Wednesday, August 30, 2017

Using Genomic Tests to Detect Genetic Abnormalities in Beef Cattle

Christian P. Lewis
South Dakota State University undergraduate student

Rapid advances in science and technology are appearing throughout agriculture. One of the newest technologies that has worked its way into the cattle industry is DNA testing and the use of genomic data.

Practical Uses of Genomic Data

Genetic abnormalities are not a common problem in beef cattle production, but they do appear if precautions are not taken. Most frequently, a genetic abnormality appeared because both the cow and bull were carriers of a recessive allele that causes the abnormality. An animal is termed a “carrier” when they have a dominant allele that is masking the recessive allele. Figure 1 illustrates how an abnormality can appear by mating two carriers. Genetic abnormalities will appear when a calf has two copies of the recessive allele that it got from its sire and dam.

A
a
A
AA
Aa
50% chance the calf will be a carrier
a
Aa
aa
25% chance the calf will have the abnormality
Figure 1: Mating two carriers (Aa) of a recessive allele (a) that is completely masked by the dominant allele (A)

Without a DNA test for an abnormality, the only way you will know an animal is a carrier or not is when you mate the suspected carrier to a known carrier and offspring with the abnormality are born. If you want to test for a genetic abnormality, the first thing that you should do is contact your breed association to see how they want DNA collected for a test and where to send DNA samples.

DNA Collecting Basics

There are three common ways to obtain DNA samples from cattle: blood samples on FTA cards, tissue samples, and hair samples. If testing young calves, a blood sample is often preferred. There are several videos online that demonstrate how to collect DNA samples if you are new to DNA testing.

Collecting blood samples


Collecting tissue samples


Collecting hair samples




Managing Known Defects

After you receive the results, there are three possible ways to keep the tested abnormality from appearing again:

  1. Cull the carriers.
  2. Make sure not to mate two known carriers.
  3. Utilize crossbreeding.

Culling the known carriers and not using carrier bulls will eliminate the abnormality from appearing in your herd again. By always using non-carrier bulls, none of your calves will ever present the abnormality.  If the genetics from the known carriers are too valuable to cull, you must plan your mating decisions so that two carriers are not allowed to mate. If you use a carrier bull, all calves sired by this bull should either be sold after weaning or tested for carrier status before they are bred. Crossbreeding may be the easiest way to avoid genetic abnormalities. It’s very rare for one abnormality to segregate within two breeds, but it’s not unheard of. For example, Tibial Hemimelia (TH) segregates in both Shorthorn and Maine Anjou, as some of the same sires were used in both breeds. So, mating Shorthorn with Maine Anjou presents a risk of the TH abnormality appearing in calves.  Further, if both the sire and dam share a breed (e.g., both sire and dam are Angus-influenced), mating these individuals could still result in the appearance of a genetic abnormality.

DNA Test Available

Producers can often order tests for genetic abnormalities along with other DNA tests. These DNA tests are priced based on how many tests you want them to perform. Most DNA tests for genetic abnormalities cost approximately $25 per head, but the cost per head may be lower if you test for more than one genetic abnormality or purchase another DNA testing product (e.g., Igenity Profile, PredicGEN).  If you wish to learn more about genetic abnormalities and available DNA tests for these abnormalities, you can visit websites maintained by Zoetis Animal Genetics https://www.zoetisus.com/animal-genetics/beef/index.aspx or Neogen Corporation http://genomics.neogen.com/en/genetic-health-and-conditions.  Both of these companies provide DNA testing services for the beef industry.  A more comprehensive list of DNA test providers can be found in the article titled “Managing Genetic Defects” authored by Dr. Alison Van Eenennaam (see references list). 

Conclusion

In today’s production environment, it is often easier to take precautionary steps than fix something after it becomes a problem. Genetic abnormalities may not appear in your calf crop this year, but they could down the road. If your cowherd is at risk (e.g. you know you have used carrier bulls in the past), testing your cowherd for abnormalities will at the very least give you peace of mind. It might even save a calf from developing an abnormality, which in turn, will lead to more pounds to sell at weaning time.

References
Van Eenennaam, A. 2015. Managing Genetic Defects. http://articles.extension.org/pages/72662/managing-genetic-defects

As part of our USDA-NIFA local adaptation grant, Michael G. Gonda at South Dakota State University has developed a course titled "Applied Beef Cattle Breeding." Christian wrote this article while participating in that course.

Tuesday, August 29, 2017

Videos from Applied Reproductive Strategies in Beef Cattle

Several of my colleagues from the University of Missouri are attending the Applied Reproduction Strategies in Beef Cattle conference today and tomorrow in Manhattan, Kansas.
The Beef Reproduction Task Force is posting live videos of the talks on their Facebook page. Farmers and ranchers can either watch the talks live or view recording of the talks.

David Patterson spoke at the conference this morning.


Proceedings from the conferences are available here.

