Tuesday, August 15, 2017

Angus Announces New Lower Price, Development of Angus-Specific DNA Test

Allen Moczygemba, CEO of American Angus Association announced in a memo Monday August 14, 2017 that the price for Neogen GGP-LD and Zoetis i50K tests would be reduced to $37, effective immediately.

The motivation for this price reduction is even more notable. In November of 2017 Angus Genetics Inc. (AGI) and Neogen will launch a new genomic test (SNP panel) called AngusGS™. This test will use 50,000 (50K) DNA variants, designed specifically for Angus cattle. DNA variants are included based on their frequency in the Angus breed, rather than across many breeds like most DNA panels currently used in the industry.

Further, AGI has increased the number of DNA markers in stretches of DNA believed to be involved in fertility, feed efficiency and tenderness. The more detailed genotyping of these chromosome segments will enable more refined research of these important traits.

For example, AGI could include increased markers in regions believed to harbor embryonic lethal DNA variants. An embryonic lethal is a DNA variant that when an embryo inherits two copies (one from the sire and one from the dam) the embryo is aborted, usually early on (less than 45 days after conception). In an analysis of about 4,000 Angus cattle, researchers at the University of Missouri found evidence for 7 embryonic lethal haplotypes in Angus (haplotypes are DNA variants close together that are inherited in a unit or a pattern). With 300,000 animals genotyped within the AGI database, AGI scientist have the ability to repeat and expand this analysis. The dairy industry has been using these haplotype tests for several years.

Dr. Stewart Bauck, Neogen vice president of agrigenomics, stated, "This project was a real collaboration, leveraging the resources and insight of AGI with the expertise of Neogen in chip design and processing, along with input from key external scientists so that the final product is an important step forward in Angus breeding and genetics." Bauck continued, "The novel tool, coupled with low cost pricing puts access to the technology within the grasp of every producer and removes barriers to broad scale genomic testing, not just for sales bulls and herd sires, but replacement heifers as well.  Broad scale testing, along with good phenotype measurement, coupled with the move to the new one-step program for the genetic evaluation, positions AGI, the American Angus Association and Angus breeders everywhere to continue to prepare the breed to meet demands for beef production in the 21st century."

The motivation behind an Angus-specific genomic test is that if we get the right DNA variants in the test, the genomic prediction performs better. More is not better. It is about getting the right 50,000 DNA variants.

50,000 DNA markers, a magic number?

We often hear discussions about 50K this or 50K that. Is 50,000 DNA variants some sort of magic number? No and Yes.

The number 50,000 is not magically. The technology frequently used for DNA marker testing (genotyping) easily fits about 50,000 to 60,000 DNA markers. The first genomic panel widely used for genomic selection included 54,000 DNA variants. This panel, released in 2008, was created by Illumina, the USDA, the University of Missouri and the University of Alberta and was called the Illumina BovineSNP50. In the last nine years, while the space available on the chips has not vastly increased, the prices have gone from $150 to $37.

However, 50,000 DNA variants is an important level to reach. We need between 20,000 and 50,000 DNA variants to accurately describe the variation and relationships within a breed of cattle.

Response from competitors

Will we see a response from competitors?

First, Zoetis has already matched the new price point for Angus genomic-enhanced EPDs (GE-EPDs) set by Neogen. Dr. Jason Osterstock, Executive Director and Head of Global Genetics at Zoetis, commented, "Zoetis is pleased to be able to increase the value of i50K and GeneMax Advantage to producers, just in time for the Fall season." (The GeneMax Advantage test now sells for $28.)

Zoetis in many regards has already been offering Angus-specific products. The Zoetis HD50K was designed for Angus cattle, by adding additional content to the BovineSNP50. The i50K is a subset of the HD50K designed as a more cost effective panel. Osterstock added, "Zoetis has been the primary source of genomic predictions for the Angus breed globally for many years, and have been incorporating Angus-specific content to maximize imputation accuracy in low density tests for quite some time. With the introduction of single-step genetic evaluations, we are excited to have the opportunity to allocate our resources and expertise from building calibrations to creating products with even greater value to producers." (The switch to single-step no longer requires recalibrations, which were conducted by scientists at Zoetis.)

Further, will other breed associations be able to decrease the price point for their GE-EPDs?

