Category: Genomics

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.

America 4-circle cattle. What? How?

Is it possible to combine all economic relevant traits in one package? Maybe so.

Aug 22, 2019

By Tom Brink

Thirty years ago, the beef cattle industry debated whether calving ease and growth could be decoupled. Some animal geneticists shrugged and said “no way.” If we are going to have fast growing cattle, we’ll have to stand more birth weight. Circa the 1980s, many believed that situation to be a permanent predicament.

Fast forward 15 to 20 years of active selection using EPDs, and the industry did produce many bulls in multiple breeds that offered both superior calving ease and excellent growth. The old paradigm was shattered forever.

That reminds me of a quote by James Baldwin: “Those who say it can’t be done are usually interrupted by others doing it.” This quote speaks to the issue of impossibility versus possibility.

In many areas of life and business, there’s an ongoing debate about what is and is not realistic. What cannot be done pitted against what can. Just like the value of EPDs.

There’s yet another can versus can’t discussion active today. Can we truly breed cattle that do almost everything well? Or is doing so impossible?

To break the argument down into simple terms, we will group the economically-important traits into four categories—calving ease, maternal, growth and carcass. These trait groups are presented in the illustration below, with each concentric and larger circle encompassing more traits.

Some breeders today stop at just a couple of these trait groups and suggest that going further in one animal or one herd is just not possible. Others take a different, less limiting view, believing it realistic to combine all the economically relevant traits.

Tom Brink4 circles of genetic success

Stepping through the circles

To get our minds around this subject, suppose, for example, a certain bull is being marketed based solely on his merit for calving ease (represented by the small black circle). He’s being sold that way because that is all he offers genetically.

Will the seller receive a reasonably high price for this bull? Unlikely, because he only brings one trait to the table and commercial cow-calf producers are looking for more.

We move next to the green circle, which encompasses both calving ease and maternal traits. There would be additional value in a 2-circle bull that fits this description. He would be more marketable than the 1-circle bull, but probably still wouldn’t bring a high price on sale day, because, again, most producers are looking for more.

The red circle encompasses calving ease, maternal and growth. A bull that legitimately covers those bases is going to attract a lot more attention. More interest = more bids = higher selling price.

Commercial buyers are also going to be more satisfied with a bull like that, and satisfying customers should top the list for seedstock breeders.

Finally, we come to a 4-circle bull that offers a tremendously complete package genetically speaking. Assuming he also has good structure, good feet and a favorable disposition, he should sire both great steers and replacement heifers. He just might top the sale, because he fulfills more commercial cattlemen needs.

The critical question thus becomes: Are 4-circle cattle even possible? Can such cattle be intentionally bred and should they be pursued as part of your seedstock breeding programs?

The 45 highest-selling bulls in the Red Angus breed so far in 2019 tell an interesting story in that regard. These bulls all sold for a $23,228 average and undoubtedly combined phenotypic excellence with a strong package of EPDs. They were indeed 4-circle cattle as a group, averaging in the top 30% for Calving Ease Direct, top 35% for Heifer Pregnancy and Stayability, top 10% for Yearling Weight and the top 10% for Carcass Weight, Marbling and Ribeye area.

The take-away message is that buyers (especially premium bull buyers) are seeking more than one or two areas of genetic competence. They pretty much want it all, which is more closely aligned what 4-circle cattle have to offer.

The human element is always interesting insomuch that what some people believe can’t be done often becomes a motivator for those actively engaged in breaking old paradigms. Creation of 4-circle genetics may be scoffed at by some, but for those making it happen, such opinions are little more than background noise.

Brink is CEO, Red Angus Association of America (RAAA). Source: RAAA, which is solely responsible for the information provided and is wholly owned by the source. Informa Business Media and all its subsidiaries are not responsible for any of the content contained in this information asset.

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.

Cow’s Mothering Rating

Cow’s Mothering Rating

Posted July 28th, 2018 — Filed in Stockmanship

I have been following a thread on another e-mail list comparing the mothering rating of the cow that tries to attack anyone who gets close to their new-born calf as opposed to the cow that is OK with this. The consensus seems to be that the mellow cow is not as good mother as the cow that will try to eat you. I disagree with this.

Bud and I found that when you work livestock properly – that is, by using pressure/release methods instead of force and fear, the cows learn to respect but not fear you.  Since they don’t feel you are a threat to them, they also don’t think you are a threat to their calf so they don’t “get on the fight” when you need to handle their new baby.

When we lived in Canada we were involved with a Beef Booster cow herd.  In case you aren’t familiar, this is a composite breed.  Some of the herds were rated “Maternal.” Their main function was to produce heifers to go into the cow herd, another raised “Terminal bulls” to use on the herds that would market all of their calves, etc.  The man we worked for had about 100 head of cows that were designed to raise “Terminal bulls.”  He wanted to change over to a “Maternal” herd so he swapped his herd with a neighbor.  When these cows were delivered the neighbor also delivered a list of ear-tag numbers of cows that would kill you if you tried to handle their baby calf.   The only way they could weigh and tag the calf was with a bucket loader on a tractor.  A man in the bucket would get the calf, then the tractor operator would try to raise the bucket before the cow could climb in, too.  We received these cows in October.  We handled them quite a lot.  If the feedlot shipped a pen of cattle and there was still feed in the bunks, we’d put these cows in the pen for a while to let them clean the bunk.  Through the winter we tried to move their straw bed every few days to make it easier when they farmed the ground in the spring.  This usually meant we had to drive the cows to the new bed a couple of times to discourage them from going back to the old one, etc.  When spring came the owner was able to weigh and tag every calf with no aggression from any of the cows.

The first year we worked on the elk ranch In Texas, we didn’t see an elk calf until it was a couple of weeks old.  The following year, the cow elk would bring their newborn calves with them when we drove through the pasture, scattering hay.  We even had one calf born in the corral.

Bull Selection Breeding Programs That Suit Operational Goals

Editor’s note: The following is part one of a four-part series that will help you to evaluate different breeding programs, which bulls are optimal for your herd, and how much they’re worth.

There are a range of different beef operations in Canada, and there is no one breeding program that is optimal for all operations. Breeding programs will be determined by operational goals and the management practices that fit those goals.

Here are some examples.

A producer that sells weaned calves at auction may choose a crossbreed program with high calving ease and a focus on performance gained from hybrid vigour; or they may prefer the uniformity of a purebred program with reputation premiums.

A producer that retains heifers and is looking for maternal replacements may be focused on maximizing the performance through inbreeding and outcrossing within a single breed; or they may develop FI crosses with higher reproductive performance and longevity.

These choices may be limited by the number of breeding fields available or the number a producer is willing to manage. There are a variety of breeding programs available, and effective sire selection requires an understanding of the characteristics of the available genetics as well as your own operation.

Each breed of cattle has distinct traits that allow them to excel in different geographical or management environments (Table 1). Depending on the goals of the operation, a sire can be chosen that has the potential to make positive changes for your operation in the areas you’ve identified for improvement.

Table 1. Comparison between beef cattle breeds in Canada (Adapted from Agriculture Victoria, 2017)

Indicators:
• E: Early, A: Average, L: Late
• S: Small, M: Medium, L: Large
• 1 = high/desirable; 5 = low/undesirable

Source: http://agriculture.vic.gov.au/agriculture/livestock/beef/breeds/breeds-of-beef-cattle

Also see Beef Improvement Federation’s across breed EPDs

Purebred

The advantage of the purebred or straight-bred approach of using only one breed is a homogeneous herd where cattle responses to environmental and nutritional factors are easier to predict. There will be consistency in nutritional needs, weaning, yearling, or finishing weights, and days on feed. The largest advantage is the ability to market a relatively uniform product, but ease of planning, and providing breeding stock forcommercial operations intending to maximize hybrid vigour may also be considerations.

When the parents have very similar genetics, the calf is more likely to have two sets of identical genes (homozygosity), which can have beneficial effects if the genes are associated with superior performance. However, negative traits can also show up with homozygosity. This can lead to the expression of abnormal traits, such as lethal recessives (e.g. curly calf syndrome, dwarfism, neuropathic hydrocephalus, etc.) It can also have more subtle effects on overall performance by increasing the amount “inbreeding depression” in the population.

Inbreeding depression is a reduction in performance due to the mating of highly related individuals, and it most negatively affects reproductive traits, followed by growth traits, but seems to have little effect on carcass traits. It is associated with an increased percent of open cows and stillbirths, with decreased levels of survival, growth, and overall performance (Northcutt et al). Generally, caution must be exercised when inbreeding as there is a high risk of performance reduction if the breeding program is not managed very carefully.

Three common purposes of inbreeding are to:

  • to test a bull for the presence of undesirable genetics that show up with inbreeding
  • develop inbred lines for a crossbreeding system
  • linebreed, or to maintain the genetic contribution of a genetically superior individual in the larger population

Linebreeding seeks to preserve and continually improve upon the genetics of a high performing ancestor. While linebreeding mates closely related individuals, it seeks to minimize the level of homozygosity (and thus inbreeding depression) while maintaining a high level of relationship to the high performing ancestor. Linebreeding is typically merited when there is difficulty finding outside bulls with sufficient performance to improve the herd.

Key components of a successful linebreeding program include:

  • individuals selected for a linebreeding program must be of superior quality with no genetic defects
  • meticulous record keeping of breeding history, parentage records, and animal performance
  • aggressive culling at signs of defects or lower performance – the starting herd should be as large as possible to accommodate aggressive culling
  • keeping inbreeding levels low

To keep inbreeding levels low, the recommendation is to keep the genetic contribution of the same ancestor to 50% or less (van der Westhuizen, 2016). To illustrate, the progeny of mating a daughter to her sire will have 75% of genetics from the sire. Generally, matings that involve full siblings and parents to offspring are discouraged. Instead, matings of uncle/niece, half siblings, and first cousins are potential strategies.

Outcrossing, or the breeding to non-relatives or distant relatives (i.e., at least 4 generations away) within a breed, is the most widely used mating strategy in purebred herds. Outcrossing can be used to increase performance levels, avoid inbreeding depression, and restore performance lost to inbreeding depression (Evans and McPeake). The more genetically dissimilar the animals, the larger the potential benefit. One drawback of this system is that, if the outcrossed progeny were to be mated, it is more difficult to predict the phenotype of the calves due to the variation in genetic background.

Crossbreeding

With crossbreeding, cattle from different breeds are mated. As the genetics from both parents can be very different, both the positive and negative effects seen in outcrossing are magnified with crossbreeding. Crossbred herds are much more unpredictable in terms of calf weight, maturity time, and nutritional demands. However, there are two key advantages:

  • Heterosis or Hybrid vigor – this is the opposite of the performance reducing effects of inbreeding depression. Heterosis provides improvements, especially in the area of reproduction and growth. The effect of hybrid vigor is dependent on the animal having two different copies of a gene, where the more unrelated the breeds, the larger the potential improvements.
  • Breed complementarity – where the strengths of two different breeds are combined. For example, when mating Charolais bulls to Hereford-Angus crossbred cows, the Charolais bull contributes growth and performance genetics, while the Hereford-Angus cows have desirable maternal and carcass quality attributes. This may not be seen in every individual animal, but is observed in herd averages.

Studies (Gaines et al., 1966; Turner et al., 1968) have found that compared to purebred, crossbred cows have a 10% increase in calf crop and calves weaned, with the calving percentage of the crossbred cows being consistently higher than their parents. Gregory et al. (1978) found crossbred cattle to be 7 kg heavier and 9 days younger at puberty than their purebred counterparts.

Crossbreeding improves reproductive performance, longevity, and maternal ability of the cow. This is manifested through increased calf survival rate, as well as increased weaning weight. Overall, the performance improvements from crossbreeding can have significant impacts on the bottom line of beef producers.

There are many crossbreeding strategies, for example:

  • 2 or 3 breed rotation,
  • terminal cross,
  • bull rotation, or
  • composite breeds.

A terminal cross is where both parents are purebreds of different breeds, and the resulting calves are a 50:50 mix. However, to maintain this specific breed ratio, replacement breeding stock from purebred herds must be used instead of rebreeding the offspring.

Another strategy is mixed breeds, where multiple breeds are used without maintaining specific ratios of each breed in the progeny. While this strategy does not require complex breeding management, there is lower uniformity and a higher level of uncertainty regarding calf performance.

The optimal strategy will depend on the operation itself; for example, if calves are sold at a pre-sort sale or are part of a large group and able to fill an entire feedlot pen, uniformity becomes less important.

For further reading on crossbreeding, NBCEC (2010) introduces an overview of different strategies and Gosey (1991) presents a more in-depth discussion.

There are also challenges and considerations associated with a crossbreeding system (NBCEC, 2010):

  • a small herd (i.e., less than 50 cows) can limit choice in crossbreeding strategies
  • a higher requirement for breeding pastures and bull breeds for the more complex crossbreeding strategies (e.g., rotational systems)
  • more record keeping and cow identification as the current breed composition of cows can affect sire and heifer replacement selection
  • less uniformity in progeny
  • no crossbreeding system can overcome low quality bulls

There is no one-size-fits-all solution or breeding program that is best for all scenarios, as the right genetics depend on the individual operation. Key determining factors include: the management style of the operation, heifer retention (i.e., terminal versus maternal sires), number of breeding fields, and time of marketing. For example, a farm that auctions their calves at weaning may choose a mixed breed program with high calving ease, while a farm that direct markets their beef may prefer the uniformity of a purebred program.

There are many different types of bulls available, and effective sire selection requires an understanding of the characteristics of the available genetics as well as your own operation. Deliberate alignment of the bull’s genetics to your operational goals will contribute to enhanced revenue and reduced costs.

Editor’s note: Stay tuned for part two in this four-part series.

