December 2014

Genotyping Cattle for More Efficient Breeding anda Higher Quality Food Supply
GeneSeek uses Infinium® iSelect® BeadChip-based tools to help breeders measure genetic meritand select superior breeding stock.
Introduction
Founded in 1998, GeneSeek is focused on performing
high-quality, cost-effective genotyping for animal agriculture.
Based in Lincoln, Nebraska, the company originally offered
STR-based parentage, coat color, and defect testing forthe beef and dairy sectors until it partnered with Merial
Animal Health in 2003, broadening its portfolio of products
and services.
The real breakthrough for GeneSeek came in 2007 when
the complete bovine genome was sequenced and theBovine HapMap became a reality. Immediately, Illumina
formed a consortium of individual, university, and government
scientists to identify SNPs across the genomes of several
major cattle breeds and later launched the BovineSNP50
BeadChip. GeneSeek recognized the impact this productwas going to have on the marketplace. “We concluded that
Illumina BeadChip-based SNP genotyping would be theleading application for the future,” said Stewart Bauck, DVM,
General Manager of GeneSeek. “That decision more thananything else turned the corner for GeneSeek and started it
on its current path of expansion.”
Dr. Bauck partnered with GeneSeek in 2003 bringing
genomics experience tracing back to his days as a country
manager for Merial in Canada. “I was looking at newopportunities in animal health and decided that we would
be remiss if we didn’t get into genomics,” Dr. Bauck said.
GeneSeek is now a subsidiary of Neogen Corporationand has grown to become a leading provider of genetic
diagnostics for identity and trait evaluation in the agricultural
biotechnology industry. It currently performs these services
using iSelect Custom BeadChips and will soon be offering
sequence-based diagnostic capabilities on the MiSeq® andNextSeq® 500 Systems. iCommunity spoke with Dr. Bauckto learn more about how genomic diagnostics is changing
the beef and dairy industry.
Q: What is the mission of GeneSeek?
Stewart Bauck (SB): Our primary goal is to provide
high-quality, low-cost, robust genotyping services for theagricultural sector, primarily animals, but also plants. Thethree pillars of our business are reliability and accuracy

Stewart Bauck, DVM, is the General Manager at GeneSeek, part of
Neogen Corporation.

of the results; turnaround time, with a goal of sending
genotyping results to customers within 14 days; andcost-effective, value-added products and services.
Q: You’ve recently doubled the size of your laboratory inNebraska. How does that enhance the services you provide
to customers?
SB: We didn’t just double the size of the laboratory, we also
moved into a scalable building that enables us to conduct
genomic testing efficiently. We now have a customized
genotyping facility with room for expansion. The layout isdesigned to move samples efficiently from reception all theway through to genotyping and data analysis. We needed toexpand our footprint to accommodate additional platforms
such as sequencing. We’re in the process of installing aNextSeq 500 System, alongside the MiSeq System, andiScan and HiScan® array scanning systems that we are
running currently.
Q: Why did you choose the Illumina products and systems
as your genotyping platform?
SB: Illumina has been agile in terms of expanding with us.
We started with the BovineSNP50 BeadChip. The iSelectBeadChip has now enhanced our product offering, enabling
us to expand from catalog to custom products. The flexibility

December 2014
allows us to build low-density, low-cost products for routinecommercial genotyping, and high-density products forresearch applications. The processes are compatible withthe high-volume throughput in our lab.
The iSelect BeadChip enables us to serve our mission ofdata reliability and accuracy with fast turnaround time.
The quality of the product means that we can rely onIllumina to perform the QC on each iSelect BeadChip.
After the BeadChip comes to us, we have a high degree ofconfidence that it will deliver time and time again. There’s
essentially no variability in performance.

“The great thing about Illumina
technology is its reliability,accuracy, and robustness.”
Q: Is the bulk of your genetic testing for bovine
breeding associations?
SB: We service virtually every major breed association in
North America and around the world, including the Holstein,
Jersey, and American Angus associations. We think about
the breed associations as a B2B (business-to-business)customer segment. Members send samples to theirbreeding associations, and the associations gather themup and send them to us for genotyping.
We also have a significant B2C (business-to-consumer)
customer segment where we have a direct business
transaction and information delivery to individual cattle
producers. These range from ranchers that send us single
samples for a low-density genotyping or parentage testing,up to the largest commercial ranching operations in North
America. We offer services to virtually all of the major ranching
operations in North America and many around the world,including Australia, New Zealand, and extensively throughout
Europe. We even have business operations in Brazil andChina. It’s a diverse mix of customers, particularly on thebovine side.
In addition, we provide genetic testing services for various
other species including dogs, fish, pigs, poultry, and horses.
We also offer services for testing specialty crops, as well as
trees that are used for pulp and paper production, such as
eucalyptus and pine.
Q: How do they use the genetic information?
SB: Most of what we do is tied to genotyping of animals forthe selection of superior breeding stock. It ranges from simple
parentage testing to the development of a genomic-enhanced
breeding program, where we use Illumina technology primarily.
In the case of the cattle industry, there is a measure of genetic
merit that’s referred to as the expected progeny difference(EPD). This is a measure of the impact that a sire or dam will

