June 2014

Breeding the Best Angus Cattle Begins with theBest Genomics Tools
A genotyping tool based on the BovineSNP50 BeadChip provides Three Trees Ranch withgenomic data to make the best breeding decisions.
Introduction
Dick Beck learned a lot about raising cattle growing up on a cattle
farm and family meat business in Pennsylvania. His desire forknowledge took him to Pennsylvania State University, where heexcelled in deciphering the science behind optimal herd management.
Graduating as the outstanding senior in the College of Agriculture, hebecame a strong proponent of carcass merit analysis technologies,
such as ultrasound, to inform breeding decisions. Widely used since
the mid-1980s, ultrasound measurements provide information about
mature cattle (ribeye size, fat thickness, and intramuscular fat) andenable ranchers to make fat and muscle predictions in young calves.
Fast forward to 2005. After several years as a regional manager for
the American Angus Association, and a few decades marketingseed stock for cattle operations, Dick became General Managerof Three Trees Ranch1, headquartered in the rolling hills of Coweta
County, Georgia. The multi-state operation runs herds in Georgiaand Wyoming. With more than 3,500 head of cattle, the limitationsof ultrasound technology became apparent. Despite its many
advantages, the ultrasound process takes time and is prone to humanand instrument error. By 2010, Dick began transitioning Three Trees
Ranch to genomic tools. Today, Three Trees Ranch uses the Zoetis
HD50K tool based on the Illumina BovineSNP50 BeadChip2.
iCommunity spoke with Dick about the transition and what Three Trees
Ranch and its customers are gaining from the use of genomics toolsfor breeding assessment.
Q: What’s the history behind Three Trees Ranch?
Dick Beck (DB): The Three Trees Ranch herd started with purebredAngus. We’ve since introduced Brangus cattle into the herd.

Dick Beck is General Manager of Three Trees Ranch, headquartered in
Sharpsburg, Georgia.

Brangus are a cross between the Brahman and Angus breeds. The
combination delivers the hardiness and disease resistance of theBrahman, with the superior fertility and meat quality (carcass traits) ofthe Angus.
Our Brangus cattle are from the Camp Cooley Ranch herd, acontinuation of the famous Brink’s herd developed by Glen Brinkman.
Glen was a visionary and pioneered the collection of ultrasound datain live animals for measurements of rib eye area and fat dispersion(marbling) in meat. The Brink’s herd has 20 continuous years ofultrasound carcass data, more than any other beef cattle herd inthe world.
Three Trees Ranch uses varying percentages of Angus and Brangus
to breed heat-tolerant, high-carcass–value cattle. We refer to these as
Angus+ cattle, and they are in high demand in the southern U.S. right
now and have great export potential.
Q: How severe has the drought been in the southeast
United States?
DB: While not as severe as what Texas and Oklahoma have endured,
we’ve been in drought conditions for more than five years. That puts
stress on cattle seed stock programs, where we’re trying to provide
cattle with as much opportunity to express their genetics as possible.
Q: When did you start using genetic selection and why?
DB: I’ve been working with bovine genomic technologies as longas they’ve been available, and currently rely on the Zoetis HD50K
tool manufactured by Illumina. Three Tree Farms ramped up its data

Illumina BovineSNP50 BeadChip-based tools are enabling Three Trees
Ranch to breed heat-tolerant, high-carcass–value Angus+ cattle.

June 2014
collection in about 2005. We submitted our first genomic test to theAmerican Angus Association in December 2010 using the Igenity
IG384 platform. At the time, it was the only genomic platform forpurebred Angus breeders. We were among the first to use genetic
selection services from Pfizer using the HD50K tool when it became
available. We were certainly the first ranch in Georgia to use genomics
on a large-scale basis.
Q: How quickly did you transition to genomic selection tools toinform your breeding decisions?
DB: We deployed genomic technologies incrementally. Our
management system is based on using the latest reproductive
technologies, such as embryo transfer and in vitro fertilization (IVF),
to multiply our superior genetics cattle. These, in turn, drove ourimplementation of genomic selection to improve the genetic base of
our herd.
The first step was to evaluate our herd bulls. Since January 2011, wehaven’t bred a cow to a bull that was not HD50K-tested. The second
step was to evaluate the donor females whose exemplary genetics
we were multiplying with embryo transfer. Over the last three to fouryears, every cow at Three Trees Ranch that has been flushed (oocyte/egg collection) has been tested genomically. During the last few
years we’ve added selection criteria, so some of the cows have beentested twice.
We are so committed to genomic selection that if a rancher wants
us to purchase the genetics (sperm or egg) of one of their herd
individuals, they need to profile it with the HD50K or we’re notinterested. We’re no longer in the gambling business. We’re in
the predictability business and we think genomic tools give usthat predictability.

