Wednesday, August 15, 2018

Show-Me-Select Rules Require Genomic Tested Bull EPDs

New sire selection rules for Show-Me-Select Replacement Heifers improve reliable calving-ease genetics.

“Bulls used in the heifer program will carry DNA-tested EPDs (expected progeny differences),” said Jared Decker, University of Missouri Extension geneticist.

The rules going into effect Feb. 1, 2019, were set by the SMS governing board of farmers.
“DNA tests add reliability to EPDs for selecting herd bulls,” Decker said.

Bulls for pasture-breeding heifers will carry genomic-enhanced EPDs. In the past, EPDs were based on pedigree and production tests. “Now GE EPDs combine DNA, pedigree and production data into a single tool,” he said.

“DNA tests give results similar to 28 calving-ease production records,” Decker said. “More data boost confidence in a sire.”

With DNA tests, EPDs result from checking blood drops, tissue samples or hair root bulbs. Blood or tissue tests are preferred, Decker said. A one-time test adds data on young bulls equal to years of production testing. It lasts a lifetime.

Bulls bought before Feb. 1 will be grandfathered in, but those bulls must get GE EPDs by Feb. 1, 2020.

Seedstock producers advertising their bulls as “Show-Me-Select qualified” draw more bidders. Sires promoted as Show-Me-Select now must have GE EPDs.

SMS heifers gained fame for calving ease that cut death losses and labor at calving. Spring and fall SMS auctions across the state bring higher bids for calving-ease genetics.

Buyers pay premiums to lower assisted births with first-calf heifers. In the past, high death losses took out heifers entering the herd.

In recent SMS sales, heifers with genomic tests bring highest premium prices.

More genetic data beyond calving ease, especially on carcass traits, came into SMS over time. Quality beef brings premium prices.

SMS was started 21 years ago by Dave Patterson, MU Extension reproduction specialist. Now, SMS brings buyers to Missouri for replacements in cow-calf herds.

Only Missouri produces SMS heifers. Herd owners enroll in a yearlong MU Extension education program. Regional livestock specialists guide the heifer program.

SMS teaches management as well as genetics. “The program goes beyond typical heifer development,” Decker said.

One example: Reproduction tract scores on all heifers before breeding. Then pregnancy checks follow within 90 days after breeding starts.

Veterinarian tract scores rank stages of puberty, from one to five. Heifers slow to develop can be culled. That cuts costs, boosts conception rates and shortens calving seasons.

Bulls used for pasture breeding or AI breeding must meet required EPDs.

SMS heifers meet a goal of predictable results as 2-year-olds, Decker said. First-calf heifers often have problems. Those difficult first births can lead to late rebreeding.

“Genomic testing adds EPD predictability and reliability. That cuts risks,” Decker said.

“We know this adds cost to market registered bulls, but time is right for change,” he said. Since 2010, cost of DNA test fell from $150 to $37.

Show-Me-Select sales show repeat buyers bid more for added genetic data.

“Seedstock producers provide this as more customer service,” Decker said. “There are many strategies for meeting the new rules.”

Herd owners join SMS through county MU Extension centers. For more information on SMS, go to http://agebb.missouri.edu/select/.

Contact Jared Decker at 573-882-2504 or deckerje@missouri.edu. For a detailed explanation of the rules see http://blog.steakgenomics.org/2018/08/SMS-GE-EPD.html.

Tuesday, August 14, 2018

Show-Me-Select Board Approves Genomic Testing Requirement for Natural Service Sires


All bulls purchased after February 1st, 2019 for use as natural service sires in the Show-Me-Select Replacement Heifer Program must be DNA tested to have genomic-enhanced EPDs. All bulls used as natural service sires after February 1st, 2020 must have genomic-enhanced EPDs, regardless of when they were purchased. Seedstock producers classifying bulls as Show-Me-Select qualified in sale books must have genomic-enhanced EPDs on those lots.

Bulls purchased prior to February 1st, 2019 will be grandfathered into the program, as is the common practice with all natural service sires. However, this grandfather grace period will end February 1st, 2020. At that time for a bull to qualify for use in the program, it must have genomic-enhanced EPDs.

Why the change?

The Show-Me-Select Replacement Heifer Program has the goal of producing premium heifers that perform predictably as 2 year olds. The program has a history of requiring Show-Me-Select producers to go beyond typical cattle production practices. This has included requiring Reproductive Tract Scores on all heifers, and requiring pregnancy checks within 90 days of the start of the breeding season. The program has also specified which bulls qualify for use as natural service sires and which bulls do not. These requirements are in place to provide as predictable performance as possible.

Genomic testing increases the predictability and reliability of EPDs. In order to decrease the risk of a natural service sire not truly being a calving ease bull, we now require the use of genomic-enhanced EPDs. DNA testing provides approximately the same amount of information as 28 calving ease records or 21 birth weight records on calves out of a bull. This additional data will increase the probability of natural service sires truly being calving ease bulls.

We realize that this will add cost to the marketing of registered bulls. However, the time is right to make this change. Since 2010, the cost of DNA testing registered cattle has dropped from $150 to $37. Seedstock producers are encouraged to view this practice as an added measure of customer service for their bull buyers. We also note that there are multiple strategies to meet this requirement. 

Contact Jared Decker at 573-882-2504 or deckerje@missouri.edu if you have questions.

Friday, June 22, 2018

BIF 2018: Experiences with Implementation of Single-Step at American Angus, One Year In

Steve Miller


Angus Genetics Inc has four research scientists. They do single-step genomic evaluations for Angus, Canadian Angus, Charolais, Canadian Charolais, and Maine-Anjou.

Angus switched to single-step on July 7th, 2017. Miller feels like the switch to single-step was a monumental switch, should have made the Time Magazine year in review!

When breeders see bulls re-rank, they then understand was a correlation of 0.9 really means! On July 7th, Steve Miller talked to two breeders. On July 8th he was feel cool and casual like Ferris Buller. The next week, then the calls came.
"I've seen this before, in a couple of months it will all blow over" a friend told Miller. And that proved true.

The switch to single-step was kind of like the stages of grief with getting a flat tire.
Quiet phase: Listening, evaluating, asking yourself if you have a flat tire.
Expressive phase: Cussing, kicking dirt, frustrated.
Have to Move Forward phase: Fixing the tire and getting back on the road.

Communication was crucial, both before the changed occurred and phone calls after the change.

There is no way AGI would go back to the methods used before the switch to single-step. The new evaluation is that much better.

On July 7th, Angus changed to single-step. But they also made a lot of other changes to the evaluation. The changes were frequently due to the changes in the carcass model, by accounting for the selection bias in which animals had carcass and ultrasound data.

Single-step is now a brand.

Any genetic evaluaiton is only as good as the data behind it.

Genotyped database has doubled in 96 weeks. On June 16, 2018 they reached over 500,000 samples. They receive over 3,000 samples per week since November 2017.

So, after the storm of single-step passed, what questions now cause the phone to ring.
How can two flush mates have this different of EPDs?

The power in the pedigree. Creating the famous A matrix, the relationships between all of the animals in the evaluation. When we use pedigree data, we use the expected relationships between animals. But, with genomic data, we actually use the real relationships between the animals.

