Thursday, June 29, 2017

Thompson Research Center Field Day Announced

The Thompson Research Field Day will be Thursday, September 21, 2017. This year we will be having an evening program, hopefully to better accommodate more people's schedules.
See the flyer below for program details. Dinner will be provided.

Wednesday, June 7, 2017

Show-Me-Select heifer sales end with highest prices at Palmyra


PALMYRA, Mo. – The fourth and final spring Show-Me-Select heifer sale topped the average price of all at $1,928.
“Buyers were light, but bidders came to buy heifers,” said Daniel Mallory, University of Missouri Extension livestock specialist, New London.
He noted that many new buyers came from northern Missouri and Iowa. Consignors were mostly longtime members of the MU Show-Me-Select Replacement Heifer Program.
“That shows the quality of the program,” Mallory said. “Farmers see the added value built for the past 21 years.”
The Palmyra sale sold 120 heifers from 12 consignors. They went to 16 buyers.
The top price was $2,550 at F&T Livestock Market, June 3. That was for a single black-baldy heifer from Richards Farm, Keytesville. She was a Tier Two, AI-bred.
Price averages for the other sales: Farmington, $1,813; Fruitland, $1,764; Joplin, $1,714. Tops at the first two sales were $2,500 per head. The top at Joplin was $3,200. Those were for a new class of SMS heifers called Show-Me-Plus. Those heifers were tested with a genomic prediction panel.
Increasingly, bigger premiums are paid for heifers with advanced genetics. The Tier Two heifers bred AI now bring a $400 average premium over Tier One heifers bred to bulls.
All who consign take part in a yearlong education program from the University of Missouri, Columbia. The program teaches management as well as genetics. Producers learn the value of ultrasound pregnancy checks soon after breeding season.
Pre-breeding exams help cull heifers that may not work as replacements.
Growing popularity goes to timed artificial insemination. That allows picking from the top proven sires in a breed. With timed AI, all cows are bred in one day. That brings a uniform calf crop in age and size. Those sell for more to feedlot buyers.
The spring sales offer heifers bred to calve in the fall.
Weather affected sale attendance more than usual this year. The southeastern Missouri sale met heavy flooding in the area. The southwestern Missouri sale conflicted with an F1 tornado.
Weather hit the Palmyra sale. Many potential bidders stayed home to plant soybeans or finish delayed haying. Wet weather early delayed farm work. With a good day, many stayed home to work.
Fall sales will have bred heifers for next spring’s calving.
The idea of Show-Me-Select was brought to Missouri by David Patterson, MU Extension beef specialist. The work with heifers built on earlier MU work on production testing of bulls.
Only heifers enrolled in the program can wear the trademark SMS logo ear tag.
Heifers are checked on arrival at the sale barn by graders from the Missouri Department of Agriculture. This assures they meet standards.
Fall sale dates will be at agebb.missouri.edu/select. Sale summaries are posted now.
Producers can enroll their herds through their regional MU Extension livestock specialist. Contact can be made at local extension centers.
 

For more than 100 years, University of Missouri Extension has extended university-based knowledge beyond the campus into all counties of the state. In doing so, extension has strengthened families, businesses and communities.


MU Extension news: extension.missouri.edu/news | News feed: extension.missouri.edu/news/feed

Tuesday, June 6, 2017

BIF 2017: Evaluating Sustained Cow Production: Alternative Definitions of Stayability

Guest post by Tamar Crum, University of Missouri


Scott Speidel
Colorado State University

The concept of stayability was developed ~23 years ago. Stayability is simply, generally, the survivability to a certain age given the opportunity to reach that age.

Multi-breed stayability analyses are difficult because of different definitions of stayability.

  • Is the female present in the herd at 6 years old? (basic/generic definition)
  • Did she wean a calf at 6 years old?
  • Did she wean a calf at 6 years old while also calving at 2 years of age?
  • Did she calve 5 consecutive times within the same calving season?

Successful females for stayability varies depending on which of the definitions of stayability the breed association has adopted.

It is shown that stayability to 6 years of age is a heritable trait.

Stayability is a HUGE driver of herd profitability and accounts for 53-77% of the value of of the maternal indices.

Currently, stayability is recorded as a binary trait. This means that a '1' means that the animal is successful at staying in the herd past 6 years of age and a '0' means the animal was not successfully in the herd at 6 years old.