In the beef industry, we often talk about heterosis, also known as hybrid vigor, being the only free lunch. In my opinion, genomics has brought us a new free lunch—imputation. Imputation is the process of using tested DNA markers to infer the genotypes at DNA markers that were not tested. In other words, fill in missing data based on patterns in the observed data. DNA variants are inherited on strings of DNA (chromosomes) they are inherited in units (haplotypes). These haplotypes create patterns in the DNA genotype data. We can use these patterns to infer the genotypes at untested DNA markers.

Imputation means we can buy a test with 20,000 DNA variants and get the same amount of information as buying a test with 50,000 DNA variants. This is how the Zoetis i50K and the HD50K work together. Variants from the i50K are used to impute DNA variants that are on the HD50K (but not included on the i50K).

Last fall, Neogen launched a new product called the GeneSeek® Genomic Profiler™ Ultra-Low Density (GGP uLD). This product was designed to increase imputation accuracy while decreasing the price of the assay. This assay would be a viable option for breed associations looking to decrease the price of their genomic testing. The GGP-uLD is an available solution for decreased GE-EPD cost for many breed associations.

The other option for decreased genotyping costs is to buy DNA tests in bulk. The Irish Cattle Breeding Federation (ICBF) bought 1 million DNA tests during a single purchase. This allows ICBF to sell DNA tests to producers for €22/head (~$26/head). They began the program in 2015, and in April of 2017, they had genotyped over 1 million cattle.

Wrap Up

It is an exciting time to be a part of beef cattle breeding! We are reaching a critical mass of data that allows us to create new products and implement new approaches.

Tuesday, August 8, 2017

TBCSC 2017: Useful Scoring System: Teat, Udder, Disposition, Feet and Legs

Tommy Perkins
International Brangus Breeders Association

You must measure every animal in your population. Weaning weight is a must. Actual birth weights (not a tape weight or a windshield weight), yearling weight, mature weights are also valuable and relatively inexpensive.
Genomics is here to stay.
Other traits, like feed efficiency and scan data, are more expensive.

Today, Perkins will talk about visual scoring systems.

Calving ease scoring system is easy. If a cow comes in with a calf, she is a 1, no difficulty, no assistance. But, what we need are 3 and 4 scores reported to the breed associations. A C-section is a score of 4. A Calving ease score of 1 is no assistance. A calving ease score of 2 is an easy pull. A calving ease of 3 is a hard pull, with a crank/calf puller used.

Brangus is going to start using a 1 to 5 calf vigor scoring system. 1 is standing up and nursing in 30 minutes. 2 is standing up within 2 hours and nursing without assistance. 3 is nursing with assistance. 4 is no suckle reflex.

Udder suspension and teat scoring system. This needs to be recorded within 24 hours. See this fact sheet from UNL for more information (http://beef.unl.edu/learning/udder_score.shtml).

Brangus is using a 1 to 5 foot angle scoring system. They are also using a 1 to 5 scale for claw set. They also have two scores for leg set, front/rear leg set and side leg set.

We can also use hair shedding scoring. See http://blog.steakgenomics.org/2017/01/ebeeforg-hair-shedding-scores-tool-to.html for more info.

We also have docility and sheath scoring systems.

Collect these scores and turn them in to your breed association.


TBCSC 2017: Creating a Bull Market

Bill Pendergrass
Beefmaster Breeders United

Over the last 20 years there has been a terminal influence.

What about the next 20 years?

  • Efficiency (not the biggest, not the smallest, who gets it done with the least inputs)
  • Feedyard
  • Brood Cow (Does she get breed every year? Does she get bred in the first 30 days? How are her daughters?)
  • Sustainability
  • Maternal Traits
  • Crossbreeding
Pendergrass said, "If they are a smart commerical cattlemen, they are crossbreeding. Period."

How do you get your share of the bull market?
  • Identify your market
  • Know your customer
  • Produce a quality product
  • Advertise effectively
  • Stay current with technology
  • Younger set of decision makers on the way

You have to have a sharp knife. You have to castrate those calves who don't have the quality to be bulls.

"You may not like it, but EPDs are the language of the industry." Pendergrass says.

We have a new generation of decision makers. Who are these new bull buyers?
  • Top tier: successful early retirees
  • Business, marketing savvy
  • They don't know cows but know numbers
  • Family progression
  • More educated on performance data
  • Think outside of the box
  • More technology driven
Current generation is consistently questioning numbers. "I don't believe that number, I don't believe that number." Next generation is much more accepting of numbers.

Your ability to market bulls will determine if you stay in the business. If you can sell bulls, it will go a long ways towards your female sales.

Have to take advantage of reproductive technology. Need to AI. Seedstock producers have to stay ahead of the commercial producers. 

Seedstock producers are held to a higher standard.
  • Herd health, vaccination protocols
  • Deates were worked
  • Breeding Soundness Exams, stay current!
  • Trichinosis Testing Requirements
  • Interstate Health Papers
Are your bulls ready to ship?


No one likes to buy an ugly bull. Have to be eye appealing, sound and functional. 

3 kinds of bulls:
  • Fancy bulls with bad numbers ... there's a buyer
  • Ugly bulls with great numbers ... there's a buyer
  • Fancy bullw with great numbers, bring all the money!
Accurate data is essential. Whole herd reporting, register your calves, submit data to your association, weight/scan records, genotyped (GE-EPDs), and selection indicies. Decision support software is what is coming next.

Have a handout when your bull customer shows up. 

Know your customer
  • Herd calls
  • Production environment 
  • Annual rainfall
  • Forage base
  • Supplemental feeding strategy
  • Marketing program
  • Weaknesses?
You need to sell them cattle that match their production.

Identify and contact key influencers
  • Veterinarians
  • Sale Barns
  • Order Buyers
  • Video/Internet Sales Reps
  • Extension personnel
  • Build a network
AI is the single cheapest way to stay current in the beef industry. Genomics now has purebred and commercial applications.
Be the data interpreter for your customers. Teach them how to read the numbers.

TBCSC 2017: Selling Replacement Females

Fred Schuetze
Buzzard Hollow Ranch

The major problem with new seedstock producers is that they don't have a plan. You need to treat seedstock production as a business.
"This has to be a data-driven business. If you don't have the data then you can't successful market in the long run," Schuetze said.

Marketing females is no different than marketing bulls.

There needs to be planning. This is for a minimum of 3 years.

You need to do some soul searching. You need to think outside the box.

Do all your purebred cows produce females that are good enough for your replacement or for fellow breeders?
How many replacement females do you need to maintain herd size?
How many females are of quality to market to fellow breeders?
How many bulls produced are of the quality to market as herdsires or commercial bulls?

First of all, computers are smart. But, they have a problem. You have to tell them what you want! You have to have training data for genetic evaluations.

You have to make a decision.
Are you going to manage the cow herd as one unit? Everything is for purebreed cattle
Or, will you split the group in two? Those cows that can producer purebreed cattle and those cows that produce commercial replacement females and market steers.
When spliting the group in two, you breed the lower quality cows to a different breed to produce crossbred females that reap the benefits of heterosis.

Have to develop heifers properly. Need to be weaned in a low-stress manner. They are developed on high quality forage and grain supplementation.

At 14 months or so implement synchronization program. Choose AI sire and then use quality clean up bull for 45 days. Open heifers to be sold to auction.

The customer has to be a partner. If he doesn't make money, he won't be back.

You have to keep good records.

  • Birth, weaning, & yearling weights
  • Ultrasound scan data
  • Breeding records
  • Palpation records
  • Vacination protocols
  • EPDs

You have to have a good reputation. You have to be able to stand behind your cattle.

At Buzzard Hollow, they AI to proven bulls. They turn out AI sire candidates that are two year olds out as clean-up bulls. They get data on these young bulls and find out if they are going to be exceptional AI bulls.

Brand recognition and integrity are the two keys to staying in business in the seedstock industry.
One of the most important parts of marketing
Developed over several years by producing quality cattle
Seller integrity
Participate in local, area, state, & national cattle events
Potential customers need to know who you are and what your program is

The customers impression is reset the moment they drive through the gate. Is the gate sagging? Is the grass mowed? Are things in repair?

Cattle need to be in excellent condition and ready to be shown at all times.

Schuetze used SimAngus cattle to change the perception of his Fleckvieh cattle. Value was added to the Fleckvieh cattle by using Angus bulls. Value was added to the Fleckvieh cattle by using Brahman cattle. The reputation of the Fleckvieh cattle increased based on their hybrid offspring.

"Don't get so narrow minded," Schuetze said.

"Be honest with yourself when you are making those management decisions", he continued.

"You better learn about single-step." (I suggest you read up here: http://blog.steakgenomics.org/2016/11/brangus-journal-understanding-genomic.html.)