Recombination between paternal and maternal chromosomes cause unique chromosomes being inherited by the progeny of a bull.

We can look at 4 bulls.

Bull Rank Whole Chromosome 6 Top Half of Chromosome Bottom Half of Chromosome
Bull A 1 6 9
Bull B 51 7 167
Bull C 58 187 1
Bull D 183 171 184
Rank out of top 193 Sires for Birth Weight genomic value.

Look at variation in calf crop. One quarter of the variation comes from the dams. On quarter of the variation comes from the sires. One half of the variation comes from Mendelian sampling, the random shuffle of genes and chromosomes between generations.

As a breeder, we should love variation. Variation is what makes genetic progress possible.

Theory and what AGI is putting out the door matches. up.

Consider two full sib ET bulls. Pedigree says they should share 1/32 of their DNA with Shearbrooke Shoshone. But, what does the DNA say? Calf with higher birth weight EPD is 15% more related with ancestors is the pedigree with higher birth weight EPDs.

BIF 2018: How Does the Dairy Industry Handle Information?

Chuck Sattler
Vice President, Genetic Programs, Select Sires Inc.

Data is fuel for breed improvement programs. Data drives the machine. Noise in the data is like water in the fuel.

Data has value! However, individual records have very little data. We have to share data for it to achieve its value. "We are not good at investing in data. It's not sexy," Sattler said. We need to invest in data collection.

We need to share data thoughtfully. Have a written agreement and think strategically when sharing data.

Genomic evaluations are a big data success story! "We marvel at the technology that makes this all possible," he said. As much as it is a story about DNA technology, it is also a story about bring large amounts of data together. It is also a success of big data.

If we had to do it over again, dairy industry might re-think Dairy Recording Processing Centers. Dairy Recording Processing Centers control the data and sometimes the breeder's voice is not heard.

Stakeholders share data with Council Dairy Cattle Breeding, this is done guided by Material License Agreements. This shared data is used for national genetic evaluations. CDCB can share data but only with stakeholders permission.

Dairy used somatic cell score as an indirect measure of mastitis. In 2000, the genetic trend for mastitis reversed from a negative slope to a positive slope. They are now launching a direct mastitis genetic prediction that will help further reduce the incidence of mastitis.

Operations of CDCB funded by genomic evaluation user fees. Those that collaborate in providing data pay smaller genomic user fees.

Dairy industry is working on new ways of collecting data. They have become complacent and are looking for new opportunities.
One of the areas they need to improve is individual ID. Have to have unique IDs to make the data come together.
They are also working on how they use on-farm computer records in genetic evaluations. Zoetis lead the way in this by collecting data directly off the farm.

They also need to improve in harvesting and using data from automated data collection systems.


Thursday, June 21, 2018

BIF 2018: Positioning for the Future of Beef Production, Bringing it All Together

John Pollak
Emeritus Professor, Cornell University

50 years is a milestone in time that provides an opportunity to reflect on accomplishments. It is also an opportunity to reset the clock.

The process for selection

  • Establish a goal
  • Create a breeding objective
  • Collect data for traits defined in the objective
  • Utilize the data to predict genetic merit
  • (other steps I missed)


What was the goal to motivate selection we performed over the past 50 years?
Pollak could not identify a consistent goal over the last 50 years.

We can look at genetic trends and see that genetic change has been accomplished. Change has happened, but can we articulate the goal that lead to these changes?

What goal should motivate the selection we perform ove the next 50 years?
The temptation is to continue on perhaps the same path on before. Doing the same things better. We should avoid this.

If Pollak were to define the goal for the beef industry's breeding objective it would be increase the sustainability of beef production.

There has been inadequate consideration of reproduction, eating quality, healthfulness of beef, disease resistance, feed intake, lifetime performance, etc.

There are economically relevant traits (ERTs) and indicator traits for ERTs.

The beef industry is not one synchronized enterprise but rather is comprised of a multitude of independent businesses. In Pollak's view, this doesn't remove the value of a breeding objective, but perhaps different economic weights in different scenarios.

Genetics is driven by the seedstock segment. Can we provide incentives or subsidies to broaden the scope of a breeding objective.

The ability to collect data is going to improve over time with the develop of technology. One of the focuses of precision management is the recording of data. There are also valuable datasets, such as health data in feedlots, that are not feeding into national cattle evaluation.

Are there trends in the industry that change the value of traits that are measured?

Genomics is impacting genetic evaluations. Genomics can help us add new traits into the breeding objective.

How are we measuring success? We can look at genetic trends by monitoring change in EPDs over time. Are there alternatives? Alternative could include is the public happy with how beef is being raised. Example is green house gas emissions. Herd size has declined, production per animal has gone up, and thus green house gas emissions have gone down.

BIF 2018: Focus on Traits Not Considered

Dorian Garrick
Professor and Chief Scientist, Massey University

This is a one bull or two bull meeting. This means it cost about the profit from one or two bulls to pay for the attendence of this meeting. Beef producers need to leave this meeting with information and thoughts about how they will change and improve their operation.

We would like to think that you use index selection, but we know that you are probably using independent culling levels or phenotypic selection. However, we can look at genetic trends to see how traits have changed.

Weaning weight and yearling weights have increased over time. However, the rate at which these growth traits were changing slowed in 1990, when ultrasound carcass measures were introduced. So, Hereford breeders were still selecting for growth, but were also putting emphasis on other traits.

An average 2017-born daughter eats $57 more feed per year than an average 1980 daughter. This possibly outweighs improvement in terminal profitability. Mature weights are increasing by 10 pounds per year.

What do you measure?
Calving traits (calving ease scores and birth weight)
Early growth traits (weaning weight and yearling weight)
Reproduction
Ultrasound predictions of carcass traits
Mature Cow weights and condition scores
Actual Carcass characteristics
Actual feed intake
As we move down this list, we have a decreasing number of records.

We need to have a goal.
With that goal, what do you want to change? This is your breeding objective. A breeding objective is a list of traits (EPDs) and their economic value. Identifying the list of goals is easy. When we look at the economics value, we realize that some traits are indicator traits and not economically important.

You then need to look at the selection criteria. What traits are you measuring to produce EPDs?

You then need a breeding scheme, a dissemination system, a mating plan, and than an economic analysis. In this economic analysis we think about the overall benefits and the overall costs of this breeding program. The most expensive breeding program is likely not to be the most profitable breeding program.

So, what should our breeding objective be, what traits are we selecting?
reproduction and longevity
income over feed cost
animal welfare
environmental footprint

We have done a good job on income over feed costs (growth, marbling, calving ease, etc.) We do a very poor job on the rest of this list. The tangible traits like growth and calving ease smack us in the face when they are bad. The less tangible traits like reproduction or cow efficiency receive less intention.

Why aren't traits being adequately considered?
Not selecting on total merit indexes (e.g. for maternal systems)
Not measuring enough of the less tangible attributes
Cannot be measured

Value proposition
Among bull breeding sector
Too many animals being recorded
Not enough traits being recorded
Not being rewarded by bull buyers (price or demand for less tangible traits)
Breed association structure might be impeding innovation
-routine EPDs provided on all animals regardless of phenotypic measurement or not

How might more balanced selection occur?