In the traditional model for evaluation of stayability the following un-successful females would have been equivalent under the basic definition of stayability.
0 = Did not calve in that year
1 = Calves in that year
- = No data


Year of Age 2 3 4 5 6
Unsuccessful Female #1
1
0
-
-
0
Unsuccessful Female #2
1
1
1
0
0

Unsuccessful female #1 calved at 2 years of age, did not calve at age 3, and was subsequently removed from the herd. She earns a stayability score of '0' at year 6 for not successfully being present in the herd at 6 years old.

Unsuccessful female #2 calved at 2, 3, and 4 years of age but did not calve in year 5 so was subsequently removed from the herd. She, too, earns a stayability score of '0' at year 6 for not being present in the herd at that point.

Which female is clearly more valuable? The problem with the traditional model of stayability does not take this into account and considers both females equivalent when it comes to stayability.

Phenotypic data records for stayability causes quite a bit of time lag. A bull will be at least 7 years of age before stayability data is able to be recorded. Daughters of the sire have to reach 6 years of age to be considered successful for stayability.

New models for the evaluation of stayability, using a random regression model, allows us to account for these differences in value of females.

While females might not meet the criteria or definition of stayability at year 6, their value and performance in years prior is still considered in the new model.

Monday, June 5, 2017

BIF 2017: Field Testing $BEEF in Purebred Cattle

Guest post by Tamar Crum, University of Missouri


Tom Brink
Red Angus Association of America

Fitting that the Georgia peach is in the logo for this year’s BIF, as we have learned throughout the conference that the industry has been provided with many types of “fruit” to choose form when it comes to our technology and genetic tools.

Do EPDs work?  Are you a skeptic? If so, you are not alone! Believe it or not there are still skeptics out there.

Numerous studies have been completed on carcass traits, milk, and weaning weight EPDs in the late 1990s and 2000s.  After that period, the research coming out proving EPDs worth got a little sparse.  Why? We convinced ourselves and our scientists that EPDs work, but skeptics remained in the industry.  They wanted to belief in EPDs but still need to see more.

This study was in conducted in conjunction with Gardiner Angus Ranch, Zoetis, and Top Dollar Angus. The field test wanted to make comparisons between high end $BEEF and low end $BEEF indices and demonstrate in a real-life setting that EPDs and indices work.  All to prove that high value cattle could be created!

High $BEEF animals and low $BEEF purebred Angus embryos were implanted.  The calves were born between April 8 - May 22.  They were pastured with their dams through weaning and then put on wheat pasture and supplemented with grower ration until early June.  They were then moved to a feedlot setting and placed on feed.  There was a targeted equal fat endpoint - without consideration for age or day on feed.  Study contained a total of 43 head.

The results were High $BEEF outperformed low $BEEF counterparts in EVERY metric evaluated!  

The predicted pedigree difference was $93.69 between the two groups.  Since the individual was being evaluated and not the progeny, the EPD values were multiplied by 2. 

The predicted difference per individual between high $BEEF and low $BEEF was $187.38.
The value observed between the two groups was $215.47!

Feeding to same fat endpoint high $BEEF cattle finished significantly quicker.  This means money saved in feed, equipment, yardage, etc.  They also had significantly heavier carcasses, were better marbled, and had more muscle but with no statistical difference in backfat compared to the low $BEEF individuals.

$BEEF worked extremely well in projecting real-world value differences in purebred Angus cattle.

Results suggest that, if anything, EPDs and mathematical calculations that drive $BEEF are conservative compared to current cattle market valuations.  Actual value will always be a bit larger than the predicted!

Take-home Message: 
Use EPDs and indexes because they work very well in creating real-world performance and financial advantages. 



Friday, June 2, 2017

BIF 2017: Making the most of genetic selection in a challenging environment

John Genho
Livestock Genetic Services

In challenging environments, we need to use heterosis. We need cross-bred cows in these challenging environments.

Deseret Ranches
Deseret Ranches uses three different herds. They have a Simbrah sired cowherd, Brangus sired cowherd, and a Deseret Red sired cowherd. A Deseret Red is 3/8th Red Poll, 3/8th South Devon, and 1/4 Brahman. The Simbrah sired cows are breed by Brangus bulls, the Brangus sired cows are mated to Deseret Red bulls, and Deseret Red sired cows are mated to Simbrah bulls.

King Ranch
The Santa Gertrudis breed was developed at King Ranch 90 years ago. They have a seedstock Santa Gertrudis herd where they perform selection with an internal EPD system. They then have a multiplier herd where they make Red Angus x Santa Gertrudis F1 bulls. These bulls are then used in the commercial herd. Replacement females are developed from the commercial herd. They have Heifer Pregnancy EPD and Breed Back EPD from their internal EPD evaluation.

