A Steak in Genomics™

Larry Kuehn and Tara McDaneld
U.S. Meat Animal Research Center

Bovine Respiratory Disease may be hard to diagnosis. Have to keep in mind that prey animals, like ruminants, have evolved to hide being sick.

What are the BRDC pathogens?
Bacteria

Mannheimia HaemolyticaPasteurella multocidaMycoplasma bovisOthers
Virus

Parainfluencza-3Infectious Bovine RhinotracheitisBovine Viral DiarrheaBovine Respiratory Syncytial VirusBovine Coronnavirus (implications relatively recent)

Viruses typically aren't severe on their own, but they are often the gateway for bacteria infections to start.

Difficulty of BRDC treatment records as phenotypes
Disease incidence measured as 0 or 1
Subclinicals/shedders analyzed as healthy

How do we overcome these difficulties?
Large sample sizes are needed. USDA MARC is not using a subset of USMARC Germplasm Evaluation Program. MARC is also working to improve the quality of diagnoses/necropsy. They are also looking for indicator traits. They are collecting nasal samples …

Jeremy Howard
Smithfield Premium Genetics 

Smithfield Premium Genetics is the nucleus that provides sows (over 1 million) for Smithfield and the sires of the terminal market pigs. At Smithfield, they mate a Landrace to a Large White to produce the commercial F1 sow. These sows are then breed to a Duroc. The terminal pig then has maximal heterosis (maternal heterosis and direct heterosis). SPG uses single sire semen of Durocs to mate to commerical farms in Missouri and North Carolina. They collect 60,000 carcass data points per year.
On the maternal side, it is had to get stayability data because generations are turned over so quickly. They use commercial test herds to collect this data on sows.
Howard said that genomic information on purebred animals prior to selection allows them to better predict performance in a commercial setting. This genomic data also allows them to figure out if problematic meat is produced at a company owned farm or an outside source.

Big data is driven by volu…

Mark Trotter
Central Queensland University

His research is outcome, not technology driven. It is not finding shiny new tools and asking how can I use it. Rather, it is looking at problems in the industry and finding solutions, including technology, to help it.

Northern Australia is much more similar to central America that it is to the United States. Southern Australia is similar to the southern US.

There are several tools for stocking rate management, but there is a need to get good tools into these systems. There is now high spatial and temporal satellite data  that is now basically available for free. There are emerging radar satellite systems.

There's a lot of hype around "smart tags" and other agtech, but what's the actual need and value? There are three key bits of information producers would love to have from a sensor system:

LocationBehaviorHealth
Producers see lots of applications for smart tags.

Location
We went from big backpacks on cattle to neck collars whi…

John Genho
Neogen GeneSeek

Why do we use a crossbreeding system? To gain the advantage of heterosis, the cross outperforming the parent average. Retained heterosis is the amount of this advantage that is maintained after multiple generations of mating crossbreed animals (not mating the purebred parents).

Dominance, over dominance, and epistasis likely all contribute to heterosis.

In general, traits with higher heritabilities have lower heterosis and traits with low heritability have higher heterosis.

Why don't commercial producers use crossbreeding? The average herd size is 40 head and 9% of herds have >100 head. It is harder to implement a crossbreeding program in a smaller herd.

Researchers in Canada have developed genomic indicators of retained heterosis. They use the genomic data to infer the breed proportion of the animals. They can then square these breed proportions, add them up, and subtract from zero to estimate the retained heterosis. Another approach is to count the n…

Jeremy Taylor
University of Missouri

Taylor is going to cover several things:

GGP-F250ImputationHaplotype diversityEmbryonic Lethals

The GGP-F250 is a very unique assay compared to other SNP panels. All of the other available assays (SNP panels) use common variants. The GGP-F250 has many rare variants, most of which are located in genes or other functional elements.

Why is rare variation important? Most of the variation in mammalian genomes, including the genomes of cattle, contain rare variation. Most of the DNA differences between different individuals are rare variants. We can't tag this rare variation with the common variants included in most SNP panels. To accurately measure genetic differences (and predict EPDs), we have to account for rare variation.

Imputation is the process of:
1. Sorting DNA variants onto each chromosome (phasing)
2. Filling in missing genotypes

We can impute from 50,000 SNPs to 700,000 SNPs to 15 million variants. But, we can't do this accurately for …

Alison Van Eenennaam
UC-Davis

United States beef cattle inventory has decreased since the 1970s. However, over that same time period, we have produced more beef. This means we are more efficiently producing more beef per cow. This is very different compared to other countries such as Brazil and India.

We have seen inflection points in the genetic progress of beef production as various technologies have been adopted? Will gene editing be that next inflection point?

Gene editing technologies are simply scissors that cut DNA. There are various types, such as Zinc Finger Nucleases, TALENS, and CRISPR/Cas9. CRISPR has become very popular recently because it uses a guide RNA to make the cut at a specific location. CRISPR can make site-specific variants (mutations) as the cell repairs the double stranded breaks. CRISPR can also be used to insert new sequence from a different animal, species, or kingdom.

There are 13 papers that describe edits for 12 different traits in cattle.

Gene editing fo…

Brent Mason
Mason-Knox Ranch

Mason-Knox Ranch develops heifers to market bred heifers. They like to purchase the heifer calves back from their customers. They also like to breed heifers to producer heifer calves, because we know that heifer calves are lighter compared to bull calves. Mason also sees an opportunity to quick change a cow herd by using sex sorted semen.

Mason said, "Those who know me, know I'm a nervous nelly." The first time they did split time AI, Mason looked at all of the heifers in the hold pen and was nervous. Dave Patterson told him to eat dinner. Mason ate dinner, came back, and still very few heifers in heat. Patterson said, "Just let them be." Next morning, lots of heifers were in heat.

Mason also sees opportunity for sexed-semen in seedstock. Think about breeding that cow who always produces a great bull, to male select semen.

"There is a difference between burlap and satin," Mason quoted a friend. Mason believes in using quali…

Jordan Thomas
University of Missouri
NAAB Symposium

Why do we care about sex sorted semen?
For any on mating, one sex of calf is always more valuable. This is due to genetic potential and your marketing program.

What is the value difference?
What is the true cost of using sex sorted semen?
Does the value difference justify the cost?

In a perfect world, pregnancy rates would be identical between conventional and sex-sorted semen. But, this is not true. Further, the bull you want to use may not have sex-sorted semen available due to sorting or fertility factors. Sex-sorted semen is also very sensitive to the timing of estrus in a timed synchronization program. Lastly, sex-sorted semen is not free! There are direct costs (cost per straw of semen) and indirect cost (lower pregnancy rates, estrus detection, more complicated protocols).

Unlike the dairy industry, we have a fixed breeding season in the beef industry. If a dairy cow is not breed using sex-sorted semen, we just AI her another ti…

George Perry
South Dakota State University
NAAB Symposium

Assume that a cow breeds 30 cows per year for 4 years. Regardless of the year, bull price per calf sired was higher than the cost of semen.

We could have different bulls for different groups of cows. Bulls for heifers, bulls for maternal calves, and bulls for terminal calves. Consider breeding a calving ease bull to mature cows- you are giving up additional growth with that mating.

Sexed semen causes the differences in sexes of the calves that we would expect to see. The number of bulls and heifers in a calf crop can be skewed even if we do one round of artificial insemination followed by natural service.

Perry's groups used 6 herds with 878 cows breed to 5 different bulls. They used conventional semen and sexed semen from each bull. Gender skewed semen had a pregnancy rate of 52.4% and conventional semen had a pregnancy rate of 67%. When cows have displayed estrus (been in heat) at time of AI, pregnancy rate was 69%. Cows th…

Reprinted from the American Red Angus Magazine.

Written by Jaclyn N. Ketchum, Cliff Lamb, and Michael F. Smith, Division of Animal Sciences, University of Missouri,and Department of Animal Science, Texas A&M University
Efficiency, sustainability, productivity and profitability – these words are used in conversations around the world including among cattlemen. How do cattlemen assimilate these goals into their herd? One way is by implementing a defined breeding season.

“Heifers that conceive earlier in the breeding season will calve earlier in the calving season and have a longer interval to rebreeding. Calves born earlier in the calving season will also be older and heavier at weaning,” stated Robert Cushman of U.S. Meat Animal Research Center. He added, “Heifers that calved early in the calving season with their first calf had increased longevity and kilograms weaned, compared with heifers that calved later in the calving season.”
Increased longevity and heavier weaning weights are t…

Join the AGI team for an informative webinar on the upcoming $Value changes

What: Tune into the “$Value Changes” webinar hosted by Dr. Dan Moser, Dr. Stephen Miller and Kelli Retallick as they walk through the upcoming changes to the $Values.

When: Mark your calendar for 6 – 8 p.m. CDT on Monday, May 20, 2019.

Where:  Click below to register for the webinar. After registering, you will receive a confirmation email containing information about joining the webinar.

Don't forget, www.Angus.org/Index serves as an educational resource for all $Value update information.


Register Today!

Jared E. Decker
Associate Professor, Division of Animal Sciences, University of Missouri

Reprinted with permission from The Cattlemen and Santa Gertrudis Breeders International.

Can we be frank for a minute? It is quite simple: EPDs work. When we use EPDs to make selection decisions (which bulls to buy, which females to keep and cull), the performance of our herd improves. Let’s discuss why EPDs work, how they can be used, and pitfalls to avoid. Defining EPDEPD stands for Expected Progeny Difference. “Expected” in this context is a loaded word. We use it here the way a statistician would use it. Expected means we are describing a prediction of the future. Expected also means we are discussing an average, not a single observation. What is the average that we are predicting with EPDs? We are predicting the average progeny, or the average of an animal’s calf crop. Finally, when we are discussing EPDs we are discussing differences. Either the difference between two animals or the difference b…

