of shared genes, he shares 25.8 percent of his genes with his paternal grandsire and 15.4 percent with his maternal grandsire. Based on actual data from a popular AI sire.

It is important to remember that EPD stands for expected progeny difference. Expected refers to a statistical expectation, which means a prediction or average. Thus an EPD is the predicted average difference between a sire’s calves and the EPD base. EPDs predict averages, because for a large group of calves the Mendelian sample term approaches zero. An individual calf can have a very different genetic merit from the sire (a large Mendelian sample term) due to the random sample of genes it inherited.

In conclusion, a calf shares 50 percent of its DNA with its sire and 50 percent of its DNA with its dam. On average, two full siblings also share 50 percent of their DNA. But, which DNA variants are shared between a parent and a calf or two full sibling calves at birth is unknown. Because of this parent average EPDs are used for young calves. It is only when more data are collected that we are able to estimate this random sample of genes (i.e. the Mendelian sampling term). Genomics provides information that enables the Mendelian sampling term to be estimated. Genomic-enhanced EPDs use DNA information to estimate the random sample of genes inherited from the parents and result in more accurate and reliable EPDs for young animals. The random shuffle of genes and chromosomes puts the expected in EPDs.

The Random Shuffle of Genes: Putting the E in EPD(opens in new window) was originally available on eXtension.org.

Buying A New Herd Bull? Do These 4 Steps First

W. Mark Hilton 2 | Feb 29, 2012

Bull purchases represent a significant investment in a beef herd. Whether that investment results in a “nest egg” or a “goose egg” depends highly on a bull buyer’s preparation. Let’s discuss some basics.

Step 1: Don’t buy a new disease. While I’ve never had a producer intentionally bring a new cattle disease onto the premises, in reality this is how most new diseases enter a herd. Be sure the bull is a virgin or is tested for trichomoniasis if you live in a “trich” area. Bear in mind that trich is a devastating disease that is spreading into areas where it once was either absent or rare.

What about Johne’s disease, persistent infection with bovine viral diarrhea (BVD) and campylobacter? Ask the supplier if he’s ever had a positive diagnosis and, most importantly, get permission for your herd health veterinarian to call the seller’s veterinarian to discuss the health of the seller’s herd.

Be sure to ask specific questions about diseases you want to avoid buying. If the seller doesn’t allow this communication, I’d look elsewhere for genetics.

Step 2: Buy genetics that fit your herd goals. If you’re using bulls on virgin heifers, calving ease is a high priority. Using across-breed EPDs (Angus base), select a bull below +1 for BW EPD for a high likelihood of unassisted calvings.

For bulls to be used on cows, you should buy a bull with growth, maternal and carcass traits that fit your goals. I see many producers still looking primarily at calving ease when selecting a bull for cows. This is counterproductive as you’re likely limiting the growth of the calves and decreasing pounds sold.

As a general rule, low-birth weight EPD bulls tend to be lower in weaning and yearling EPD. Buy a bull for cows that will improve hybrid vigor (which improves health), growth and carcass.

We all want cattle that will thrive in their given environment; a calf with poor vigor at birth starts life with a huge black mark. Calves should be born quickly and stand to nurse on their own within 30 minutes. Anything less isn’t acceptable, and such calves have a greater chance of morbidity, which can be a tremendous labor issue. Ask about calf vigor before you buy.

Step 3: Quarantine for 30 days. Every farm or ranch has pathogen exposure and most animals never show clinical signs of sickness. Their immune system fights off the disease and you never even know they were exposed.

However, take that “normal” animal, stress him, and put him right in with your cows with their normal pathogen load and the new bull gets sick. Thus, 30 days of quarantine is a small price to pay for improved health.

Your herd health veterinarian will likely recommend a vaccination and parasite-control protocol during quarantine based on the bull’s health history and diseases common in your locale. Call your herd health veterinarian to get advice on these preventive health procedures.