Eldon Farms, Virginia
Kentucky 31 based forage, so they deal with the stress of fescue toxicosis.
Their breeding objective is average daily gain on fescue forage. They develop bulls on fescue over the winter. These bulls do not look good in the spring. As the fescue starts to grow in the spring, some of the bulls snap out of it over the summer. They shed their wooly coats and look good. Other bulls never snap out of it and are culled.

BIF 2017: Factors affecting feedlot profitability

Gary Fike
Tri County Steer Carcass Futurity Cooperative

The Tri County Steer Carcass Futurity Cooperative first helps producers collect growth and carcass data. They help them benchmark their cattle related to the industry. It is hoped that this information will be used to make genetic improvement. The cooperative also works to help encourage and educate about retained ownership in the beef industry.

It all comes down to profit.

From an analysis of 25 states, the most profitable group make $216 per head, the least profitable group lost $120 per head. Out of 6 groups, the 4th and 5th groups basically broke even.

What are the big things that drive whether or not a consignment of cattle was profitable?
The least profitable group came in as the heaviest group. The most profitable cattle cost the least as feeders (bought cheap and sold high). The most profitable group had the fastest growth rates and were heaviest at slaughter. The most profitable cattle gained well during the warm-up period. The most profitable group also had the highest average daily gain over the test period. The most profitable cattle had the least expensive cost of gain, this includes health treatments and yardage.

Older calves are healthier in the feedlot. One of the best ways to do this is to have calves that are more similar in age. [Estrus synchronization!]

Cattle that are treated twice were less likely to grade Choice or qualify for CAB. Cattle that were treated twice lost between $200 to $365 per head. "I don't know if you'll agree with me, but that is a big chunk of money," Fike said.

Meat tenderness was also better for those cattle that were never treated for illness.

.


BIF 2017: Investing in the future, heifer development for longevity

Justin Rhinehart
University of Tennessee

A step-by-step guide for heifer development:

  • Breed early in the first breeding season
  • Minimize calving difficulties
  • Wean acceptable calves
  • Breed early in the second breeding season
  • Optimize profit
  • Improve genetics

In our nutritional development, we can have steady growth, fast early growth then plateau, slow early growth and fast late growth.

We can develop heifers to a lower target weight and still get good pregnancy weights.

If we have range development vs feedlot development of heifers, we see higher pregnancy rates in the range developed heifers. The range developed heifers also stay in the herd longer.

One month before breeding season, reproductive tract scores heifers and cull heifers that have not reached sexual maturity. Estrus synchronization is also a great tool for jump starting heifers using the progesterone in a CIDR.

With a limited approach to heifer development, using estrus synchronization is very important. It will aid those heifers to be successful.

To have a great cross breeding scenario, it is easiest to buy cross-bred heifers and breed them to a terminal approach. From a systems perspective, this is an optimal approach. We can learn from crop or other livestock production in terms of utilizing hybrid vigor.


BIF 2017: The Power of Index Based Selection

Donnell Brown
R. A. Brown Ranch

Darrh Bullock
University of Kentucky

Larry Keenan
Red Angus

In the history of selection, we used used visual appearance and local adaptation to create some breed creation. We then moved to actual performance. We started weighing and measuring cattle. Then scientist used statistics to analyze this data and produce sire summaries and EPDs. We have now added genomics to this process. Prior to the release of Milk EPD there was no change in milking ability in Angus cattle.

We started with visual appraisal. We then did visual + actual weights, visual + adjusted weights, visual + EPDs, visual + EPDs for economically relevant traits, and visual + GE-EPDs. Now, we need to move to visual + economic selection indexes.

Don't overload producers with too much information!

We don't need to be double reporting data. Genomics goes into GE-EPDs; no need to publish genomic percentiles. Indexes simplify the information we present to commercial producers.

Prior to the release of Hereford's  BMI index, there was improvement for maternal profit. After the release fo the BMI index, genetic progress was even more rapid.

There was a field-test for $B. They breed two sets of steers. One from a low $B group of bulls and a second from a high $B group of bulls. The value difference predicted from the index was $187. The actual profit differences were greater than $200.

There are terminal, weaning/replacement indexes, and overall indexes.
The industry needs to improve terminal indexes. It is important that we have calving ease direct and feed intake need to be included in these indexes.

There are a small number of weaning/replacement female indexes. These are lacking calving ease maternal. Further we need further improvement in fertility and maintenance EPDs.

There are lots of all-purpose indexes. These carry it all the way through. From conception through slaughter.
Most of these indexes contain a measure of fertility. However, sometimes the EPDs used for fertility are indicators of fertility, and not direct measures of the economically relevant traits. We also need to work on adding feed efficiency to these all-purpose indexes.