have on their offspring. It’s used frequently for the selection ofsuperior breeding stock. It greatly enhances the rate of genetic
progress by removing animals from the breeding populationthat aren’t contributing the desired mix of alleles. More breed
associations are embracing the GeneSeek Genomic Profilers(GGP) built on the iSelect platform to develop and deploy tools
to achieve genomically enhanced EPDs for individual traits.
Q: How are cattle traditionally evaluated?
SB: The conventional way to measure the genetic merit ofprogeny is to raise a cow, impregnate her, and have her raiseprogeny. It takes several years to evaluate the progeny anddecide whether she’s any good. With genomics, the producer
can take a tail hair or other tissue sample when she’s a day oldand get exactly the same information.
If I have a young bull and I want to evaluate his genetic
merit, traditionally I put him out with a group of heifers, heimpregnates them, and they calve. Their progeny grow up, areweaned, and put into the feedlot, where they are evaluatedas they’re prepared for market. By the time I get the data on
the first progeny that bull has sired another set of calves andhe’s out in the pasture working on his third set. That’s a risk
management situation. I want to know before I put him out thefirst time whether he’s any good. I don’t want to wait until he’s
3 or 4 years old and sired three set of calves, before I realize
I’ve made a mistake.

“The iSelect BeadChip has now
enhanced our product offering,enabling us to expand from
catalog to custom products.”
Q: What are some emerging genotyping applications?
SB: The part that is emerging is the concept of markerassisted management. We’ve seen increasing interest andinvestment into selecting the animal based on its genomic
profile, and altering its management as a consequence.
For example, consider a steer that’s going into the feedlot
rather than for future breeding. What I do with him in thefeedlot and how I manage him could be very different if he has
the genetic potential to produce highly marbled, high-quality
beef for a steakhouse, as opposed to hamburger for fast
food. With marker-assisted management, we would know thisessentially from birth. Soon, a steer will arrive at the feedlot,
walk off the truck, and pass a reader that scans the electronic
ID in their ear. Their record will pop up on the screen and theappropriate gate will swing open for the high-quality (Primeor Choice) or mid-quality (Select) beef pen based on theirgenomic profile.

December 2014
Q: What percentage of cattle is being genetically tested now
versus 10 years ago?
SB: Five years ago it was fractions of a percent of the total
cattle population were being tested. Today we’re probably
in the range of about 5–6% and it is growing exponentially.
Within the purebred sector, genetic testing is becoming
commonplace for bulls sold to commercial producers. Many
people are using some genomic profiling for their sire or
dam selection programs. Increasingly, there are progressive,commercial producers who are using genomic profiling for
producing beef for the marketplace. Within the poultry andpig industries, it’s become virtually commonplace. Soon a
producer won’t be able to consider themselves to be a global
player in those categories without a comprehensive genomic
selection program.
Q: How do you partner with Illumina to meet the genetic
testing needs of breeding associations?
SB: We’ve been working with Illumina around the conceptof custom BeadChips. Because of our knowledge of themarketplace and the direct daily interaction we have withcustomers, we can anticipate their needs on a geographic
basis, even by segment. We bring our custom designs
to Illumina and work with them on the development ofBeadChips, which we deploy within our lab. Illumina helps
us meet the fast turnaround times and lower costs that ourcustomers demand. It makes sure we’re operational andable to process samples in a timely manner. Having a partnerthat can provide that level of focus and customer service
enables us to be successful delivering genetic services tothe marketplace.
Q: Is the BovineSNP50 BeadChip the foundation of theGeneSeek genomic profile test?
SB: Illumina developed a low-density version of theBovineSNP50 BeadChip (called the BovineLD BeadChip)
containing approximately 7,000 SNPs that we use as
the foundational product for most of our bovine genomic
profiler products. We’re now working on an iSelect 150,000
SNP custom array built with those original 7K SNPs of theBovineLD BeadChip as the foundation. Since the introductionof the BovineSNP50 BeadChip, we’ve learned more about
the bovine genome and specific markers, and used thatknowledge to build enhanced products.
Q: Did you evaluate other array technologies?
SB: We evaluated other microarray-based platforms. The
Illumina BeadChips come in various sizes, ranging from 8–24samples. It’s a relatively simple process to obtain samples
in combinations that allow us to run 24 samples. Otherproviders have 384-sample arrays, which are too large formany applications. We like the flexibility from Illumina, wherea relatively small number of samples are required to completea chip.

Q: How is GeneSeek distinguished among its competitors?
SB: We have several competitors in our space. If you were toquery our customers, they would tell you we are distinguishedby our focus and our flexibility. We process DNA and performgenotyping, and are capable of accommodating projects ofvarious sizes. We work with our partners to deliver the data
in a form that makes sense for them without proprietary
limitations. Customers can get the data back in the form thatthey want, at the right price, in a timely fashion, and they cancount on its reliability.

“We like the flexibility from Illumina,
where a relatively small number ofsamples are required to completea chip.”
Q: What are the trends in genetic testing?
SB: We definitely see a trend towards sequence-based
applications. We see some of our microarray-based
genotyping moving towards a genotyping-by-sequencing(GBS) application. We have a MiSeq System on hand and areinstalling a NextSeq 500 System. Going forward, our serviceswill include BeadChip genotyping, as well as GBS and othersequencing applications.
Q: What are the next steps in GeneSeek’s growth?
SB: We intend to keep growing geographically, replicating theGeneSeek model in other countries and for other applications.
We are expanding our portfolio of products and our customer
base by leveraging some of Neogen’s core competencies infood safety. We’ll also be building a range of product offerings
to serve the agricultural sector effectively and intend to expand
into more plant applications.

December 2014

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1370-2014-013 Current as of 18 December 2014