Step 4: Are you buying for Maternal or Terminal crossing. Study the EPDs. Make sure they fit in with what you are trying to accomplish. If you are wanting to keep your Cows on the smaller side – do not breed for frame size and growth/milk. That will lead you away from your desired outcomes.

Comparing Cattle for Crossbreeding

Across-breed EPDs and the value of shared metrics

Imagine you want to buy a horse. But you’re a tall guy, so you want a tall horse. In your search, you find advertisements for two likely potentials. They both look like great ranch horses, but one is listed as 72 tall while the other is described as 132 tall.

If you chose based on those numbers alone, without knowing the measurement systems being used in each case, you would be short-changed if you chose the second horse because of its seemingly larger height number.

If you knew the measurement system each number was coming from—inches and centimeters, respectively—and knew how to convert those systems to make them comparable, it would be clear that the first horse is taller despite the seemingly lower number (72 in. versus 132 cm, a.k.a. 52 in.). If both horses were measured using the same system—let’s say, hands, making them 18 hands versus 13 hands—to begin with, it would make finding the taller horse even easier.

Expected progeny differences (EPDs) in the cattle world are a lot like our hypothetical tall horses problem. Most breeds’ EPDs are on different bases. An EPD basis is analogous to a measurement system; it’s the system in which their measurement numbers (i.e., EPDs) make sense. If you try to directly compare the weaning weight EPD on an Angus bull to the weaning weight EPD on a Hereford bull, for example, your success at getting a bull that meets your genetic goals will be about as successful as if you had chosen the second “tall” horse.

Sorting Out the Bull

February 2015

Selecting a bull today can be an overwhelming task for many cow-calf producers. Photo courtesy of Aaron Berger.

The winter and spring bull sale season is well underway. For many cow-calf producers this is when catalogs are studied and sales are attended, with the focus being on the purchase of their next herd sires. The purchase of a bull is a significant investment and represents the genetic future of the calves and in many cases replacement heifers that will go into the cowherd. The following are thoughts on a process that producers can use when planning the purchase of their next sire.

What do you want your cowherd and the calves you produce to do? What genetics will do that?

Clearly identifying goals for what cattle are expected to do and the traits and characteristics that most impact profitability for the cow-calf enterprise is a foundational first step. Are calves sold at weaning, as yearlings, or is ownership retained through until harvest? What do the purchasers of your calves want? Can you produce what they want and have a functional female if replacements are retained? What is an optimum target given the production system cows are expected to operate under? These “big picture” questions should be answered prior to the selection and purchase of a bull.

Where is my cowherd at genetically?

“Wherever you are at, that is where you are.” Randy Hunter, DVM and stocker/yearling operator from Wheatland, Wyoming uses this phrase when teaching cattle handling skills to help people recognize everyone is at a different place in their ability. Once you know where you are, you can identify a plan to move toward where you want to go. This phrase applies well to thinking about the genetics of the cowherd. What is the genetic makeup of the cowherd currently? Are you pleased with where you are? What traits or characteristics would you like to see change? What is the target for where you want to end up? How much change is needed to reach an optimum level given your resources?

Sorting out the bull breeder

Selecting the breeder and breeding program of your next bull is more important than the choosing of the bull himself. The following are characteristics in no particular order that need to be considered when deciding who will be your genetic provider.

  1. Honesty and Integrity
  2. Custmer Service
  3. Genetic Program and Focus
  4. Bull Development Plan
  5. Value Added Opportunities

Sorting through all the information

Selecting a bull today can be an overwhelming task for many cow-calf producers. Bull sale catalogs are full of information, including actual animal performance, ratios, Expected Progeny Differences (EPDs), gene testing, economic indexes, ultrasound measurements, etc. There are also individual breeders who utilize their own scoring system for characteristics such as disposition and udder soundness of a bull’s dam. Having access to all this information is great. However, trying to sort through and discern what these data mean and which information is relevant to what you want can be a bit like trying to get a drink out of a fire hose! What you want is there, but you can find yourself getting smacked in the face with more than you wanted when you go to get it.