Indexes work.

But, there are some keys to successful implementation, which include:
Develop a breeding objective

  • Management
  • Marketing
  • Environment

We need to identify selection index that most closely matches your breeding objectives.

The correlation between $W and $B in Angus is about 50%.

Darrh identified an outlier bull that had a -2 dollar $W and 170 dollar $B.

Don't make the mistake of sitting on the sidelines if the selection index scenario doesn't perfectly match your operation.

Red Angus was one of the last breed associations to adopt selection indexes. Keenan encourages the audience to learn from Red Angus' mistake. Again, don't sit on the side-line.

Do not panic if market values change, selection indexes are very robust.

Herd Builder is Red Angus' all-purpose index. If you look at HB vs HB without CED the correlation between the two is 0.97. If you compare HB vs HB witouth WW or ADG the correlation is 0.93. If you compare HB vs HB without Carcass the correlation is 0.99. If you compare HB vs HB without  Carcass of Feedyard, the correlation is 0.89. However, if you remove Stayability from HB, the correlation is only 0.74. This highlights the importance of stayability for profit.

Realize that some traits in an index have thresholds or optimum is not maximum.

What does the future hold for indexes?
Increased number of ERTs
Increased number of selection indices targeted to specific production systems
Improved genetic evaluations due to improved genomics technology and inclusion of commerical data
Multi-breed indices

Take home messages:
Selection indices are simple to use
Facilitate genetic improvement in profitability
Available for major production/marketing systems

Know what is under the hood.
What traits are included?
Is calving ease acceptable for my intended use?
Do I need to select for or monitor additional traits?

Selection indices are robust to economic changes. Use indexes!

Thursday, June 1, 2017

BIF 2017: Genetics of reproduction project

Alison Van Eenennaam
UC-Davis

The grant dubbed the "heifer fertility project" is really looking for embryonic lethal variants. These are DNA variants that if an embryo inherits two copies of the variant, that embryo is aborted. The DNA variant breaks a gene. If an animal inherits two copies, it can't live.

The project sequenced the entire genome of hundreds of cattle. This is not genotyping thousands of DNA variants, it is looking at all 2.6 billion base pairs of the genome. From sequencing these bulls, the team identified millions of DNA variants. They selected 200,000 of these DNA variants that are predicted to affect proteins encoded by genes to build a new SNP chip. This chip is called the GGP-F250.

They then genotyped 17,000 cattle with the GGP-F250 chip. Taylor then looked for DNA variants for which there are not observed in two copies. If a DNA variant is at high frequency, but is never seen as two copies, then we have evidence that this is a lethal DNA variant. There appears to be hundreds of these lethal variants in Angus cattle.

Van Eenannaam is working on the producer applications from this grant. If there are lots of DNA variants responsible for embryonic loss, we will have to strategically manage them. If we don't use animals that carry embryonic lethal variants, we will basically be practicing single trait selection. If you haven't heard, single trait selection is bad!

What is important is to never mate a carrier to another carrier of the same lethal variant. Mate selection tools allow us to do this in a sophisticated way.

For more information, see http://beefreproduction.org/.


MateSel is a software program for mate selection. MateSel works to increase genetic merit while limiting inbreeding. Van Eenannaam's graduate student showed simulations using MateSel.
There is a trade-off between never using a carrier and economic genetic progress.

BIF 2017: Implications of multi-breed evaluations and across-breed EPDs for commercial cattlemen

Bruce Golden
Theta Solutions

IGS Analysis:

  • 12 breed associations
  • 12 million pedigree records
  • 10 million observation records
  • 15 different EPDs
The IGS primary goals are:
Improve accuracy
EPDs that can be compared between breeds
Weekly run
Advanced methods

In order for the data to be comparable across breeds, there has to be connectedness between pedigrees. There have to be sires that are in Simmental pedigrees that are also in Red Angus and Gelbvieh pedigrees. With all of these breeds using Angus sires to produce hybrids, there is a good possibility that there will be good linkages between breeds.

Models seem to be robust to methods used or not used to adjust for heterosis. Have to adjust for heterosis effects, as they are not additive, to effectively predict EPDs (additive effects).

Larry Kuehen
USDA-MARC

The center uses 2,200 AI matings each year that result in about 1,000 AI-sired pregnancies. 

Adjustment factors will be coming in July of these year. Factors are also published with performance breed averages.

USDA-MARC wants to get to the point where all breeds in the IGS evaluation have the same common adjustment factor to get to the Angus scale.

The group is also working towards releasing adjustment factors multiple times a year. 
They are also working towards releasing across-breed EPD factors in early spring, before bull buying season.

