A Steak in Genomics™

Are cattle responsible for 51% of greenhouse gas emissions? How can technology help?
Head over to the Show-Me Ag website to see Jared Decker discuss beef cattle, the environment and genetics.
https://www.kmos.org/ShowMeAg/
Episode from December 12, 2019 (2019/12/12, titled "Cattle Genetics").

The Red Angus Association of America is seeking feedback on their economic selection indexes. Producers can provide feedback at this link:
https://www.surveygizmo.com/s3/5183855/RedAngusAssociation?fbclid=IwAR3qskT1DJ6UMbSIS2R3ul316FQ6L_k-Gt_DYDq8wB8omLQOgkG1yCuAGbM

To be frank, I am conflicted by this process.

On one hand, I think it is important to have translational research be a collaborative process. Further, users are more likely to trust and use a technology if they were involved in its creation.

However, often times, optimal selection decisions are counterintuitive (need to write a blog post on this). I feel strongly that selection decisions are best made when driven by data, and that includes design of selection tools.

American Angus Association went through a similar process, and it is my understanding they used the survey data to weight economic importance of traits that are hard to pin down, such as claw set and docility. Traits that are economically important, but are some…

Youth interested in the beef industry are encouraged to compete in a national essay contest. Essays should respond to the prompt “What does it mean to be a beef breeder in the 21st century?”

The winning essay will be published in one of BEEF magazine’s online newsletters (e.g. BEEF Daily or BEEF Cow-Calf Weekly). The 2nd through 5th place essays will be published on A Steak in Genomics blog. We will award $500 for first, $300 for second, and $200 for third place in the contest. New this year, we will have two age divisions, "13 and Younger" and "14 to 19". Winners will be announced at the Mizzou Youth Livestock Judging Clinic on March 7th.

Essays will be judged by beef genetics extension specialists, breed association staff, and trade publication staff.

Essays will be judged on their ability to encourage best practices and technology adoption by describing:
Trust and effectiveness of beef breeding best practices and technologies.Simplicity of using technology.The profi…

November 21, 2019 @ 7:00 p.m. CST
During winter, many cattlemen and women utilize harvested forages and even crop residues to serve as the primary diet for their cattle when most grazing forages go dormant. However, many of these feedstuffs may not meet the dietary requirements of the animal. Join Dr. Tryon Wickersham, Texas A&M; Dr. Eric Bailey, University of Missouri; and Dr. Mary Drewnoski, University of Nebraska as they cover the importance of supplementing your herd when generally lower quality feedstuffs make up a majority of the animals diet specific to regions across the U.S.

Click to Get Registered Today!Tell your fellow producers on social media!Share

I will be hosting a webinar tomorrow night, October 24th, at 6:30 PM Central Daylight Time. We will discuss EPD basics, genomic testing, selection decisions, and considerations for using EPDs.

You can join the Zoom Meeting by clicking the link below:
https://missouri.zoom.us/j/134203468

You will need to install Zoom on your computer prior to joining the webinar.

You can also join by phone for audio.

Dial by your location +1 646 876 9923 US (New York) +1 669 900 6833 US (San Jose) Meeting ID: 134 203 468
Webinar is limited to the first 100 participants.

Participants will be able to type questions in the chat box.

Looking forward to the webinar tomorrow night!

by Ryan Boldt, Director of Breed Improvement, RAAA

Selection for carcass trait performance is important to keep in mind when making bull-purchasing decisions. Most carcass traits are moderately heritable in nature. In seedstock animals, the best method to collect information about carcass-trait performance is through the use of ultrasound imagining.

Generally, ultrasound information is collected on seedstock animals at a year of age. When an ultrasound is collected, up to four measurements are taken. The most common measurements recorded include intramuscular fat, backfat, and rib eye area which serves as the best indicators for carcass marbling score, carcass back fat and carcass ribeye area.

The ultrasound information is collected via a probe that emits high-frequency sound waves. The probe is placed on the animals back and an image is created that shows the difference between different tissues under the animal’s hide. These images are captured by a certified ultrasound technician a…

Neogen Corporation announced September 19th, 2019 that it has entered into a collaboration with International Genetic Solutions (IGS). The effort is focused on heightening genomic impact in the IGS platform, the only major multibreed beef genetic evaluation available, and at the same time greatly enhancing the research and development necessary to continue to improve Neogen’s Igenity® Beef Profile.

The Igenity Beef Profile is a leading global genetic testing product that helps producers of both straightbred and crossbred beef commercial cattle select their best animals for breeding programs. IGS delivers the most credible, objectively described, user-friendly and science-based genetic predictions to enhance the profitability of beef cattle producers who look to leverage the full power of expected progeny differences (EPDs).
“As part of this partnership, Neogen will benefit from access to information that will improve the Igenity Beef Profile, and IGS will endorse and promote the use of…

For more information, see "The Random Shuffle of Genes: Putting the E in EPD".

Great short video on the use of EPDs, including the importance of the definition of EPD.


Big shout out to Jordan Thomas for making these great videos. This one features my graduate student, Troy Rowan. Also, if you aren't following MizzouRepro on social media, you should start!

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…