Know and understand what the numbers mean

The first priority is to know and understand EPDs. Research has shown EPDs are a tremendous and valuable tool for giving an indication of what a bull’s true breeding value is in terms of the genetics he will pass on to his calves. Understanding what the numbers mean and which ones are relevant for the traits which you are selecting for is important. Matt Spangler, University of Nebraska–Lincoln Extension Beef Genetics Specialist has put together a NebGuide titled “EPD Basics and Definitions” that explains what these traits mean and how they can be used to compare animals within a breed to one another. In most cases, EPDs are not comparable across breeds. An exception to this is Red Angus and Simmental EPDs which are a multi-breed EPD and are calculated in the same way.

Economic indexes are the second set of numbers to understand. Matt Spangler defines economic indexes as “A collection of EPDs weighted by their economic value such that traits with greater impact on production goals have a larger economic weight associated with them.” Understanding how different economic indexes are calculated for the breed you are evaluating can help you to know if they should be used as a tool for selection.

The third set of numbers to grasp and evaluate is an individual’s own records and performance against those of his contemporaries. These indicate how a bull did in his own right. While worth looking at and evaluating, they are secondary to EPDs for identifying a bull’s true breeding value.

Identify the bulls that meet your “numbers” criteria

Sorting through the bulls on paper and identifying those that meet your criteria is the next step. Plan to do this well in advance of the bull sale so you give yourself adequate time. The more stringent the criteria and the more values you include, the fewer bulls you will have to pick from.

Visually appraise bulls for structural soundness and phenotype

While a bull may look good on paper, when you actually see him, he may not be the type and kind that you want. Remember that this bull’s purpose in life is to get cows pregnant. That means he has to be able to move and cover cows.

Get the breeder’s opinion

A solid seed stock supplier should be a tremendous resource for you in selecting your next sire. Communicate to them what you want and ask what bulls they recommend. See if the bulls you have identified are ones they believe will meet your goals.

Set a budget and give yourself options

Bull sales can be fast moving events. Know ahead of time what you are willing to spend. Identify your options in terms of bulls you will consider. If the bulls you want quickly blow by your limit, you want to have evaluated if there are others in the offering that still meet your criteria.

Conclusion

Selecting your next herd sires is an important event. Being well prepared can help to ensure that the bull you pick takes your herd genetically the direction that you want to go. An excellent resource that further discusses preparing to purchase your next herd sire is the “Rancher’s Guide to Profit”. This set of videos prepared by the Red Angus Association is available at their website.

Aaron Berger
Nebraska Extension Educator

Using EPDs and Economic Index Values

https://beef.unl.edu/using-epds-and-economic-index-values

February 2015

Expected Progeny Differences (EPDs) have been around for decades and are the best tools available to use in selecting sires with desirable genetic potential as parents.

A recent webinar titled “Genetic Selection Tools in Beef Cattle: EPDs and Antagonisms” outlines how to understand and utilize EPDs in selection.

When selecting sires it is critical to understand potential genetic antagonisms that exist to ensure marketing goals can be met while fitting within environmental constraints. Selecting for increased milk and early growth can be detrimental in some environments and in cases where replacement females are retained and maintenance costs are a concern. Additionally, selection for decreased calving difficulty could potentially lead to replacement heifers that have slightly more difficulty giving birth during their first parity

There are scores of EPDs available and selecting to improve multiple traits simultaneously can be cumbersome – just open up any sale catalog and it is easy to become confused immediately. Economic indexes can help alleviate this confusion. They do so by combining multiple Expected Progeny Differences (EPDs), each weighted by an economic value, into one numeric value often expressed in dollars per animal.