Joe Epperly
North American Limousin Foundation

We have ~35 million calves produced each year in the U.S. beef industry. This is kind of like a salad of different centuries. A bit of this and a bit of that. However, in the seedstock industry, we look at each individual ingredient. 

While breeds have different averages, the range in performance between breeds overlaps. 

Epperly encourages use of planned matings tools made available by breed associations.

Matt Spangler
University of Nebraska-Lincoln

Why is there a desire for EPD comparable across breeds?
This helps facilitate informed decisions by commerical cattlemen.

A multi-breed does not inherently mean that EPD are directly comparable across multiple breeds.
Direct comparisons require:
  • Pedigree ties
  • Common base adjustments
  • Common trait definitions
  • Common underlying models
  • Correct accounting for breed and heterotic effects
Additive adjustment factors from USDA-MARC are needed if:
  • Breed and heterotic effects cannot be reasonably estimated from field data due to confounding of contemporary group and breed.
  • A common base is not adopted.
  • Etc.
The goal is to have all IGS partner breeds with directly comparable breeds. This assumes that each IGS partner breeds will use, adopt, and publish IGS EPDs and not breed-specific EPDs.

Q&A
Don't compare EPDs of bulls across breeds, unless we first use the adjustment factors. You will know breeds are directly comparable when the USDA-MARC adjustment factors for the breeds are identical. 

Separate software from models. BOLT is simply software. We have to have the correct analytical models for issues to be corrected.

At the end of the day, the question is-are we ranking sires correctly? If this answer is yes with a simple model, then a complex model is not necessary.


BIF 2017: Where are we going with genomics and genetic improvement

Matt Spangler
University of Nebraska-Lincoln

Alison Van Eenennaam
University of California-Davis
 
Early DNA tests with 1 or 2 markers had little predictive ability.
As tests improved, more markers were added.
Eventually there was a switch to genomic predictions. 
Unfortunately, early on, these DNA test results were published along side adjusted phenotypes, ratios, and EPDs. 
Quantitative genetic methods solved this problem by combining the molecular breeding value (MBV) with the EPD. Two approaches were used to combine MBVs with EPDs. One approach is to fit the MBV as an indicator or correlated trait. This is similar to combining carcass records with ultrasound records. The other approach is to blend the two predicts, MBVs and EPDs, as an index. 

There are two fundamental camps for implementing single-step.
  • UGA- ssGBLUP Misztal
  • Theta Solutions/ISU - BOLT Garrick, Golden, Fernando

Before, we were trying to fit genomic prediction into established genetic prediction systems. The move to single-step is the first real redesign of genetic prediction systems. These new systems will have genomic prediction at their core.

We now have the ability to do gene editing. These methods use a molecular scissors, such as meganuclease, Zinc finger, TALENs or CRISPR/Cas9, to cut both strands of DNA. When the cell repairs this double-strand break, a new deletion or insertion can be created. Or, a new piece of DNA, a donor sequence, can be introduced into the chromosome. This can allow us to move DNA from one breed into a different breed of cattle. 

"I see genome editing as the cherry on top of the breeding sundae," Van Eenennaam said. Genome editing is not a silver bullet. It will add to, but not replace, other breeding methods. To do genome editing, we have to know the DNA variant responsible for the phenotype.

An example. We could cross Belgian Blues and Nelore to get double-muscled Nelore. Or, we can edit the Nelore myostatin gene to make it match the Belgian Blue version, and create a double-muscled Nelore. Another example is creating a polled Holstein using the Angus sequence resulting in polled cattle.

Right now, the FDA has draft guidance saying that they are going to be regulating every genome edit as a new drug. This regulatory environment will limit the use of this technology in livestock production.

A lot of people believe that high accuracy sires have more consistent progeny. This is not true. 
Mendelian sampling leads to variability in a calf crop. By chance, a calf could inherit all of a bull's favorable variants, or a calf could inherit all of a bull's unfavorable variants.

Genomic predictions have not worked across breeds. [However, watch for research from my group on this subject.]

Genomic technology is great. "The entity that fully leverages trait information will win the race. Phenotype is still king," Spangler said.

BIF 2017: What the beef industry can learn about genomics from other industries

Tom Lawlor
Holstein Association USA

Lawlor cited Jerry Taylor's article saying that Holsteins are the genomic prediction poster cows. Genotyping has increased and genetic improvement has increased in the dairy industry.