are calculated by the American Angus Association and provided tous today.
Q: Has genomic testing replaced ultrasound in providing data on
the animals in your herd?
DB: For the last three years, every bull that we’ve sold, regardlessof whether that bull is going to commercial use or purebred use,
has been HD50K tested. We no longer use ultrasound technology,
because it became a losing proposition. To achieve phenotypic weight
and obtain good ultrasound data, ranchers need to feed cattle highenergy rations. That can be damaging to the long-term reproductive
health and structural soundness of the animal.
Frankly, I was tired of feeding bulls to get meaningful ultrasound measuresof marbling and rib-eye size. I decided it was much more reasonable andpractical to feed those animals for maximum longevity and reproductive
performance and use the genomic tools to tell me about their carcass
characteristics. There are volumes of research that show that feeding
rations with high energy levels to young bulls and females can adversely
affect reproduction. We like the flexibility that genomics gives us to manage
the cattle the way we think they need to be managed, while still providing
meaningful genetic data for comparison.

“We’re no longer in thegambling business. We’re in thepredictability business and wethink genomic tools give us thatpredictability.”

Q: What are the benefits of using genomic and reproductive
technologies in tandem?
DB: Genomics enables us to evaluate the genetics of our cattle at anyage, and compare them to the genetics of the entire Angus population
rather than simply a contemporary group that might skew the data.
With high-accuracy genomic-enhanced data, we have an EPD*
accuracy level of most traits for a baby heifer calf or a baby bull calfthat is equivalent to a 10-year-old proven dam or a four-year-old sire,respectively. That enables us to make selection decisions when calves
are just a few weeks of age.
We’re collecting oocytes from 10- to 15-month-old heifers andsemen from 10- to 15-month-old bulls, where both sets of parents
possess genomic-enhanced, excellent high-accuracy genomic EPD
data. Using IVF in pregnant donor cows and young virgin females
determined superior through genomics, we can significantly shorten
our generation interval.
Deploying genomics and IVF together allows us to turn generations
faster and pick up the pace of beneficial genetic change in our herd. Itchanges the game altogether.
Q: Is EPD data one of the primary values that you use inassessing cattle for breeding?
DB: EPD is the primary objective measure that we use in breedingthese cattle. We have 17 different traits and seven different indices that
* EPD = expected progeny differences

Q: Do you consider genomic data to be more objective thanultrasound technology in assessing cattle?
DB: Having worked in the American Angus Association and marketingfor lots of different people, I know that the traditional collection ofultrasound data has the potential for a huge amount of human error.
Since all ultrasound data is compared to a contemporary group, thedata is only valuable and accurate if the group chosen is a realistic
contemporary group. Financial incentives can sometimes bring out theworst in human nature, causing people to choose a group that makes
an individual or a sire group look superior for a specific trait.
In contrast, genomics yields secure data that can’t be manipulated.
When we send a genomic sample to the American Angus Association,it’s given a barcode ID. That sample goes to Zoetis where it’s assayedwith the BovineSNP50 BeadChip. The results are sent back tothe American Angus Association, which then uses the barcode toassociate the data back to the animal.
The results are an objective comparison of my animal to the 51,000
cattle to date that have been tested with BovineSNP50 BeadChipbased tools and are in the latest iteration of the American Angus
Association database. That’s invaluable for the long term. Genomics
provides a level of accurate comparison that we could only dream ofin the past.

June 2014

Beef Quality and Yield Grades
The U.S. Department of Agriculture (USDA) quality grade
is a composite of factors that affect palatability of meat
(tenderness, juiciness, and flavor)3. The USDA beef quality
grades in descending order of quality include:••••

PrimeChoice
SelectStandard

to evaluate marbling and feedlot performance. It enables ranchers
to evaluate potential replacement heifers so they can continue toimprove their commercial herds. Since our bulls are tested with theBovineSNP50-based HD50K tool, customers will get parentage data
free of charge that matches that specific commercial animal back to
its sire. That added accountability means my customers know thegenetic impact of our bulls.
In cattle ranches throughout the American West, 20–30 bulls might get
turned out in a huge group of cows. They’ll scatter across hundredsof acres, making it impossible to track progeny. Today we have costeffective tools that enable us to track every animal and know at thevery least its sire. If it’s superior, we’ll be able to propagate that sire. If
it’s inferior, that sire will get replaced in the population by a better one.