Wednesday, August 23, 2017

Southwest Research Center Field Day 2017

The Southwest Research Center Field Day will be Saturday September 9, 2017 from 9 am to 1 pm.
It will include a Beef Tour, Forage Tour, Horticulture Tour, and General Ag Tour. It will feature airplane rides, pumpkin patch, grass maze, face painting and other children's activities.

Beef Tour

  • Tim Evans, The value of a veterinary diagnostic laboratory to Missouri agriculture — 9 & 11 a.m.
  • Eric Bailey, Mineral supplementation for beef cattle — 9:30 & 11:30 a.m.
  • Danny Shilling, Cattledog demonstration — 10 a.m. & noon
  • Jared Decker, Selecting for profit — 10:30 a.m. & 12:30 p.m.

Forage Tour


  • Ryan Lock, Baleage supplementation — 9 & 11:30 a.m.
  • Tim Schnakenberg, Bermudagrass: could it be a game-changer in our hayfields and pastures? — 9:30 & 11 a.m.
  • Will Knuckles, Novel endophyte fescue — 10 a.m. & noon
  • Stacey Hamilton, Measure-monitor — manage your pasture with paddock track: technology to improve your bottom line — 10:30 a.m. & 12:30 p.m.

Horticulture Tour

  • Patrick Byers, Blackberry research and production — 9:30 & 11 a.m.
  • Kelly McGowan, Overview of elderflower research — 9:45 & 11:15 a.m.
  • Grant Bolton, Trapping and control of spotted-wing drosophila — 10 & 11:30 a.m.
  • Shon Bishop, High tunnels and Brussels sprouts — 9 & 10:30 a.m.
  • Dean Volenberg — 9:30 & 11:30 a.m.
  • Leon Riggs, Introduction and history of bees — 9 & 11 a.m.
  • Hannah Hemmelgarn, Mushroom cultivation — 10 a.m. & noon

General Ag Tour

  • Rick Rath, Missouri Department of Conservation — 9 & 11 a.m.
  • David Brune, Sustainable seafood production in the Midwest — 9:30 & 11:30 a.m.
  • Jacquie Howell, Nutrition — 10 a.m. & noon
  • Reagan Bluel, cannulated cow
The Southwest Research Center is located at:
14548 Highway H Mt. Vernon, MO 65712

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.

TBCSC 2017: Genotyping Embryos

Matt Barten
Embruon

Growing out of DNA testing for genetic conditions, Barten decided to develop a company that could biopsy embryos and DNA test embryos (rather than waiting for calves to be born).


In embryos, there is the inner cell mass that is going to become the calf. There rest of the embryo (trophectoderm) will become the placenta. They biopsy the trophectoderm as it will heal and the embryo will develop normally.

Now, with the DNA from the biopsy, they can DNA test the embryo.

Illumina needs minimum of 150 ng of DNA.
1 Cell can yield ~7 pg of DNA
1 biopsy yields ~70 pg DNA (~10 cells)
Have to amplify this DNA 2,100 times.
This is like amplifying a bushel of corn into a semi truck load of corn.

Half of the variation in the population is expressed between full siblings. From an embryo flush, you can see tremendous variation in the genomic predictions of the embryos.

By genotyping the sire and the dam, GeneSeek and Embruon can correct the messy genotypes from the embryo biopsy. They can get high quality genotypes from the small starting quantities from the biopsy.

Using risk assessment software, the return on investment in embryo biopsy was 49%. Typical embryo transfer was about 43%.

Embruon has now took over a lab that was previously used for human In Vitro Fertilization (IVF), and is now used for cattle IVF.

Embruon can test for:

  • Gender
  • Genetic Condition
  • Gender and Genetic Condition
  • Genomic-enhanced EPDs

The cost is around $140 per embryo, plus shipping cost.

Monday, August 7, 2017

60% Off 50K Test for A Limited Time on American Simmental Association Cows

$20 Genomic test including parentage

The American Simmental Associations strives to leverage all its resources to provide the industry with the best prices and most robust science.  The Cowherd DNA Roundup is a perfect example of a breed association that works for its members and customers.

Breeders who submit a DNA sample on their entire cowherd can get genomic-enhanced EPDs and parentage for $20/test.  Like how that sounds?  There's more!  Breeders who submit cow weights with either body conditions scores or hip heights get an additional $5 off per test - an amazing price of $15/sample.

This project marks a major investment from the American Simmental Association towards research and development.  The $15 test is only available for the first 15,000 samples with phenotypes submitted.  There is no estimate of when the results will be available on samples submitted.  Donor cows and bulls do not qualify.  No additional DNA tests are available with this offer.

Leoma Wells, ASA's DNA and Total Herd Enrollment (THE) Specialist, will transition from DNA Services to ASA's point person for the Cowherd DNA Roundup project. When asked about the transition, Wells says, "I am excited and grateful to be a part of this revolutionary project. It combines two of my favorite areas, DNA and data collection on females. The wheels are turning and I absolutely can't wait to get started and smash the goals we have set."  In September, ASA will welcome Carolyn Wild to the DNA department to help with the daily DNA services.

Contact Leoma Wells or Jackie Atkins for more information 406-587-4531.

Source: ASA Weekly Newsletter

Decker's Take Home Message
I love programs like this that strive to create win-win situations. The American Simmental Association needs mature cow weights to accurately describe cow nutritional requirements through a Mature Cow Weight EPD. This EPD will allow another economically important trait to be added to economic selection indexes.
Further, this project will increase the number of genotyped cows. This will ensure that more herds are genotyped from the bottom to the top, and not just the top cows and bulls.

TBCSC 2017: Live Animal Evaluation - What to Look for and Where

Sam Womble
Texas A&M AgriLife

Visual structure evaluation is best evaluated from the ground up.
Go from hooves, heels, pasterns, knees, hocks, shoulders, hooks, pins, rump and back.
"Be very critical of how they get out and travel." Womble said. For cattle with ample forage and feed, structure may be a little less important. For cattle on rough range that have to get out and look for forage, structure is more important.

Simply, sounder cattle last longer.

When cows slop too much in their hip, they get their legs up under them.
Cattle that are correct have their feet securely underneath them. They have about a 45 degree angle to their shoulder.
Cattle that are too straight on their front and hind legs look good standing still. But, when we put them on the move they really struggle.

We want a 90 degree angle from the point of the shoulder to the top of the shoulder and from the point of the shoulder to the elbow. If this angle is great than 90 degrees, the cattle are too straight, too upright in their shoulder. Cattle that are too straight often have toes that point to the sides instead of straight forward.

When looking at the back legs, we should be able to draw a straight line form their pin bone down to the ground past the hock and the pastern.

Cattle can be sickle hocked. The legs are underneath the animal, and there is too much angle to the hock.

Post legged is when the hock is too straight. There is no angle to the back legs. These cattle do not stride smoothly.

From the rear, the hind legs should be straight and toes should point straight forward.

If a bull toes out, the hocks are closer together than the feet. These cattle often have swelling in their hocks.

Cattle can also be bow legged. The hocks are out wider than the toes.

We want big feet with lots of surface area for stability. We want depth to the heel.

Cattle that hump up (roach up) as they walk are likely compensating for being too straight.

Decker's Take Home
Until we have EPDs for structure, use visual appraisal to find cattle that are structurally correct. Look for cattle that can cover their stride (back hoof falls in the hole left by the front hoof) and are correct from the ground up.

TBCSC 2017: Genomic Enhanced Expected Progeny Difference -Do they Work?

John Genho
Livestock Genetic Services

Livestock Genetic Services does genetic evaluations for several American (eared) breed associations.

When comparing EPDs and raw performance, the relationships are always better when using genomic information, compared to pedigree information only.

King Ranch marketed a bull named KR Ricardo 182/20.
KR Ricardo 182/20
This bull had four brands on his shoulder. Two stars, as he had two copies of the favorable DNA variant (allele) for the GeneStar Marbling test and two T for the GeneStar Tenderness tests. Now that we use 50,000 DNA markers, branding is not really practical!

As we adjust

Sometimes we see that calf, and the cow looks mad, so you say, that calf looks like 80 lbs. Or, you don't take the time to collect weaning weights and yearling weights.
How can geneticists adjust bad data? We can't. If you want better EPDs, you need to turn in clean data!

What if Genho went in for a physics and IQ test. The first time he went in, Albert Eistein and Stephen Hawking were the two others taking the test that day. He looks like he is 30 points below average on that day. He decides to go in for a second test. On this day, his contemporaries are Justin Beiber and Homer Simpson. On this day he scores 30 points above average! Did Genho's intelligence change between these days? No. But his contemporary group did. We need to make sure that we have large and well formed contemporary groups. Contemporary groups are formed using breeder, year, age and other information. However, breeders control how contemporary groups are formed.
1. Breeders can report management groups.
Calves that are managed differently (different pastures, some being fitted for show) need to be reported as different contemporary groups.
2. Breeders can control which calves are reported.
When the bottom of the calf crop is not reported, the middle of the calf crop (contemporary group) looks like it is below average. The middle of the group looks like poor performers, because the poor performers weren't reported!

"We get excited about this new model and this new test. What we need to do is make sure we collect clean data." says Genho. We need to make sure that we are reporting complete, clean data.

We can remodel a house with a hammer, hand saw, and screwdriver. Or, we can remodel a house with a circular saw, pneumatic air gun, and electric driver. We can remodel the house much quicker with modern tools. It is still important to be a good breeder. The more powerful tools mean we need to be better breeders.

Decker's Take Home:
Trust EPDs and use them. And, just as important, turn in clean and complete data.