But, not everyone is happy. From The Bullvine website:

  • "How Genomics is killing the dairy breeding industry"
  • "What the Experts Won't Tell You About The Future of the A.I. Industry"


The dairy industry has had to change their data structures and analysis methods. Everyone in the dairy industry is winning, but some breeders are winning more than others.

The Holstein breed is rapidly turning over their population and seeing more profitable animals.

Genomics also allows them to look at genetic merit, inbreeding, undesirable genetic defects, and breed composition.

One in five animals are expected to be a carrier of a genetic defect causing early embryonic loss. We have to abandon our old beliefs about not using animals with genetic defects. These are at too high a frequency in the population to not use carriers. What is required is getting the information out for breeders to use. They specifically call them haplotypes, e.g. HH0, HH1, etc., is to allow marketing of these animals.

The Holstien bull Storm's best chromosome is chromosome 11 inherited from his dam. However, this chromosome 11 also carries the Haplotype associated with Cholesterol Deficiency (HCD). Breeders still need to use this bull, but they need to work to create descendants that don't carry HCD.

Holstein breeders are doing this! They are much more likely to breed a non-carrier cow to a carrier bull. They are working to blend the best genetics while also systematic and methodically removing genetic defects.

In the German Holstein industry, in 2011 10% of their matings used genomic bulls (young bulls with genomics). By 2015 that percentage was up to 30%.

S-S-I Partyrock Profit-ET has 5 generations of ancestors that have been genotyped. Very aggressive use of the technology to make improvement.

Breeders were looking across the world for the best genetics. But, with genomics, there is more emphasis on developing the best genetics in the world. Top sires now have most of their ancestors being owned and breed by a single farm. The best Holstein genetics are now coming almost exclusively from the United States.

Registration of offspring of the bulls from companies with an aggressive genomic program increased 16%. These companies have great market share. Companies are doing this by controlling access to their top genetics. They have pre-release semen, early access to the top young bulls is being limited to a "select group". If a bull is born from one of these matings, the company has first right to this bull. Once the bull is released, most of the semen sold is for female selected sex-sorted semen. This is great for commercial producers, because then can make sure they have the best females.

This is also used as a limitation of competitors access to a company's best genetics. However, this has not been effective, as a bull's top son's often come after the pre-release period is over.

There are also "Free Agents". These are bulls with high genomic profiles, but no contract on that bull.

AI stud ownership of female genetics is now common.

The dairy industry has seen growth of large National Genetic Evaluations, there has been a move away from the Interbull model of "pooling data".  If you contribute phenotypic data, you pay $15 for a genomic evaluation of a bull calf. If you are not contributing phenotypic data, you pay $150 for a genomic evaluation of a bull calf. Typically for AI service the fee is $575. If it comes from a third party, the cost is $1200.

Only the best cows have been DNA tested for genomic-enhanced predictions. This can cause a bias in the prediction. Single-step removes the bias that comes from only the best cows being genotyped.

How do you invert a matrix that is 760,000 by 760,000? You don't. You use the APY method. This method selects a core group of animals, say 15,000 animals. You invert this 15,000 by 15,000 matrix and use it in a recursive method.

The United States needed a commercial entity to do genetic evaluations. Genetic predictions moved from the USDA to CDCB.

There has also lead to fragmentation of genetic evaluations. Zoetis, ABS Global, GENEX, and CDCB all have separate evaluations for health traits.

The big take home from Holstein genotyping, is not that they have done a lot, but that each year the rate of genotyping increases. This also allows an extra boost in improving the lowest heritable traits.

Lawlor sees a renaissance period in dairy breeding. There has been great improvement in health and other hard to measure traits.

The competition between breeds has increased. Holsteins and Jerseys have a stable outlook into the future. Other breeds may struggle to stay relevant. Do not be a beef breed that does not have a genomic evaluation!

Genomics also allows us to check breed ancestry. A top Jersey bull, FARIA BROTHERS RAWLS {2} was identified as 20% Holstein. Most of the top Jersey bulls have Holstein genetics 3 to 5 generations back.

With genomics, the dairy industry sees a larger gap between progressive and less progressive herds. Progressive herds are widening the gap.

The phrase used to be genetics program. The phrase is now "genomics program". Sire selection is key to this! Advanced reproductive technology, such as IVF, is essential to a genomics program. They are seeing on-farm IVF facilities and use of beef semen on bottom tier of dairy cows.

A cow's ability to make eggs for embryo transfer is now a trait of interest.

There is no set practice for the use of genomic testing in large herds, varies between 0 to 100%.

Imputation is very important.

They can identify differences between bulls that have consistent progeny and bulls that have more variable progeny. Consistent progeny is desirable in a commercial setting. More variable progeny is desirable in a seedstock setting in which you are striving for genetic improvement.