Marketing is the name of the business, but you have to have the data to back up the marketing.

TBCSC 2017: So You Want To Be A Seedstock Producer

John Ford
Executive Director
Santa Gertrudis Breeders International

Why be a seedstock producer?

We see producers that join a breed association, make a big splash, and then disappear.
Why?
This is likely because they were not focused on things that make a seedstock producer profitable and successful in the long run.

We talk about successful youth programs, premier sales, and national champions. But we do not talk to them about the complexities of seedstock production. We do not talk about producing cattle for a commercial customer.

We have to focus on performance.
We have to focus on data collection.
We have to focus on new tools available to us.

The mom-and-pop grocery has given way to 5 major grocery chains. Those customers are looking for a consistent meat product. Those grocery chains are telling the four packing plants what their customers are wanting. Those four packers are talking to the 5% of the feedyards that feed 80% of the industries cattle. The feedyards are talking to the commercial cattlemen and asking them to produce efficient,productive cattle that will be profitable for the feedyard, packing plant, retailer and meeting the customers need. Those commerical producers are then turning to the seedstock producers and asking them to help reach these goals.


Seedstock producers develop breeding plans and stick with the plan.
A breeding plan provides a clear picture of herd direction and allows informed breeding decisions to be made. We need a road map. The successful seedstock producer has a road map. They know what they are producing.
If you get to chasing fades, you will see your program going backwards.

Long-term economic viability depends on focusing on improving traits that either lower the cost of production or increase revenue.

"Technology has changed the game." Ford said. We have the tools available now that you can identify those animals that produce profitable cattle.

Breed associations are now giving breeders power tools.

Objectives for animal improvement can only be reached based on sound genetic information and performance data.
Genetic selection tools have not eliminated the need to measure and collect data.

Seedstock producers speed genetic progress by using reproductive tools and commit to artificial insemination. In beef breeding, we can't turn over generations very quickly, especially compared to competing protein sources. But, reproductive technologies allow us to improve our genetics. Seedstock producers can use embryo transfer, In Vitro Fertilitation, and artificial insemination. Artificial insemination is one of the most underutilized tools in seedstock production.

"You need to be fluent in the language of your breed," Ford said. What was your breed's average weaning weight last year? What was it ten years ago? You also need to be fluent in your herd.
Further, you need to be fluent in other breeds. When someone is taking about retaining heifers and another breed's terminal index, you need to point out to them the issue here.

Who is your target bull buyer? If your target audience if everybody, your potential buyer is nobody. Most times, bull customers live within 200 miles of their seedstock supplier. Know your neighbors and friends. Know their operations.

Seedstock producers are customer oriented. In today's marketplace it is not about the breed, but the breeder. Customers are more like partners in our genetic package.

There is not a better marketing tool than producers that can say they will buy back their customers calves.

Visibility is the greatest marketing tool. Websites, social media platforms, and print media are essential in today's busy environment. However, no form of advertising impacts marketing like industry networking.

Seedstock production is complex. It is data driven. Our goal is to accomplish genetic improvement to affect the industry from producer, feedyard, packer, retailer, and consumer.


TBCSC 2017: History of Veterinary Genomics

James Womack
Texas A&M University

Genetics is like looking at a flower or two. Genomics is looking at the entire garden.



Genomics really grew out of gene mapping.

Genome was first coined in 1920 as a combination of gene and chromosome. It was meant to describe all of the genes along a set of single chromosomes.

The term Genomics was coined during a meeting in Bethseda Maryland ("Beer, Bethesda, and Biology: How "Genomics" Came Into Being").

Built off of information and technology built for human genetic and genomic research.
In 1981, we knew of 4 linkage groups. Blood type was linked with hemoglobin. Alpha-, beta-, and kappa-casein were known to be linked on the same chromosome.

By 1985, we had 25 linkage groups for cattle (cattle have 31 chromosomes, 29 autosomes, X and Y).

In 1990, there was a conference at Cold Spring Harbor about mapping genomes in cattle (mapping is figuring out the recombination that occurs between spots on a chromosome. These DNA variants are inherited in patterns, not independently).