Q: Is the Angus database as large as some of the dairy cattle
databases?
DB: The dairy breeds have a huge head start on us, but the Angus
database is growing. There are a lot of lessons that we’re learningfrom dairy farmers about how they have used genomic data. Hopefully
we’ll avoid some of the pitfalls and will learn the shortcuts to make themost progress.
The American Angus genomic database is significantly larger than
all the other beef breeds combined. It was initially developed torecord the parentage of the animals. About 25% of the annual Angus
production is documented genomically, so the predictive value of thisdatabase is growing. It’s becoming more than just a historic record. It’sevolving rapidly into a predictive tool.
Q: How has the use of genomic technology impacted the qualityof Angus cattle herds in general?
DB: Genomic technologies are enabling us to make real progress in
improving cattle and are providing us with the data to prove it. About
10 years ago, knowledgeable people in the industry said that thegoal for a beef cattle operation was to produce 70% USDA Choiceor Prime rated cattle. That means that 30% of the herd will be USDA
Select and won’t command a premium price (see Sidebar). With
genomic tools like the BovineSNP50 BeadChip, those same people
are now saying the goal should be 70% Premium Choice** or USDA
Prime, a level of marbling that qualifies a carcass that meets the black
hide color criteria for Certified Angus Beef.
During a recent commercial sale of bulls, Gardiner Angus Ranch
introduced a customer who had closed out a pen of cattle thatwere 100% Premium Choice and USDA Prime, something that wasabsolutely unheard of before we had genomic tools. People usedto say that cattle ranchers couldn’t offer high quality on a consistentbasis. I think genomic tools have changed that, enabling us toproduce a beef product that’s very predictable.
Q: How do genomic tools like the BovineSNP50 BeadChip help
you ensure predictable product?
DB: Genomic tools provide higher accuracy assessment at a younger
age. We’re now going to the next generation of tools. The American
Angus Association and Certified Angus Beef4 offer a tool called
GeneMax5 that’s based on SNPs derived from the BovineSNP50
BeadChip. It’s designed specifically for the Certified Angus Beef andAmerican Angus Association breeders for use in commercial cattle**Medium to High Choice“Genomics provides a level ofaccurate comparison that wecould only dream of in the past.”

Q: With a herd of thousands of cattle, how do you keep track of
the steers and cows?
DB: Every animal in our Three Trees Ranch breeding herds has apermanent tattoo in its ear that’s applied at a young age. We use
DNA to verify the parentage so we’re absolutely sure that we know
exactly who its sire and dam are. We have our own database inhouse. In our case, 95% of our cattle are also in the American Angus
Association database.
In the future, there’s interesting radio-frequency identification (RFID)
technology coming down the road. The new, smaller batteries can
now power RFID technology at a reasonable cost. They’ve developed
RFID tags for cattle that can be read from two miles away. At somepoint, the technology will become economically viable for progressive
breeders to implement it.
Q: Do you still need to educate your customers about the value ofgenetics over phenotypic assessment?
DB: That’s the biggest challenge that we have for the next five years.
I think the technology has evolved and advanced faster than we havebeen able to educate people. These tools can make you a better
breeder and that can improve your bottom line. Education remains
a big part of seeing this technology used pervasively to assess theAngus population.
Q: How do you see genomics playing into the future at Three
Trees Ranch?
DB: I see genomics as a primary tool going forward. It’s how we’re going
to position and package our product. Things have come a long way since
the mid-1980s. Today, Illumina is providing us the tools to accurately
assess and accelerate improvement in our herds.

June 2014
As the technology evolves, so will we. The dairy industry, with a few years
more experience than we have, has recently begun looking at wholegenome mapping, and the identification of haplotypes†, SNPs, andgene interaction that single gene testing can’t identify. They’ve identified
haplotypes associated with excellent fertility and others with infertility. As
we continue to grow the Angus database, we hope to add haplotype data
for the traits that we can’t identify with single markers.
We need new paradigms for a new generation of consumers that wantassurances that the meat they consume has been sustainably raised.
The beauty of Illumina BeadChip tools is that they will someday enable
us to measure disease resistance and allow us to more rapidly eliminate
some of the conditions that put our herds at risk. Genomic tools could
be designed to identify cattle that are prone to certain diseases, such as
bovine respiratory disease. We’ll then be able to selectively mate aroundthose markers and avoid them, rather than having to administer antibiotics
to affected animals. Genome technology offers an elegant solution to solvethese problems.

References
1. Three Trees Ranch, http://www.threetreesranches.com/(5 June 2014)
2. Illumina BovineSNP50 BeadChip, illumina.com/products/bovine_
snp50_whole-genome_genotyping_kits.ilmn
3. USDA Beef Quality and Yield Grades, Texas A&M Agriculture andLife Sciences, meat.tamu.edu/beefgrading/ (5 June 2014).
4. Certified Angus Beef, www.certifiedangusbeef.com (5 June 2014)
5. GMX GeneMax, www.cabpartners.com (5 June 2014)

haplotypes = blocks of genes that are inherited together†Illumina, Inc. • 1.800.809.4566 toll-free (U.S.) • +1.858.202.4566 tel • techsupport@illumina.com • www.illumina.com
FOR RESEARCH USE ONLY
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Pub. No. 1370-2014-004 Current as of 17 June 2014