BIF 2017: The Promise of Genomics for Beef Improvement

Daniela Lourenco
The University of Georgia

Before genomics, we were fairly happy with genetic prediction. Traditional evaluation combined pedigree, individual performance and progeny information. This was equal to summing all of an animal's genetics effects and dividing by 2.

SNPs are used as markers for genes, or regions of the genome that impact production. The color of a banana peel (green vs. yellow) is a marker for banana ripeness. SNP markers are used in the same way.

Marker assisted selection did not work. Why? Most traits are polygenic, meaning they are controlled by hundreds or thousands of genes. Trying to predict quantitative traits with a small number of DNA markers doesn't work well.

What is 100,000 times cheaper now than in 2001?
Airline flights are 2 times cheaper.
Computers are 5 times cheaper.
DNA sequencing is 100,000 times cheaper now than in 2001.

A Holstein bull named Freddy was the best bull according to genomic predictions in 2009. In 2012, when trait records on his daughters came in, he was still the best bull.

Genomic information is simply an extra source of information about an animal.
This information can either be used to predict genomic merit and use this prediction as an indicator or correlated trait in EPD prediction. This is called multi-step genomic prediction.

Another method is to use the genomic information to measure genetic similarity between animals.

There are two software implementations of single-step genomic prediction, Georgia's software and Bolt's software. Which software should be use?

One of the ways to improve genomic predictions is to have additional animals.
The US Holstein association has 1.6 million genotyped animals.

Increasing the number of DNA markers, 50,000 vs 500,000, we only see a 2% improvement in genomic predictions.

There are small gains with more SNPs. This does not help to improve relationship measurements, because 50,000 DNA markers is already enough. Further, with limited trait information (phenotype records), adding additional markers simply divides the pie into smaller slices.

Genomics does allow us to select animals at an earlier age. The genomic information has the same effect as more progeny information. This allows us to shorten the generation interval. This allows more rapid genetic improvement.

There is no magic here. Phenotypes are still essential. Only using genomic information is like running up a credit card bill with out earning cash. Phenotypes are the cash that keeps the system solvent.

More information always equals higher accuracy. Genomic-enhanced EPDs, which combine pedigree, performance and genomics, is more accurate than genomic predictions alone.

Before 2015, the max load for UGA's software was 150,000 animals. Their new APY method allows millions of genotyped animals.
Single-step with APY has been used by American Angus, Zoetis Holsteins, and US Holsteins.

"Keep genotyping and phenotyping if you want more reliable GE-EPDs," Lourenco said.

There is another parameter in genetic evaluation, which Lourenco calls delta. Delta is the trust in the genetic advisor. If there is no trust in the genetic adviser (delta = 0), then there is no genetic improvement. If there is great trust in the genetic adviser (delta = 1), then genetic improvement can be maximized.

When PIC switched to genomic prediction in 2013, their rate of genetic improvement increased 35%.

Wednesday, May 31, 2017

BIF 2017: Economic Impact of Estrus Synchronization and Artificial Insemination

Justin Rhinehart, standing in for Les Anderson
University of Kentucky
University of Tennessee

Why don't more producers use estrus synchronization and AI?

Labor/Time
39%
Cost 17%
Too Complicated 17%
Lack of facilities 11%
Other 14%
Does not work 2%

The cost per pregnancy for a bull costs between $60 and $75 depending on pregnancy rate. The cost per pregnancy is approximately similar between AI and natural service, if calculated on an equivalent production basis.

Estrus synchronization and AI improve profitability. Study looked at 1,197 cows from 8 herds. 

Herds that used fixed time-AI saw a higher weaning percentage, shorter days to calving, greater weaning weight per cows exposed, resulting in AI herds being $49 more profitable per calf. 

The greatest benefits of AI are realized after multiple generations. Part of this is improved genetic merit of cow herd from picking replacements from AI sired heifers.

Goal was to increase pounds of calf weaned per pound of cow exposed. In two herds used in long term demonstration project, cows were large, breeding season was long, and operation efficiency was low.

Over 9 years of fixed time AI, cow weights decreased from 1550 pounds to 1350 pounds. However, due to the use of selection of sires, weaning weights increased from 450 to 550 pounds. Pounds weaned per cow exposed increased from 340 pounds to 440 pounds. 

Estrus synchronization and AI is profitable in both the short and long term. Returns are greatly increased if producers take advantage of added value of their product.

Decker Take Home Message:
We have heard several times, including at BIF, that weaning weights are not increasing in the beef industry. This demonstration project clearly shows that wean things are done the right way (artificial insemination, use of EPDs for sire selection) we do see improving efficiency in terms of cows weights and weaning weights. Genetic selection works! Access to better bulls through AI works!