  • New technologies
  • Subsidies by government (USDA grants are an indirect example of this)
  • Local regulations
  • Market requirements

New business structures to capture value (small collectives on like minded breeders)

Reproduction and Longevity
Inadequate use of puberty data
Inadequate use of post-partum anestrus interval

Feed Cost
Forage intake (behavioral aspects - walking distance - grazing time -sward selection)
Feedlot intake
Complex trait where animals can rank differently based on sex, diet, etc.

Animal welfare
Disease resistance

Environmental footprint
Urinary nitrogen excretion
Greenhouse gases
Soil Damage

New Zealand now has limits on amount of urinary nitrogen that can be excreted by a farm.
We can reduce the amount of greenhouse gases that an animal releases.

We want to move the cloud. We need to think about traits that are underrepresented (reproduction, animal welfare, environment).

We really need to improve the efficiency of beef production.
Selection is a proven and cost-effective mechanism for improvement. Needs to be based on whole-system indexes. The best way to do this would be to look at indexes and nothing else.

BIF 2018: Focus on Sustainability

Sara Place
Senior Director, Sustainable Beef Production Research, National Cattlemen's Beef Association

Does less beef mean less heat? Is meat, especially beef, not good for the planet?
We see the marketing of plant based burgers. We also see work for lab grown beef.

In the United States, agriculture and forestry are net carbon sinks (they capture carbon). In the US, beef is responsible for 2% of emissions. However, pasture is responsible for 3.9% of carbon capture. Agriculture is a net help in carbon emissions because of carbon capture! Further, carbon emissions are improving over time in agriculture.

However, the news media is not telling this story.

Emissions are not going down due to decreased consumption of beef. Emission are going down because of technology advancements. Productivity is a key driver in improving sustainability. We would need many more cattle, with much more emissions, if we produced cattle in 2017 they way we did in 1976.

If we continue on current trends, global cattle herd will increase by 7%. However, if rest of world matched rate of improvement we see in U.S. cattle herd, we would see a decrease by 27%! If rest of world matched U.S. productivity, world cattle herd would decrease by 53%!

What is the pounds of feed per pound of product for beef, chicken, and pork. Beef takes 13.8 pounds of feed per pound of product. Chicken is at 1.6 and pork at 2.5 pounds of feed. However, beef uses 1.6 pounds of human edible feed. Chicken uses 1.4 pound of human edible feed and pork uses 2.0 pounds of human edible.
However, what is the net protein contribution of these meats? In other words, how much protein does the animal eat and how much does the animal produce. Chicken and pork both eat more protein than they produce (0.85 for chicken, 0.70 for pork). Cattle contribute 2.53 pounds of protein for every pound they eat! Cattle take sunlight and turn it into protein.

Further, cattle can produce food (protein) on land that cannot be used in any other way to produce food.

A lot of feed used for beef production is used for maintenance of cattle (maintenance of cow, maintenance of growing steer).

How can we improve sustainability of beef production?
What can we take from our monogastric friends?
Focus on both components of feed to gain ratio. We are likely no where near biological efficiency of cattle. Focus on red meat yield, decrease whole industry maintenance energy costs including improved fertility rates, and avoiding extra fat.
How can we take further advantage of ruminant cattle?
Can we add more total gain on forage and reduce use of human edible grains?

Beef's sluggish response to sustainability concerns left open an opportunity for "alternative protein".

We need to tell the story of a self replicating technology that can take energy from the sun in the form of plants and turn it into protein. This technology is beef.


BIF 2018: Focus on Quality

Mark McCully
Vice President, Certified Angus Beef LLC

Within Certified Angus Beef they market over 1 billion pounds of beef and certify over 5 million cattle.

Quality can have a broad definition. For this talk, McCully will focus on Quality Grade (marbling).
Consumer satisfaction improves with high marbling. Beef with a Prime Quality Grade has a nearly 100% consumer satisfaction.
We have improved tenderness in the industry through multiple avenues (genetics, management, beef handling, beef cutting and processing). Because of improvement in tenderness, McCully feels marbling becomes even more important.

The percent of cattle that are grading Choice and Prime has increased over the past 10 years. For a long time we were increasing carcass weight with little change in quality grade. In the last ten years, we have seen a significant improvement in quality grades.

We have increased the amount of Prime beef pounds by 92.8%. We have increased Premium Choice by 72%. Select quality grades have decreased by 40%.
Percent of boxed beef sales have increased from 10% of sales to 20%.

The spread between Select and Choice is $10. The spread between Choice and Branded is $5.50. The spread between branded and CAB is $6. The spread between CAB and Prime is nearly $20. Even though there has been a 21% increase in tonnage of Choice and Prime, the spread between grades has stayed consistent. This likely reflects the strong demand for quality beef.

Yield Grade 4 and 5 discounts have decreased over time, allowing feeders to more aggressively chase Quality Grades.

Five Rivers looked at performance differences between low grading and high grading cattle. There is no difference in average daily gain, feed to gain ratio, and cost of gain. We can increase the quality of our product without sacrificing efficiency.

Is marbling a free trait? Are there unfavorable genetic correlations for other traits, including maternal traits? Right now the data says there are not unfavorable correlations and we can improve marbling without harming other traits.

Bigger supplies are allowing customer access. This is allowing retailers to promote quality beef in their advertisements. Further, ground beef is no longer quality grade neutral. Retailers are marking Prime Grade ground beef.

We have added value to the beef carcass. We have identified new ways to fabricate a carcass. More of the carcass is being marketed as a steak item, rather than a roast. This means there is increased value of marbling beyond the middle meats.

As we look at export opportunities, quality grades will be a driver of demand.

What are our industry targets?
What should they be?

NBQA 2016 Targets 2018 Year to Date Should be our goal?
% Prime 5 7.6 15
% Upper 2/3 Choice 35 23.3 45
% Low Choice 35 48.1 30
% Select 25 17.6 10


BIF 2018: Efficient Red Meat Production

Michael Genho
Elanco Animal Health

From the business dictionary, efficiency is "the comparison of what is actually produced or performed with what can be acheived with the same consumption of resources (money, time, labor, etc.)"

Production Metrics

  • Feed Conversion Ratio
  • Residual Feed Intake


What's missing?
Level of input and output.
What is the optimal within a given context?

These (FCR and RFI) fail to take economic situation into account.

Elanco has a calculator to measure the optimal days on feed.
In an example, feeding a set of cattle for 28 more days would have been more profitable because of increased margin profit from the gain of those cattle. This was true even though the feed conversion of this pen would have gotten worse over those 4 weeks.

Elanco is working to help customers move up the analytical ladder. Move from standard close outs to statistical analyses to predictive analyses.

Elanco looked at drivers of closeout profitability comparing lots to other lots in a region. The two leading drivers are in price and out price. These account for 50% of the profitability difference. The third highest was average feed conversion. It was even larger than ration price. Feed conversion is the largest production measure influencing profitability. Confounded with feed conversion is health.

Average feed conversion has stayed fairly flat over the last 17 years. However, in the last 17 years, days on feed has increased which can drive down feed conversion.
Even when breaking groups out by days of feed, feed conversion has gotten worse over the last 17 years. 

We can estimate empty body fat using back fat, carcass weight, quality grade and ribeye area. Empty body fat ranges from 24% to 34% on a lot basis. However, if we look within a lot, there is much variation within  lots of endpoint empty body fat.

So, what do conversions look like if we control for endpoint (empty body fat), sex and end weight?
We have cattle that are very good at feed conversion, quality grade and growth. Many of these lots of cattle are getting ahead of people. They are reaching their endpoint before managers realize.

Conclusions
Efficiency is best measured measured in context of what is optimal. Have to consider costs and output level.
Average feed conversion is the single largest performance driver of feedyard profit and loss (accounts for 10% of variation).
Feed conversion should be optimized within endpoint targets (empty body fat).


Wednesday, June 20, 2018

BIF 2018: GeneSeek Genomics Symposium

Stewart Bauck
Neogen Vice President of Agrigenomics

This is the 50th aniversary of the BIF Symposium. Fifteen years ago at BIF, the sequencing of Dominette for the first cattle genome sequence was announced.
GeneSeek now has laboratories all over the world. They have worked with customers and collaborators to develop over 50 custom assays (DNA tests).

There are 3 pillars of GeneSeek's success:

  • High quality data
  • Fast Turn-Around Time
  • Fair Pricing

Dr. Mitch Abrahamsen
Executive Vice President, Chief Scientific Officer
Recombinetics
Precision Breeding for Animal Health and Productivity:
What does it take to deploy technology in the market place?

Recombinetics has 3 product lines. Two are focused on applications of gene-editing to human medicine. 
The agriculture product is called Acceligen. Acceligen uses gene editing to move DNA variants from one breed to a different breed. 
Recombinetics has 22 patents. 
To date, all genetic progress is the result of traditional animal breeding programs.
  • Mate best animals together
  • Select the best progeny based on data available
  • Repeat
Gene editing allows us to focus on animal welfare traits and to make rapid and intentional progress. "We don't have to wait on random chance," Abrahamsen said. 

Gene editing is a complementary tool to use in addition to traditional and genomic selection.

What are the drivers for innovation in Animal Agriculture?
  • Consumer Expectations
  • Interest in how food is raised 
  • Animal Welfare
  • Environment impact
  • Evolving regulations for animal production
We are in the Green Revolution 2.0 in Animal Agriculture:
  • Accelerated productivity
  • Sustainable 
  • Global food security

This is done through big data, genetic improvement by genome prediction, and genetic improvement by gene editing.
Recombinetics Acceligen is focused on health and welfare traits.
They have produced 
1. Naturally hornless (polled)
2. Naturally-cool (slick mutatation)
3. Naturally-casturated

Have to influence with science and passion. Just science information will not be enough.
Acceligen will have macro-traits that they share with all of their collaborators and customers. Later down the road they will also have micro-traits that are specific to certain scenarios, will be proprietary, and provide a competitive advantage.

Semex and Recombinetics have announced a partnership to focus on animal welfare traits.

Acceligen's position is to regulate the product not process at USDA. Currently, this happens by the FDA regulating the process. 

Gene-editing using natural processes to introduce existing mutations into breeds. For example, introducing existing Angus polled mutation into elite horned Holsteins.

"We need to take steps that are really paradigm shifts," Abrahamsen said. "At some point we have to start doing things differently."

Matt Barten
Embruon, LLC

With intact embryos from embryo transfer, we see pregnancy rates around 65%. With biopsied embryos, pregnancy rates are around 50%. 
However, the biopsies are small and have very little DNA. GeneSeek has to amplify this DNA. This is like taking a bushel of corn and copying it to two semi trailer loads of corn.
This allows us to select which embryos we transfer and which we never use. We can choose to only implant embryos for those that will become desirable animals.
See more about Embruon at these blog posts:


Dr. J.R. Tait
GeneSeek
Biology, the random sampling of genes and chromosomes, leads to variability produced by a good bull. GeneSeek is working with commercial customers to identify appropriate tools to make decisions about which animals to select.
There is significant variation even between cattle that are closely related. From a set of full siblings (same mother and father), one calf can be in the bottom 10% and another calf can be in the top 10%.
Production systems on commercial operations often doesn't allow for BIF adjustments.
  • We don't know the age of the calf
  • We don't know the age of the dam
  • We may not match the calf to the dam
  • The cow may not have an ID
  • Calf weights may not be taken in the right age window
In other words, commercial producers don't have management practices like a seedstock producer. However, DNA testing can provide genetic predictions for commercial producers without the difficulties of acting like a seedstock producer.

Neogen has a product called Igenity Beef.
Angus, Red Angus, Hereford, SImmental, Gelbvieh and Limousin were used in the development of these products. 
Igenity Silver has 6 traits plus parentage.
Igenity Gold has 13 traits plus parentage.
Often these results are reported on an online dashboard. Customers can also create a custom index. 
50 to 70 years ago dairy selection emphasis was all on milk production. Does this mean fertility didn't change... No, fertility got worse over this time period. We have to practice multiple trait select and we need to select on all the important traits.

Igenity has launched an Igenity Production Index. This index assumes the producer is keeping their own replacements and marketing cattle on a grid. They are also going to soon release a maternal index and a terminal index.

The Igenity Production Index focuses on certain production traits. But, we see favorable genetic trends for a suite of traits.  

Igenity Beef are the multi/crossbreed products (Igenity Gold and Igenity Silver).
They also have breed specific panels including:
  • Igenity Angus
  • Igenity Gelbvieh
  • Red Navigator
  • Igenity Brangus
  • Igenity Santa Gertrudis
  • Igenity Beefmaster

Wednesday, May 16, 2018

Crossbreeding Considerations

Simplicity, management key to successful program 


Story by Lisa Henderson
Reprinted from Cattlemen' s News.


Fewer open cows, less death loss, more growth, more milk and more efficiency. Those are the significant economic advantages crossbreeding can offer your cattle operation.

“A crossbred cow is 25 percent more productive over her lifetime compared with a straight-bred commercial cow,” says University of Missouri animal scientist Jared Decker. “Not only do we see increased growth performance out of crossbred cattle, but we see significant impacts on fertility and reproduction.”

Decker adds bluntly, “All commercial operations should consider using crossbreeding.”

While the popularity of breeds can rise and fall over time, crossbreeding remains an advantageous practice for commercial herds.

Heterosis, or hybrid vigor, and breed complementarity are the primary benefits realized from a properly planned crossbreeding program. Heterosis is the increase in performance or function above what is expected based on the parents of the offspring.
Through crossbreeding, beef producers can also take advantage of breed complementarity.

“With breed complementarity, the strengths of one breed are matched to the weaknesses of another and vice versa,” Decker says. “Or, the optimum in the middle is achieved by using one breed with a high level and another breed with a low level.”

Clay Mathias of the King Ranch Institute for Ranch Management at Texas A&M University, says crossbreeding is always a high leverage choice. “The choice of which breeds to use is basically free. However, the returns of a crossbreeding program are substantial. Crossbreeding improves fertility, age at weaning, weaning weight and longevity.”

Before implementing a crossbreeding program, however, animal scientists suggest you should:

  • Define your current situation in relation to markets, breeds, nutrition, environment and management.
  • Define what market, or markets, you are aiming for and determine breeding objectives.
  • Define the management and nutrition levels it is possible to achieve in your environment.
  • Decide which breed types will perform best in relation to your desired production traits.



One of the important considerations in a crossbreeding program is consistency, Decker says. “The ‘breed of the month’ club memberships have been revoked long ago. A crossbreeding system should use a small number of breeds (two or three), and should use the same breeds year after year.”

As an example, Decker says, “I marvel when I drive by a corn field how consistent the plants are. Yet, every plant in that field is a hybrid. Beef producers need to aim for this same level of consistency in their crossbreeding programs.”

The success of a crossbreeding program will depend on its simplicity and ease of management, according to animal scientists. Several factors and challenges need to be considered when evaluating choice of crossbreeding system, including:

1) Number of cows in the herd
2) Number of available breeding pastures
3) Labor and management
4) Amount and quality of feed available
5) Production and marketing system
6) Availability of high-quality bulls of the various breeds

Various research studies show the design of any crossbreeding program should take advantage of both heterosis and breed complementarity. An ideal crossbreeding program should 1) optimize, but not necessarily maximize, heterosis in both the calf crop and particularly the cow herd, 2) use breeds and genetics that fit the feed resources, management and marketing system of the operation, and 3) be easy to apply and manage.

“An often overlooked system for crossbreeding is to buy females in place of developing replacements from your own herd,” Decker says. “And, a producer could purchase a maternally oriented crossbred female, and then those crossbreed females would be bred to a terminal sire with 100 percent of the resulting calf crop marketed for beef.”

Again, however, Decker emphasizes that producers should evaluate their marketing endpoint and marketing system before launching a crossbreeding program.

“The choice of breeds needs to match the marketing goals,” he says.

Crossbreeding doesn’t necessarily mean you will sacrifice some traits for others. For instance, Decker says, “I have received reports of producers achieving 70 percent of their calf crop grading Prime while using a three-breed crossbreeding program.”

While such testimonials support crossbreeding, Decker admits that color might affect prices for calves at some auctions.

“If calves resulting from crossbreeding are not black, producers may need to be more strategic about marketing their cattle,” he says. “However, several programs are now in place to market crossbreed calves, such as the Red Angus Association of America’s Feeder Calf Certification Program or the American Hereford Association’s Hereford Advantage program.”

The Red Angus Feeder Calf Certification Program (FCCP) is a USDA Verified Genetic, Source and Age Program. The FCCP builds a reputation through source verification to the ranch of origin and, coupled with group age verification, provides producers with access to export market premiums.

The Hereford Advantage program on the other hand uses top-ranking Hereford bulls mated to British-cross cows with a focus on gain and end product merit.

Friday, May 4, 2018

Link Round Up, May 4th, 2018

Red Angus Association of America announces release of Dry Matter Intake (DMI) and Average Daily Gain (ADG) EPDs.
https://www.progressivecattle.com/news/industry-news/8383-red-angus-association-releases-two-new-epds-aimed-at-increasing-efficiency

Why not release a RFI EPD? The animals ranking for feed efficiency changes based on how we express the trait. http://blog.steakgenomics.org/2014/08/improving-feed-efficiency-feed.html The best way to account for the cost of additional feed intake is through an economic selection index in which we balance both growth and intake.


"Five Reasons to DNA Test Your Cows"
https://hereford.org/2018/05/five-reasons-to-dna-test-your-cows/
Head over to the American Hereford Association website to learn more about DNA testing your cowherd.

Speaking of DNA testing cows...

Leoma Wells provided an update on the American Simmental Association's Cow Herd Roundup (CHR) on their Facebook page. https://www.facebook.com/AmericanSimmentalAssociation/videos/10160437412475066/


Did I miss important beef genetics and genomics news? Send me a message on Twitter or Facebook.

Thursday, April 19, 2018

Recruiting Summer and Fall 2018 Loewenberg Interns

We are currently recruiting students to join the Loewenberg Internship program. Download the application here: https://missouri.box.com/v/LoewenbergApp.

The Loewenberg Beef Cattle Management Internship is an opportunity born from the generous gift of Mr. Bruce Loewenberg. Mr. Loewenberg donated his herd of Salers cows to be used for research and teaching purposes in the Division of Animal Sciences at the University of Missouri. The intent of this internship is to give a select group of motivated students the opportunity to manage and make business decisions on a herd of Fall and Spring calving cows. Decision‐making for this herd will be a team oriented effort by the four to six students selected for each internship session. The vast majority of labor will be provided by the internship students. This includes, but is not limited to, moving wire during rotational grazing, working cattle for herd health, setting up cows and heifers for AI breeding, and other common practices in the business of cow‐calf operations in the Midwestern United States. Students will be advised by a committee from the Division of Animal Sciences and Mr. Loewenberg. Preference will be given to students with strong organizational skills, willingness to work through complex business decision‐making, a commitment to a team management model, and those with some large animal handling experience.

Hard copy or email applications will be accepted. Applications and a current resume can be returned to Cinda Hudlow in S102 ASRC or via email at hudlowl@missouri.edu. Please direct questions to Dr. Jared Decker via email DeckerJE@missouri.edu.


Internship requirements and preferences

  • Four to six students per academic session
  • Open to any CAFNR undergraduate student
  • Minimum GPA of 2.5 at commencement of internship
  • Two consecutive academic sessions required
  • Preference to students with Junior or Senior standing


Internship sessions

  • Fall September 26 ‐ December 31, 2018
  • Spring January 1 – May 15, 2019
  • Summer May 16 – August 15, 2019


Important Application and Selection Dates

  • Applications due on or before May 4, 2018
  • Interviews will be scheduled for the week of May 7-11, 2018.


Monday, April 16, 2018

April 19 Webinar by Genetics Experts to Give Cattlemen Guidance on Creating the Best Herd

Fourth, final webinar in series focuses on bull selection

DENVER, CO (April 12, 2018) – This year’s edition of the NCBA Cattlemen’s Genetics Webinar Series comes to a close April 19, with a special presentation that puts a focus on honing bull selection.  The National Cattlemen’s Beef Association teamed up with six genetics specialists from across the country to offer this series, which kicked off Jan. 18.

The Genetics Webinar Series was designed for producers who would benefit from genetics knowledge, from the experienced seedstock breeder to someone who might be new to the cattle industry and needs to better understand genetics. It is being coordinated by the NCBA producer education team. Earlier webinars were “The 4 S’s of Crossbreeding: Simple, Structured, Successful and Sustainable,” “Show Me the Money! Are there EPDs for Profit?”, and “Fake News: EPDs Don’t Work.” These webinars can be accessed at www.NCBA.org under the Producer Education tab.

Titled “Putting the Tools to Use: Buying Your Next Bull,” the April 19 webinar puts the genetic concepts covered in the first three seminars to work, as attendees will go to a virtual bull sale and select the best bull from a sale catalog for two distinct production scenarios. The webinar begins at 7 p.m. CDT.

Leading discussion on the topic at the webinar will be Matt Spangler, Ph.D., associate professor and extension beef genetics specialist at the University of Nebraska – Lincoln, and Bob Weaber, Ph.D., professor and beef extension specialist at Kansas State University. Joining in the discussion will be other members of the eBEEF team, a group of six genetic specialists from five academic institutions who have invested time and resources in the advancement of the cattle industry through genetics.

According to Josh White, NCBA executive director of producer education, the genetics webinar series has been an effective extension of NCBA educational webinars, which was started several years ago. “Some of the largest participations in our webinars have been for genetics topics in the spring,” said White. “This 2018 partnership with the eBEEF team has been a terrific addition to the education we can provide.”

Cattle producers are invited to join the webinar live, although “homework” for the seminar – available at www.NCBA.org – is advised. The homework includes the eBEEF bull sale catalog and the eBEEF bull selection scenario.

For more information, go to the Producer Education tab of the NCBA.org website.
###

The National Cattlemen's Beef Association (NCBA) has represented America's cattle producers since 1898, preserving the heritage and strength of the industry through education and public policy.  As the largest association of cattle producers, NCBA works to create new markets and increase demand for beef.  Efforts are made possible through membership contributions. To join, contact NCBA at 1-866-BEEF-USA or membership@beef.org.

Questions?
Contact Producer Education at producered@beef.org
 







Friday, March 23, 2018

Cattle Raisers Convention 2018: Breed Characteristics, An Overview

Robert Wells, Noble Research Institute

What breeds should you consider?
Types
Heterosis
Complementarity effects


There are two species of cattle:
Bos taurus
British breeds (Angus, Hereford)
Continental breeds (Charolais, Simmental, Limousin, Gelbvieh, etc.)

Bos indicus (Zebu, humped cattle)
Brahman
Nelore
Gir


Angus (British)
Reputation is carcass and maternal. Also has a reputation for growth.
"They wanted to be everything to everybody," he said. The problem with this is the increased mature size in these growthier Angus cattle.

Red Angus
Reputation for carcass and maternal. Before the 1950s, all Angus were Angus, regardless of coat color. The Red Angus breed has not chased growth as much as black Angus.

Hereford (British)
Reputation for maternal, easy fleshing, and longevity. Hereford don't typically have a lot of maintenance requirements.

Shorthorn (British)
Reputation as maternal and carcass. Shorthorn was previously a dual purpose breed of meat and milk. This is why Shorthorns have been used in a lot of composites such as Santa Gertrudis.

Simmental (Continental)
Reputation for maternal and growth.

Gelbvieh 
Maternal and growth

Limousin
Reputation for growth and lean tissue. Great for yield grade.

Charolais
Reputation for growth, but they also do a decent job on quality grade.

American Brahman (Bos indicus, composite of several breeds from India)
Maternal, lean, hardiness, insect, disease and heat tolerance.

Longhorns
Reputation for hardiness and lean beef. Horns are a by-product that can marketed to hang in steak houses.

Corriente
Reputation for hardiness and roping stock. Once referred to as a goat in a beef cattle hide. Often used for calving ease, but their are probably better options to get calving ease without the discounts for Corriente cattle.

Waygu
Marbling

Akaushi
Larger framed than Waygu. Known for marbling and fertility.

There are more breeds out there can you can imagine.

Composites
Santa Gertrudis
Mix of Brahman and Shorthorn. Has to fit breed type to be registered.

Beefmaster
Maternal heterosis and growth. Longevity, fertility and efficiency. Can be any color.

Brangus
Carcass, Growth, Maternal and Heat Tolerance.

Balancer
Gelvieh and Angus hybrid

LimFlex
Limousin and Angus hybrid

Simbrah
Simmental and Brahman hybrid

Black Baldy
Hereford and Angus hybrid. Great longevity and maternal.

F1 Tiger Stripe
Hereford and Brahman hybrid.

Super Baldy
F1 Tiger Stripe with Angus influence.

Commercial Angus

Ultrablack
Brangus and Angus cross. Less Brahman influence than Brangus.

Crossbreeding
Crossbreeding leads to increased hybrid vigor, also known as heterosis.
Crossbreeding can lead to a lack of uniformity. We have now gone towards a straight breeding program. Straightbreeding has lead to increase consumer acceptance and carcass quality, but we have also lost some fertility and stress tolerance.

Maximum heterosis is achieved by an F1 x F1 cross. This has grandparent from 4 unrelated breeds. However, this may decease uniformity, especially in multiple bull herds.

Maternal hybrid vigor increases calving rate (6%), weaning rate (8%), weaning weight (6%), and a negligible 2% increase in birth weight.
Cow lifetime productivity is increased by 25% due to heterosis.

Keep in mind that some crossbred cows are larger than their straightbreed counterparts. May need to adjust stocking rates appropriately.

Original Scenario:
100 cows, Cow Breed A x Bull breed A
525 lb weaned calf
Average weaniing rate 82%
43,050 lbs marketed

Switch to:
Cow Breed A x Bull Breed B
Individual heterosis (+5%)
~551 lb weaning weight F1 calf
45,203 lbs marketed
+2,152 lbs/year = +$5,725.65/year

Switch to:
F1 cow x Terminal bull breed C
+WW total heterosis + 25%
656 lb calf (+131 lbs)
59,040 lbs marketed
+15,990 lbs = +$40,295

"What is that ideal cow? I don't care what color she is," Wells said. The cow needs to fit our environment and our resources.
Early puberty
Never misses a breeding season (1 calf/365 days)
Calves unassisted
Doesn't require a lot of supplemental feed
Easy fleshing
Converts forage to lbs of raised calf

Must be able to manage for the benefits.
Heterosis will not make up for poor animal husbandry/management.
Heterosis will not make up for poor bull selection.

*Note, this post was live blogged and may contain mistakes.

Cattle Raisers Convention 2018: Bull Selection Panel

Moderator:
Tommy Perkins, International Brangus Breeders Association
Panelists: 
Kelley Sullivan, Santa Rosa Ranch
Donnell Brown, RA Brown Ranch

What DNA tests do you require when you buy a bull? Parentage? Genetic Defects? Polled? Coat Color?
What trait is most important in bull selection?
Does genomic testing provide value?

Donnell Brown currently markets 4 different breeds (Angus, Red Angus, SimAngus and a 4-breed composite called Hotlander). Brown has been involved with 17 different breeds. They DNA parentage test every animal born on their place. Five to ten percent of animals have the wrong parentage assigned. Cows swap calves. The wrong straw gets pulled out of the tank. A bull comes over from two pastures over and then goes home before we ever knew he was out. Would we prefer to use a bull with one calf crop or a bull with no calves? Most producers prefer the bull with more data. Genomic-enhanced EPDs provide the same amount of information as the first calf crop out of a bull. Donnell said for seedstock producers it is more important to DNA test females, because that gives us more information on her genetic merit than her lifetime worth of progeny data.

"Just because a bull has EPDs doesn't mean he is good." Brown said. The EPDs simply reflect how the bull compares to other bulls.

Brown has never printed actual performance data in a bull catalog. No actual birth weight, no actual or adjusted weaning weight, etc. The EPDs provide much more information.

Truck manufactures report the estimated highway and city miles per gallon. These numbers aren't always exact, but they provide a great estimate to compare different trucks. EPDs are the same for comparing bulls.

Donnell Brown has been using selection indexes for 25 years.

Kelley Sullivan states that Santa Rosa Ranch is now the largest Brangus and Ultrablack breeder in the United States. Ultrablack cattle has allowed Brangus breeders to expand bull selling into new markets. The higher percentage of Angus allows them to sell into Nebraska, Missouri, etc. This
"If you are not successful, we are not successful" Sullivan says. We need to meet our customers need and produce beef for our consumers.

Before you buy a bull, you need to identify herd goals. What are you looking to do?
What are your selection priorities? You need to use the selection tools (indexes, EPDs, genomics). "Unless we know what we have, we can't sell it to you," Sullivan says.
If a bull can't move and a bull can't walk, you can't use him. He won't be able to do what he is supposed to do. Bulls need to be structural sound. You need to look at the bull, or have someone trusted look at him.

You need to find a reputable source of genetics (breeding stock). Santa Rosa Ranch stands behind every bull they sell. Do your homework. Is the seedstock producer doing what they say they are doing.

You need to make a sound investment. They price their bulls at 5 times the current prices of the calf market. Some bulls are priced higher if they have potential to go into a seedstock herd. Don't look for the cheapest bull out there.

Concentrate on factors that have the greatest effect on profitability. Performance is a function of both genetics and management. Don't single trait select.

You're investing in their program and, if they are reputable, they are investing in your program as well.

You must require a Breeding Soundness Exam (BSE) be performed before you take ownership of the bull.

What development ration has been fed? Is he fat? If he is fat, he is going to lose a lot of that condition when he is out breeding cows.

Disposition and docility is sometimes over looked. You don't want the problems associated with bad dispositions.

"One of the goals of our program is moderating mature frame size," Sullivan said. "We need her to breed back and have a calf every year."

Donnell prints only the most valuable information in the bull sale catalog. Brown's number 1 trait is $Profit. Everything that effects your profitability goes into that index. Percentile ranks helps producers better understand EPDs. If you can count from 1 to 100, you can understand percentile ranks. Is this bull average? In other words, 50th percentile. Is the bull in the top 5%? Is the bull in the 95th percentile?

Maternal is so much more than milk. Is the cow going to have a calf year after year?

"I measure as many things as I can measure," Brown said.

"I like selling 18 month old bulls. I like having a man to do a man's job, rather than asking a boy (yearling bull) to do the job."

"A bull you bought last year will effect your herd till 2034. A bull you bought is an investment in your herd," Brown said. If you buy an old junker, clunker pick up, you get the performance of a junky pickup. The same thing happens with regards to the bull you buy.

*Note, this post was live blogged and may contain errors.

Thursday, March 15, 2018

Angus Genetics Inc Releases Foot Score Research EPDs

In January, Angus Genetics, Inc. (AGI) announced the release of research Claw Set and Foot Angle EPDs. The development of a research EPD is the second step towards a production EPD.

This followed research presented in the summer of 2017 which found heritabilities of 0.34 for foot angle and 0.21 for claw set. Estimating heritability (portion of the trait influenced by genetics) is the first step towards a production EPD. This research also found a genetic correlation of 0.22 between the two traits, indicating that both traits need to be reported and analyzed.

Stephen Miller, AGI Director of Genetic Research stated, "“Angus breeders have completed a tremendous amount of data reporting in such a short period of time; this is truly a testament to their commitment toward genetic progress. We are absolutely thrilled to begin the process of rolling this breakthrough out to the membership.”

Kelli Retallick, AGI Director of Genetic Services cautioned, “Though we are getting closer to a production EPD, we encourage members to continue sending in data. Consistency of scoring within a producer’s herd is key, and luckily, we have a variety of resources here at the Association to help.”

Between herd variation, just like any other trait, is handled through the use of contemporary group effects in the EPD analysis. Thus, the main focus is consistency within a herd year after year. The American Angus Association also has partnerships with university judging teams to aid in foot scoring.

Figure 1. Genetic trend for Claw Set EPD in highly accurate Angus sires. Blue line is a linear trend. Red line is a smoothing curve (Loess regression).
 As seen in Figure 1, claw set has basically remained unchanged in Angus cattle since 1985. This may be due to the lower heritability of claw set or less phenotypic selection on claw set. An EPD should help improve the rate of genetic progress for claw set.

Figure 2. Genetic trend for Foot Angle EPD in high accuracy Angus sires. Connealy Counselor, an outlier with a Foot Angle EPD of 1.20 was excluded from this graph. Blue line is a linear trend. Red line is a smoothing curve (Loess regression).
If we compare the 30 years from 1985 to 2015, Foot Angle has also not changed in Angus cattle. However, we see foot angle getting worse from 2003 to 2008, at a rate of 0.013 units per year. However, we see improvement in foot angle from 2009 to 2015 at a rate of -0.016 units per year. This may be due to the ease of phenotypic selection for foot angle or the increased response to selection due to the higher heritability for foot angle.

Recording, Reporting, and Analysis of Subjective Scores

The American Hereford Association uses subjective scores to report Udder and Teat EPDs. They began publishing production EPDs for these traits in 2015. The genetic trend for both of these traits began to improve more rapidly in 2010 likely due to systematic recording and reporting of udder and teat scores in 2009 (Figure 3). These results show how important data collection and reporting are for genetic improvement. Further, this illustrates that subjective scores, when properly analyzed and used, can effectively improve economically important traits.
Figure 3. Genetic trends for Udder (red line) and Teat (blue line) in the American Hereford Association.

Work by Other Breed Associations

The press release pointed out that these were the first foot score EPDs in the U.S. beef industry. Angus made this distinction because the dairy industry has been reporting structure genetic predictions for quite some time. The Australian Angus Association has structural soundness genetic predictions for Front Feet Angle, Front Feet Claw Set, Rear Feet Angle, Rear Leg Hind View and Rear Leg Side View.

Breed associations in the U.S. are also working towards structure EPDs.

Tommy Perkins, International Brangus Breeders Association, explained at the 2017 Texas Beef Cattle Short Course several subjective scoring systems Brangus breeders are using to record and report data. These include a 1 to 5 scale for foot angle and claw set.

Bob Weaber, Kansas State University, provided an update on structural soundness research being conducted at KSU in collaboration with the Red Angus Association of America.

Solutions

Commercial cattle farmers and ranchers can utilize crossbreeding to complement the strengths and weaknesses of different breeds. Seedstock producers and commercial operations that straightbreed need to look for avenues of genetic improvement. This frequently requires the recording and reporting of data to produce EPDs that increase genetic improvement. At the very least, this requires systematic recording of these traits to increase attention to their impacts and expression.

Take Home Messages

Beef producers, especially seedstock producers, should learn at least two lessons from these developments.

  1. Record and Report data that affect you customers' success
  2. Subjective scores, when analyzed in a genetic evaluation framework, are valuable sources of information








Tuesday, March 13, 2018

Breed composition: it’s like chocolates you can’t tell what’s inside just by looking at them

Written by Tamar Crum, Jared E. Decker, Robert D. Schnabel, and Jeremy F. Taylor

“My mom always said life was like a box of chocolates.  You never know what you’re gonna get.” – Forrest Gump

You may be wondering how in the world does a box of chocolates relate to breed composition of livestock? Or, if you are anything like me, it’s where did I hide that Halloween chocolate, I need some! I think that there are two analogies between a box of chocolates and the breed composition of livestock. 

First, we can pick out the white chocolates and may even be able to separate the milk chocolates from the dark chocolates.  This is similar to our ability to visually evaluate breed characteristics and sort livestock into different breed or subspecies (Bos taurus or Bos indicus influenced) based on breed characteristics.  However, such visual evaluation of breed composition is not terribly accurate.  For example, biting into a piece of dark chocolate and finding a nut when you were expecting caramel.  Crossbreeding is an important tool in the cattle industry, as it enables us to capitalize on breed complementarity and hybrid vigor.  However, crossbreeding complicates our ability to accurately sort animals into breeds based on breed standard traits.  Imagine a box of chocolates that contains a few chocolates that appear to be covered in both white and milk chocolate.  Do we sort these chocolates into the milk chocolate group or the white chocolate group?  Or, perhaps a new ‘hybrid’ group, since neither of these groups really reflects the correct composition. 

Second, a box of chocolates includes a diverse assortment of “fillings”.  The “fillings” cannot typically be determined from just visual evaluation.  The different “fillings” provide another challenge to our being able to sort the chocolates into groups.  Without reading the decoder in the box (isn’t that cheating?) or just taking a bite out of each of them (no judgment on my part if that is your routine!), we cannot accurately sort the chocolates.  The “filling” of the chocolates is directly analogous to the DNA of an animal.  If we keep breeding records on our animals, we can sort the animals based on their pedigree and breed registrations.  For example, if we have offspring from a registered Angus sire and a purebred Simmental dam, we can assume that the progeny will be 50% Angus and 50% Simmental.  But, what about if we take this progeny and breed it to a registered Angus? Will the resulting grandprogeny be 75% Angus and 25% Simmental? Due to the random assortment of DNA (chromosomes) into the sex cells, these proportions can vary. Not only can they differ from the 75/25 mark in an individual, but full-sibs produced from exactly the same mating can also be comprised of varying grandparental breed proportions.  Who knew that sorting a “box of chocolates” could be so complicated?

Understanding the breed composition of animals is a challenge, especially for genetic researchers.  Not all members of a breed are identical. Each breed was formed by an initial sampling of animals that were considered to be “characteristic” of a desired breed type.  Later selection and breed development produced breeds that differed for carcass qualities, maternal ability, or even adaptability. These characteristics make the breeds valuable to the industry.  In addition, each breed may have different mechanisms underlying variation in traits, such as feed efficiency or marbling.  Differences in traits between breeds reward both the producer and the consumer when crossbreeding is used. 

However, in certain genetic analyses we often need to understand the breed composition of animals to appropriately use the data. For example, when markers are used to generate estimates of genetic merit for traits such as feed efficiency, the resulting prediction equations will only be useful within the breeds that are represented in the training data set.  So understanding the breed composition of the animals will guide us in understanding how broadly useful the resulting prediction equations will be. Because of the inaccuracies of breed identification of crossbred animals using visual measures, a method to determine breed composition based on sampling the “filling” will provide a more accurate measure.  We have developed an analytical method to estimate the ancestry/breed composition of crossbred animals based on their DNA data.

You may have heard of or even participated in the 23andMe, Ancestry.com, and other genetic tests that are used to predict your ancestry.  You know, you used to dance in your lederhosen until you found out that you were Scottish and so now you wear a kilt! Think of our method as the 23andMe analysis for cows.

So how does the analysis work? In ancestry analysis, the observed data are DNA genotypes for animals which may be full-blood, purebred, or crossbred and the inferred factors are the ancestral or “reference” breeds.  To conduct the analysis, the first and most important step is to determine a set of reference population animals that genetically define the frequencies of genotypes at each tested variant among the members of each respective breed.  As you might expect, this makes it extremely important that the breed definition for the “reference” samples is correct.  In addition to being the most important step, determining the subset of samples that represents the diversity within each of the “reference” breeds is technically difficult. 

The reason for this is that the concept of breed and breed membership is man-made, and has not persisted in nature. The creation of species is a complex and lengthy process taking tens or even hundreds of thousands of years.  On the other hand, the development of livestock breeds is a very recent concept, beginning with domestication of cattle about 10,000 years ago and leading to the formation of herd books approximately 200 years ago.  Compared to the thousands of years cattle have roamed the earth happily mating at random, we should probably only expect that regions of the genome with large  effects on traits that define breed characteristics have been subject to human selection and resulted in breed differences. However, the phenomenon of drift in DNA variant frequencies over the last 200 years has caused enough differences in frequencies among breeds that we do in fact find signal for breed identification. Our software’s output can be represented by a figure similar to Figure 1.

Figure 1: Genetic profiles for animals defined as representing 18 different breeds. Breed identification is shown below each colored block and each animal is represented as a vertical line within the figure.
 The software does not know which animals were chosen to represent each breed but simply clusters them together based upon genetic similarity. We then arrange the output according to the animals that were selected to represent each breed to produce Figure 1. Each block contains a dominant color that is representative of each breed.  There also appears to be small levels of mixture represented by the colors in the top and bottom of each block for almost all the breeds. One interpretation of this is that there is a shortage of statistical power to completely predict breed ancestry.  However, this does not seem to vary much as we increase the number of markers used in the analysis. So, this result could suggest that these samples do not represent purebred animals. But, this is not the case in the recent sense, as the animals sampled to represent each of the breeds were traced by pedigree to ensure that they were purebred.  What appears to be more likely is that this represents breeding events that took place before the foundation animals for each breed were selected. Two simple examples of these events are the polled and coat color variants found in Hereford cattle.  The polled mutation in Herefords is identical to the mutation found in Angus cattle (and other Celtic breeds) and the Hereford coat color variant is only found in white-faced European cattle (e.g., Simmental). This indicates that these variants, and therefore breeds, have common, albeit, common distant ancestries.

The current software version functions to provide estimates of the genome-wide ancestry of individuals.
Future versions may allow ancestry estimates for specific regions of each chromosome.  It provides a method for determining the breed composition of individuals with no pedigree information, and that were perhaps generated in a commercial environment employing various crossbreeding systems.  Figure 2 illustrates how the genomes of crossbred animals can be separated into components originating from their ancestral breeds, with no pedigree information included in the analysis. By establishing the ancestry of these individuals, we can determine cohorts for use in association studies or other downstream analyses such as the genomic prediction of EPDs.

Figure 2: Genetic profiles for 238 crossbred animals. Breed identification is shown by color and each animal is a vertical line within the figure.  The key indicates which color corresponds to which ancestral breed. The animals shown are mostly Angus and Simmental.


The goal of this research is to develop an analytical pipeline that will enable the detection of the breed composition of crossbred animals based on animals defined to be representative of specific breeds. We will then use this information to enhance the analysis of genetic and trait data. Opportunities for the use of this information are only limited by our imagination.  It was once stated on 23andMe’s website that, “Your DNA can tell you a lot about your family, your health, your relatives, your ancestry, your traits, and you.”  (https://www.23andme.com/dna-health-ancestry/). We hope that this software can help us do just that for cows.

Tamar Crum is a PhD student at the University of Missouri.  This research is part of a study entitled “Inference of Admixture for Cattle with Complex Ancestry”.  This article was written as part of a Walton-Berry Award given to the Decker Genomics Group at the University of Missouri, which paid for four graduate students to attend the Beef Improvement Federation Conference held in Athens, GA in June 2017.

Reprinted with permission from the March 2018 issue of SimTalk.