Updates are based on a major research effort and will be effective this June.
The American Angus Association® Board of Directors approved changes to the $Value Indexes during the February board meeting Feb. 18-21, 2019. Updated $Value Indexes will be available this June, and changes include revisions to Beef Value ($B), updating the Weaned Calf Value ($W) model to the new Maternal Value ($Maternal) and rounding all $Values to whole dollars to eliminate decimals. Quality Grade ($QG) and Yield Grade ($YG) will be removed because $QG is redundant to the Marbling EPD, and $YG is redundant to Fat and REA EPDs. In addition, a balanced index will be implemented June 2020 with a complete education plan to be executed with the membership and industry to take place over the next 15 months. “Our current $Value Index models have served us well since 2004,” said Dan Moser, Angus Genetics Inc. president. “But since 2004, technology has improved, and new EPDs have been created. So, an extensive res…

Bob Hough recently posted the following comment on Facebook (posted with his permission):
Early in my career at a breed association, the much beloved American Angus breed executive told me that the secret to success running a breed association was to have a top junior program, keep the books straight, and make sure the numbers (EPDs) don't change. This philosophy meant Angus valued stability in their genetic predictions over keeping them up-to-date with the latest science. The Angus Association also marketed extremely effectively the infallibility of their EPDs because of the size of their database. I will start with the later. Yes, a database needs certain critical mass to make sure the animals are tied, but that can be achieved in a modest size database. After that, data quality far and away outweighs data quantity in assuring the most precise and reliable EPDs possible. On the former point, Angus breeders are simply not use to change. This is not the case in most breed associati…

Reprinted courtesy of ARSBC Newsroom

Some people just don’t trust EPDs. The acronym EPD stands for “expected progeny difference” — a numerical value that represents a prediction of the average performance, relative to a specific trait, among the progeny of a breeding animal. To aid genetic selection, EPDs are used to compare the expected performance of one sire’s calves with those of another sire’s.

“But some people are suspicious. They think someone is pulling strings to manipulate the numbers,” lamented animal geneticist Jared Decker while addressing a New Mexico gathering of cattle folk. “But EPDs work. They absolutely work.”

A researcher and assistant professor at the University of Missouri, Decker returned to his native New Mexico to speak during the Applied Reproductive Strategies in Beef Cattle Workshop hosted Aug. 29-30 in Ruidoso. He talked about the value of using EPDs to achieve genetic improvement over the long haul.


Decker discussed how EPD-aided selection can work for a …

Visit the NCBA Producer Education website to learn more.

Tim McAllister
AAFC Lethridge Research & Development Centre

Microbes are part of the natural world, they occupy all parts of the world from deep sea vents, skin, digestive tract, and our food.

The rumen is one of the most microbe rich environments in the world. We use fistulated animals to have a window into the rumen microbiome. Rather than looking at the bacteria that come out of the digestive tract, we can directly sample the rumen. The microbes in cattle rumens can even digest cotton shirts!

In cattle, the majority of digestion happens in the rumen by the microbes. So, most of the time when we are feeding our cows, we are really feeding the microbes.

Cows eat 2 to 20 kg of dry matter, 20 to 80 liters of water, and 50 to 150 liters of saliva. The microbes produce 2 to 6 kilograms of volatile fatty acids (VFA). The rumen also produces 0.75 to 2 kilograms of bacteria that go into the digestive system and can be digested.

In a roughage diet, 65% of VFA is acetate. Cattle on high co…

Robin Falkner, DVM, Zoetis

Can't manage what we don't measure...
Peter Drucker said, "If you can't measure it, you can't improve it."
But if we focus on measuring stuff that doesn't matter, much , then we are managing poorly.


Can we consume our way to success? Consumerism is the attitude of "what should I buy?"  Don't go into the trade show as a consumer, go into the trade show as a producer.

We too frequently think of a health program as a calendarized list of health practices. Just because everyone believes something doesn't mean it is right. Falkner again used his recipe analogy. We have been looking at recipes for a long time. We need to be developing better cooks.

A sound animal health program is built on a foundation of:

Managing exposures to pathogensAccess to premium markets

Let's look at the history of agriculture. Dr. Roger's researched innovation in agriculture in the late 1950s and 1960s. He looked at practices in the …

At the January 4th Show-Me-Select Board of Directors meeting, new service sire EPD requirements were approved. All sires, artificial insemination and natural service, must meet minimum Calving Ease Direct (CED) EPD requirements. In addition to yearly updates, two changes were made.

First, no Birth Weight EPD requirement will be published. All commonly used breeds now have CED EPDs available.

Second, all breeds in the International Genetic Solutions (IGS) genetic evaluation are now set to a common requirement. In the summer of 2018, breeds within the International Genetic Solutions switched to a single-step BOLT multi-breed genetic evaluation. The EPDs for animals in the IGS genetic evaluation are directly comparable across breeds.

In 2017, the Red Angus requirement for CED was a CED of 8, which represents the 30th percentile. Less than 5% percent of heifers breed to a bull with a CED EPD of 8 or larger had calving difficulty.We feel that this require is meeting the need to reduce cal…