Genomics and profitability are closely tied

Hannah Garrett of Diamond Peak Cattle Company in Craig, Colo., believes in genomics and good cattle. Genomics, the study of the DNA within a living structure, is important to any cattleman hoping to improve the genetics of his or her herd.

Genomic testing, she said, deals with the changes of the base pairs in terms of the expression of birth weight, calving ease and carcass traits. Through science, research, and academia, Garrett said changes in base pairs can be directly tied to the changes that are directly tied to an operation’s bottom line.

At her Colorado Farm Show presentation, Garrett pointed to her genetic results from a site like 23 and Me. Her results showed her high percentage of Scandinavian blood but her favorite portion of the results, she said, was the 3 percent uncertain result. It’s an illustration that the science is not perfect in either the beef cattle or human segment, leaving room for improvement.

Garrett said there are three main applications for genomics in the beef cattle industry today: parentage, genetic defects and genomic profiles.

“When we think about the future and where this technology is headed, we think about things like disease detection or being able to identify calves that have a higher susceptibility to BRD,” she said. “That would be huge, right, if you’re a feedlot operator and could, from the very beginning, identify by the genome, calves that are more likely to get sick.”

Genomics and profitability are closely tied. For an operation that turns bulls out, genomics can ensure that the bulls being kept — and fed all year — are siring a reasonable number of calves to earn their keep. She said it can also shed light upon the most effective sire and dam crosses and the heritable traits that make it so.

“Maybe it’s a specific sire group that works well when you cross it on top of your cow family,” she said. “You can chase that sire group, use that sire group more, and get more of that type and kind of calves that will bring more value for you.”

This translates to dollars on the scale, as well as the ability to select and retain the highest quality replacement heifers. The cost of improved genetics in the form of bulls is a major consideration for many operations and Garrett said parentage testing can allow producers to keep heifers resulting from this investment to continue to grow the investment.

Garrett said whether a producer is retaining ownership to the rail or weaning and shipping calves, the product being produced is beef, and genomics can ensure the quality of the product is one that is high and will result in demand. Genomically enhanced EPDs is a blending of traditional EPDs with genomic information and is often referred to as a 50K. These enhanced EPDs increase the accuracy of the traditional EPDs. Single step, or BOLT, is the math behind this development and Garrett said it is the algorithm breed associations use to blend the two sets of EPD data. Single step, or BOLT, takes relatedness into consideration.

“Traditionally, we assumed you were 50 percent your mom, and 50 percent your dad,” she said. “But you’re not. You’re 52 percent your mom, and 48 percent your dad. More importantly, rather than being 25 percent of each grandparent, you’re more like 27 and 23.”

CONSISTENT RESULTS

This becomes important in cattle, she said, when determining relatedness to a dam or sire and the attributes they possess and pass on. While EPD data changes over time, she said there is less change when genomics and EPDs are combined. As a bull buyer, this allows a higher degree of confidence in EPD data. As populations grow and more data is assigned to a bull, variability decreases over time. For seedstock producers working to produce consistent results, genomics are vital.

“As Mr. Walter told me, I want to know I can sleep at night and that the bulls I sell are the bulls that go out and perform and have the calves I expect them to have,” she said. “Seedstock producers are trying to create a relationship with you and they want you to come back. In order to do that, they’re trying to offer you the most consistent product they can.”

Genomics combined with EPDs can offer producers the confidence to select for the traits that are the most likely to return on their investment but Garrett said bulls still need to be sound and able to do their job so he has the opportunity to bring profit back to the operation. It takes, she said, the variability out of sire selection.

Heifer selection and genomics can be driven by seedstock or commercial profiles to define values in terms of maternal performance and carcass traits. Information is gathered and returned on birth weight, calving ease, milk, stayability and heifer pregnancy.

“If we can identify the heifers that will make better cows and have more calves, that puts us in a higher degree of profitability,” she said. “If we know a heifer is more or less likely to fall out of the herd and not remain as a cow, that’s a big deal because we know cows have to be in the herd for at least six years to pay themselves off.”

Culling those heifers based on genomic results can save thousands of dollars for the producer and save time wasted by developing the wrong heifers.

Carcass traits determined by genomic testing can also translate to dollars, especially for those producers retaining ownership and feeding calves that may be docked on the rail. Identifying and feeding calves with the carcass traits most desirable in an operation, she said, is money in the pockets by reducing discounts.

“Not everybody is set up to retain ownership but maybe if you could use a tool to identify the top end of your calves that are going to feed, and are more likely to gain premiums, it might be something you could pencil into your operation,” she said. ❖

— Gabel is an assistant editor and reporter for The Fence Post. She can be reached at rgabel@thefencepost.com or (970) 392-4410.

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