Economic Indexes Defined

An economic index is a collection of EPDs weighted by their economic value such that traits with greater impacts on production goals have a larger economic weight associated with them. The basic equation of an economic index is:

I   EPD1  x  a1  +  EPD2  x  a2  +  EPD3  x  a3…EPDn  x  an

Where: I is the index value; EPDn is the EPD for trait n; and an is the economic weight associated with trait n.

Angus, Hereford, Charolais, Gelbvieh, Limousin, Red Angus, and Simmental all publish at least one economic index.

A recent webinar titled “Genetic Selection Tools in Beef Cattle: Economic Indexes” explains how economic indexes are calculated and provides information on a number of the breed indexes available.

A full description of all available economic indexes can be found in the University of Nebraska NebGuide G1847 Economic Indexes for Beef Sire Selection (PDF version, 374KB) and a full description of all available EPDs can be found in the University of Nebraska NebGuide G1967 EPD Basics and Definitions (PDF version, 704KB).

Matt Spangler, Ph.D.
Associate Professor and Beef Genetics Extension Specialist
University of Nebraska–Lincoln

EPDs and How to Use Them

ARSBC 2018:

Darrh Bullock
University of Kentucky

Crossbreeding should always be a consideration for commercial cattlemen. Crossbreeding has the greatest benefit for reproduction and other lowly heritable breeds.

Practical Guide to Bull Buying
Determine marketing strategy. Will heifers be retained? Make breeding decisions based on specific marketing plan. But, change marketing plan based on current situations.

It’s pretty easy to find a bull that will give you great feeder calves and market animals. When we are keeping replacement females, we are now asking a bull to create females and feeder calves. We’ve given him a new job.

Determine your management level.
What is your labor? How frequently do you visit your cattle? How much attention do you give to them?
What is your level of nutritional management?
Assure that bulls are reproductively sound with a BSE.
Check for structural soundness. This is doubly important if you are retaining females.

The tough one is to set performance levels based on resource availability.

Select for performance using EPDs and indexes.
Determine other factors included horn/polled, color, tempermant, visual attractiveness.

“For trait for which EPDs are available that is the single piece of information you should be looking at,” Bullock said. The other pieces of information including actual measurements, ratios, and genomics feed into the EPDs. Don’t try to outsmart the system!

If you are looking at actual weights and EPDs together, you are reducing your ability to make accurate decisions. Just look at the EPD!

Environment is muddying the water. If we take it out we are improving the tool to make selection decisions.
EPDs is the best tool. Uses all information actual measurements, relatives, environment and genomics. EPDs are a risk management tool, they are not perfect.

One bull has an EPD of 65 lbs. Another has a 50 lbs EPD. The first bull’s calves on average will weigh 15 pounds more.

Prior to EPDs, we basically had no opportunity to select for maternal traits. Maternal traits are predictions on the daughters of the bull.

American Angus Association started publishing EPDs in the early 1980s. Prior to EPDs there was success in increasing growth. Before EPDs you couldn’t select for milk. The rate at which growth was increasing was faster with EPD selection. EPDs allowed us to select for increased growth and decrease birth weight (decreased calving problems).

All breeds have upward pressure for weaning weight. This increased growth is also increasing the mature size of cows. Mature height is under control, it has stayed flat. However, mature weight continues to increase. Mature height does not dictate nutrional requirements. Mature weight is what drives feed needs.

The trait we need to focus on is calving ease, not birth weight. Birth weight is simply an indicator of calving ease.

We need to be careful with selecting for more milk, or we will run into issues like we did with the frame race in the 1980s. Too much milk can lead to reproductive failure.

Most DNA variants (SNPs) have very small effects. But, when we add them all together they can have large effects.

Without a genomic test, accuracies are low. But, if we send in a DNA sample and do the DNA testing, it is the same as having 24 calving ease records out of that bull.

Calving Ease Direct is the tool to look for bulls that have calves that come easy. Calving Ease Maternal tells us if the heifer has the potential to calve unassisted.