BIF 2017: The Show-Me-Select Replacement Heifer Program

David Patterson
University of Missouri

What are the challenges facing the beef industry?

  • Reluctance to adopt new technology
  • Aging producer population
  • Rising input costs
  • Declining markets
  • Increasing global competition
  • Perceived lack of incentives


However, we have several opportunities, including on-the-shelf technology not being used (that works!), increasing domestic and global demand for high-quality beef, and marketing incentives that will add value.

In the U.S., we have 69% of beef farms as secondary income, 50% using a defined breeding season, and 10 to 15% using artificial insemination (AI).

Since 1996, the Show-Me-Select program has contributed great than $120 million to the Missouri economy. Over 32,000 heifers have sold through the program. Many more have stayed on the farm.

In 1998, heifers averaged $767 in Show-Me-Select sales. In 2014, they averaged $2,944. In 2015 heifers averaged  $2,242. Base-line heifers sold through the program sell for $200 more than national averages.

The Extension and Land Grant System were founded to use and apply research based knowledge in agriculture production. The Show-Me-Select Heifer program has been a great resource to obtain funding and achieve successful research projects.

CSS certified semen has a large impact on pregnancy rates in a timed AI protocol. Herds that did not use CSS semen had lower pregnancy rates.

Through the program, they have seen increased use of ultrasound pregnancy diagnosis. This allows to tell which pregnancies are AI bred and which are natural service.

Carrying an AI pregnancy added $184 premium to heifers. Having the sire identified (Tier II heifer) added $68. Having a Tier II heifer (sired by high accuracy AI sire) and carrying an AI pregnancy adds about $400.

"Take a breath and don't stop doing these things when the market drops," Patterson said. These practices added equity into your cowherd.

In 2015, a new designation was added for heifers, Show-Me-Plus. A Show-Me-Plus heifer is a heifer with a genomic prediction. We predict that this adds a $200 premium to heifers in the sale.

From the Thompson Research Center herd, steers who graded Prime earned $169 more dollars than steers that qualified for CAB, and 286 more dollars than steers that graded Choice.

In 2010, 68% of the heifers in the Show-Me-Select program were artificially inseminated at least one time. In 2016, 91% of the heifers were AI'ed at least one time. This rate of adoption is much higher than industry average.

The heifers are managed with a health program. Further, all heifers are evaluated for a Reproductive Tract Score. A Reproductive Tract Score measures whether or not heifers are pre-pubertal. Heifers with a RTS of 1 only get bred 6% of the time. Heifers with a RTS of 2 have a 29% AI pregnancy rate. Heifers with RTS of 3, 4, and 5 have AI pregnancy rates of 48, 51, and 52%, respectively.

Heifers on an MGA protocal that were non-cycling had an AI pregnancy rate of 35%. Heifers on a 14-Day CIDR protocol that were non-cycling had an AI pregnancy rate of 47%.

Patterson made the point that the beef industry needs more and better reproductive data. Open vs pregnant is not enough. Reproductive tract scores and precise pregnancy dates from ultrasound aid in evaluating reproductive success.

Monday, May 29, 2017

Respond to Survey, Be Entered To Win $100!

We are conducting a survey looking at the attitudes and beliefs regarding genetics and technology in the beef industry.

Five survey participants will be randomly selected to receive a $100 Visa gift card.

Click on the link below to see study information and fill out the survey:

Survey is available until June 16th, 2017.




BIF Is Coming



Watch the blog Wednesday, Thursday and Friday of this week for coverage from the Beef Improvement Federation Symposium in Athens, Georgia. For those of you who have followed in the past, that means there will be LOTS of posts this week!
Also, Thursday afternoon, June 1, I will be speaking during the Advancements in Producer Applications breakout session.
You can also follow the conference using the #BIF17 hashtag on Twitter.

Also, a big THANK YOU to the American Simmental-Simbrah Foundation for helping fund four MU graduate students' attendance at BIF. If you are at BIF, please say introduce yourself to Harly Durbin, Sara Nilson, Tamar Crum and Troy Rowan.

Monday, May 15, 2017

Angus Single-Step Has Launch Date

Angus Genetics Inc will switch to single-step genomic prediction on July 7th.

Since 2010 they have been using multi-step genomic prediction. In multi-step, genomic predictions are treated as correlated traits to produce GE-EPDs. In single-step, all genomic, pedigree, and performance data is analyzed in one model. The key to calculating EPDs is measuring genetic similarity. