A Steak in Genomics™

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 carrier…

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.

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 TourTim 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. & noonJared 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. & noonStacey 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…

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 embryo…

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. …

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)FeedyardBrood Cow (Does she get breed every year? Does she get bred in the first 30 days? How are her daughters?)SustainabilityMaternal TraitsCrossbreeding 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 marketKnow your customerProduce a quality productAdvertise effectivelyStay current with technologyYounger 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 retireesBusines…

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 …

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 th…

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 variant…

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…

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. Th…

$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'…

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 s…

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.
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 Hawk…