Use EPD closest to marketing endpoint (weaning weight, yearling weight, carcass weight). Keep in mind correlated responses in calving ease, milk, and mature weight.

For maternal traits, watch for too much milk. There are Heifer Pregnancy, 30-Month Pregnant, Stayability and Sustained Cow Fertility for selection for reproduction.

Carcass traits are highly heritable and can make a lot of progress in first year of selection.

Selection indexes allows for comparison on a single value. Look for an index that matches what you are trying to do.

EPDs are breed specific. Different breed associations are continuously updating EPDs. Others are still updating on a twice a year basis.

Percentile rankings are one of the most under utilized tool in cattle selection. It is a great tool to find where in a breed a bull ranks.

Summary
Commercial bull buyers should be practicing crossbreeding
Best tools for selection are EPDs and indexes.

Link to video of Bullock’s presentation: https://www.facebook.com/AngusJournal/videos/2146961142208480/
See ARSBC Newsroom for more information. http://www.appliedreprostrategies.com/2018/newsroom.html
Note: this post was live blogged and may contain errors.

EPDs 101: Use Information to Improve Your Herd

Jared E. Decker
Associate Professor, Division of Animal Sciences, University of Missouri
http://blog.steakgenomics.org/2019/03/epds-101-use-information-to-improve.html

Can we be frank for a minute? It is quite simple: EPDs work. When we use EPDs to make selection decisions (which bulls to buy, which females to keep and cull), the performance of our herd improves. Let’s discuss why EPDs work, how they can be used, and pitfalls to avoid.

Defining EPD

EPD stands for Expected Progeny Difference. “Expected” in this context is a loaded word. We use it here the way a statistician would use it. Expected means we are describing a prediction of the future. Expected also means we are discussing an average, not a single observation. What is the average that we are predicting with EPDs? We are predicting the average progeny, or the average of an animal’s calf crop. Finally, when we are discussing EPDs we are discussing differences. Either the difference between two animals or the difference between an animal and the breed average.

The Key to EPDs

What makes EPDs special? Genetic predictions, i.e. EPDs, separate genetic variation from the total variation in a trait. There is a key piece of information that is essential to do this. We need to have some measure of genetic similarity. In the past, we used pedigree information to estimate this genetic similarity. Now we use a combination of DNA data and pedigree data to measure genetic similarity. With measures of genetic similarity, we can separated the bell curve for the variation in the trait into two parts: first, a genetic variation and second, other sources of variation. Now that we have the genetic variation isolated, we can use that informationto make genetic decisions.

Contemporary Groups

Contemporary groups are another important piece of genetic evaluations. Contemporary groups are groups of animals from the same farm or ranch that were managed the same, are the same sex, and are similar in age. By accounting for contemporary groups in genetic evaluations, we remove sources of similarity or differences that are not due to genetics. This makes the genetic evaluation more accurate. By using contemporary groups, we can perform a national genetic evaluation.

The Purpose of a Bull Sale

What is the purpose of a bull sale? What are we buying at a bull sale? What is the purpose of a bull? And, what distinguishes a great bull from a good bull?

We do not go to a bull sale to buy the environment. We do not go to a bull sale to buy management practices or feed rations. When we purchase a bull, we are buying genetics. A bull is simply a delivery mechanism for the genetic potential of our next calf crop. Bulls should be measured on the performance of their calves. The ultimate measure of a bull is not how he looks, but how his calves perform and affect our profitability.

Far too often, bull buyers try to buy management, nutrition and environment when they purchase a bull. While a bull needs to be fertile and sound to do his job, his main purpose is to provide genetics for the next generation. When we make genetic decisions based on actual performance or adjusted performance, we are trying to purchase the management of the bull. Management is not passed on to future generations. Only by using EPDs to make genetic decisions do we focus our decisions on genetic merit. Genetic evaluations take raw measures and create information we can use when purchasing a bull.

How EPDs Are Used

We use EPDs to rank animals from the most favorable to the least favorable. For example, suppose we want to increase the growth potential of our herd. We can rank potential artificial insemination (AI) sires from those with the largest Weaning Weight (WW) EPD to those with the smallest WW EPD. We would then purchase semen on the bulls with the largest WW EPD to increase the weaning weights in our herd. But, we need to discuss two pitfalls with this hypothetical example.

First, we need to avoid single trait selection. We do not want to focus on one trait. By focusing on one trait, we often take one step forward for that trait but two steps back on other economically important traits. Focusing on multiple traits can be difficult, but economic selection indexes make this easier. Economic selection indexes combine multiple traits into a single number based on each trait’s economic importance. Commercial producers should identify an index that matches their production system and marketing endpoint.

Second, extremes are not always better. For some traits, a middle or optimal value is best. We want birth weights that are small enough to avoid calving difficulties. But, we do not want calves born so small that they do not thrive as newborns. We also want Milk or Maternal (MAT) EPDs that match our forage resources. We want cows that provide adequate nutrition to their calves. However, cows with high genetic potential for Milk or MAT have high maintenance energy requirements and cannot fully express their milk production potential. These cows waste forage resources and in some environments may have trouble breeding back. EPDs can be used to select cattle that are at or near breed average; EPDs do not require selection for extremes.

Avoiding Pitfalls

EPDs can be imprecise, e.g. miss the mark, for individual animals. This is especially true if it is a young animal with very little data. There are a couple of strategies to counteract this.

First, we can turn in more data on an animal. Seedstock producers can collect as much data as possible and turn complete, clean data into their breed association. Commercial producers can work with seedstock producers who are passionate about data reporting. An easy way to get more data is made possible through technology. DNA testing a bull to produce genomic-enhanced EPDs is equal to reporting about 20 progeny records for all published traits. Genomic testing improves the accuracy of EPDs as it allows us to better measure the genetic similarity of animals in the genetic evaluation.

However, we should not double- or triple-count information. One of the ways we commonly see people do this is when selecting a calving ease bull. They often look at the actual birth weight, the Birth Weight EPD, and the Calving Ease Direct EPD to make this decision. But, this practice makes these decisions less accurate, because instead of adding information they are adding together uncertainty. Further, the Calving Ease Direct EPD contains the information in Birth Weight EPD and Birth Weight EPD contains the information in the actual birth weight. So, the best practice is to simply look at the Calve Ease Direct EPD that contains all of the available information.

Second, we can hedge our bets. Too often in beef breeding, we are looking for the “One” great bull. But, in reality, the “One” does not exists. Instead of using one bull, we hedge against changing EPDs by using a group of bulls. Because EPDs are unbiased, some of the bulls in the group will have their EPDs go up, others will have their EPDs go down, and others will stay the same as EPDs are updated with more data. The average of this group of bulls will remain the same before and after the EPD updates. However, we are at the mercy of randomness if we use a single bull. His EPDs might stay the same, go up, or go down. Because EPDs are predictions of the average, we can use this property to protect ourselves against uncertainty.

How EPDs Work in Practice

Suppose we have two bulls, Black Bull and Gold Bull. Black Bull has a WW EPD of 2 and Gold Bull has a WW EPD of 22. There is a 20 pound difference in the EPDs of these two bulls. At the same ranch under the same management and environment, we mate each of these bulls to 100 cows apiece. Fifteen months later, we wean the resulting calf crops. The Black Bull’s calves average 495 pounds at weaning, with the majority of the calves weighing between 445 to 545 pounds. The Gold Bull’s calves average 515 pounds at weaning. The 20-pound difference in the EPDs of the bulls is reflected in a 20-pound difference in the average of their calf crop. However, due to the randomness of inheritance and genetics, some of the Gold Bull’s calves under perform the Black Bull’s average and some of the Black Bull’s calves outperform the Gold Bull’s average. We cannot do much to change the shape of the bell curves. However, with the use of EPDs, we can move the bell curve in the direction we want it to go.