Womack's lab continued to pursue comparative maps, comparing mice, humans, and cattle. This allowed them to use advances in the human genome to improve information about cattle genome. If a new gene was identified (mapped) in the human genome, they could use that information to

In 1998, Womack wrote in a grant that "The bovine genome will probably never be sequenced." All of that soon began to change. The human genome was finished ahead of schedule and below budget. This lead to a call to sequence other genomes. In 2002, the National Human Genome Research Institute announced that they would help fund the cow and dog genomes. However, NHGRI said they would only pay for half of the cost of sequencing the cattle genome.
Researchers got money from the USDA, Japan, Korea, China, Canada, and Australia.
Womach got a call saying that if the cattle genome community did not come up with the money, that NHGRI was going to move on to a different organism.
Anne Armstrong set up a meeting with the governor of Texas. Anne Armstrong was known as the velvet hammer. Needless to say, the State of Texas came up with $5 million to support the sequencing of the cattle genome.

In 2009, the first cattle genome was published. It was based on an inbred, Line One cow from the Fort Keogh Research Station in Miles City, named L1 Dominette 01449.

Once we have the tools of genomics, we could begin finding the DNA variants found for simple Mendelian traits. These traits are controlled by a single gene. These are easier to find and identify.

However, most of our economically important traits in cattle production are complex traits. These traits are controlled by many genes and are influenced by the animal's environment.

There is a lot of diversity in genomes. Of the 3 billion base pairs, you likely vary from other people at 3 million base pairs. These single base pair changes are called SNPs (single nucleotide polymorphisms).

In cattle we have a DNA test (SNP chip) with 700,000 DNA markers (SNPs) on it.

Researchers have just finished a DNA project looking at bovine respiratory disease. See eBEEF.org fact sheet about the project (http://articles.extension.org/pages/73031/genetic-markers-of-bovine-respiratory-disease-complex-susceptibility).

Dairy calves in hutches were scored for different respiratory symptoms (nasal drainage, eye discharge, ear drooping, temperature and cough). Calves in hutches were identified that had severe symptoms. Then calves in a nearby hutch with no symptoms were also identified. Researchers then conducted a genome-wide association study to identify DNA markers that are associated with variation in Bovine Respiratory Disease.

The found 50 loci that were associated with BRD in different analytical approaches, geographic locations,

On chromosome 15, they identified Poliovirus receptor related 1 (PVRL1) as influencing BRD susceptibility. This gene is know to affect entry of bovine herpes virus 1 into the cell. Other strong candidates have also been identified.

TBCSC 2017: Measuring Heat Stress in Cattle

Raluca Mateescu
University of Florida

What is heat stress?
There are several sources of heat that affect cattle.

  • The first and most important is heat from the sun. 
  • This is amplified when the humidity is high.
  • Metabolic heat from digesting feed. This heat is higher for forage compared to grain.

In response to extreme heat, cows will:

  • Regulate internal heat production (eat less, reduce growth, lactation, and activity)
  • Regulate heat exchange (increase blood flow to the skin, increase sweating & panting)


We would prefer that cattle increase their heat exchange and keep their production high.

Heat stress is when the cow's internal temperature increases above normal levels.

We can also expect more areas of the country to be affected by heat and humidity. So, how do we select cattle that can cope with heat stress?

In swine, poulty and dairy production we use climate control to manage heat stress. This is not feasible in beef cow-calf production where cattle are not confined and we can't control their environment.

There is lot of genetic variation in thermal tolerance in beef cattle. This means that we can make progress through genetic selection!
About 20% of the variation in thermal tolerance is due to genetic variation.
The hard part will be identifying which animals are genetically superior for core body temperature regulation. This requires exposing animals to heat stress and seeing which ones perform the best. Need phenotypes and tools to make selection decisions.

Dr. Mateescu research is focusing on using Angus x Brahman cross cattle to collect heat tolerance traits.
They put a temperature sensor in a blank CIDR (no hormones, just the CIDR). They left these in heifers for 5 days.

Under high heat stress, only 100% Brahman were able to regulate their body temperature and stay neare 39 degree Celcius.
Under lower heat stress, Angus and 3/4 Angus could not effectively regulate their temperature, whereas Brahman, 1/4 Angus, 1/2 Angus and Brangus could regulate their temperature.

Even when looking within 725 Brangus, we see a lot of variation in internal body temperature under heat stress. Animals with smoother, finer hair had lower internal body temperatures (were cooler).

We have to select for internal body temperature using genomics because collection of the phenotype is very expensive. The cow of the future will have both high productivity and resistance to heat stress.