Conclusion

Cattle producers can use EPDs to use all the data available boiled down to information they can use. EPDs predict genetic differences and inform selection decisions. EPDs produce the desired results when used consistently and properly. Whether in good times or bad, EPDs help us accomplish our goals.

http://blog.steakgenomics.org/2019/03/epds-101-use-information-to-improve.html

EPDs Work Management Perspectives: No hype

Management Perspectives: No hype: EPDs work
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 have become complicated, the precision and reliability of the EPDs has 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 accuracy of genetic predictions.

The whole goal to 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.

Bull Selection: New Calculator To Determine The Value Of A Bull

Editor’s note: The following is part four of a four-part series that helps you to evaluate different breeding programs, which bulls are optimal for your herd, and how much they’re worth. (See part onepart two and part three).


Different traits of bulls can contribute to different impacts on the bottom line of the operation. For example, a bull with a higher calving ease EPD may contribute to more live calves. Not surprisingly, bulls with higher calving ease (or lower birth weights) sell for a higher price (Simms et al., 1997). With the large variation in bulls available, bull prices extend over a wide range from $3,000 to over $20,000 per head.

Identifying a fair price during sire selection contributes to higher efficiency in operation economics. To estimate breakeven bull price, a bull valuation calculator has been developed. The purpose is to provide a general idea of how much a bull is worth based on key farm parameters.

Bull Values – two Scenarios

The value a bull provides depends on his individual performance, the environment (ex: pasture productivity), management (cow:bull ratio) and markets (calf price). For example, large framed bulls require more feed, leading to a higher maintenance cost, but that may be offset by heavier calves at sale time.

Two scenarios were studied – a low maintenance farm versus a high maintenance farm. Table 1 shows the parameters entered for each farm. The default values in the calculator are the averages of the two scenarios.

The low maintenance farm is assumed to have a larger pasture size reducing the cow to bull ratio, multiple bulls in a field with potential for fighting as well as rough terrain contributing to reduced bull longevity, and reduced feeding costs over fewer days, resulting in lower maintenance costs. This management style is reflected in the cow herd as well with a lower weaning rate and lower weaning weights.

The high maintenance farm is assumed to have smaller breeding pastures, more labour, and more feed, which leads to a higher cow to bull ratio, greater longevity, higher weaning rates, and higher weaning weights.

Despite keeping key parameters constant like the proportion of the calf value attributed to the bull and expected calf price, there is a large variation in bull value between the two farm scenarios (Table 2).

The high maintenance farm has a breakeven bull price more than double that of the low maintenance farm. In fact, the low maintenance farm would have had a much lower breakeven price if the annual maintenance cost was similar to the high maintenance farm. However, the lower annual maintenance cost helped to offset the lower cow to bull ratio and lower weaning rate.

For the high maintenance farm, the producer can afford to pay more for a bull given the expected performance of both the bull and its offspring. The large variation in bull prices on the market reflects the different abilities of the bull to bring value to an operation. This is impacted not only by the bull but also the environment and management system used by differing operations.

Driving Factors of Bull Price

The value a bull provides is in the calves sired over a lifetime, the long-term genetic change of the herd, and salvage value at the end of a productive life. (As long-term genetic change is not readily measurable by producers, this parameter was excluded from the calculator.)

The value provided depends on:

  • cost factors (i.e., bull maintenance cost and death loss),
  • performance factors (i.e., years of service, the expected cow to bull ratio, expected weaning rate, expected weight of feeders, and proportion of the calf value attributed to the bull), and
  • price factors (i.e., expected price of feeders and salvage value).

 

 

 

 

**Download the Excel calculator here**

Note: this calculator is currently available in Excel only. A web option will be developed in the near future. 

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EPDs only one part of the genetic selection formula

EPDs most valuable when used with best practices

Find the Right BULL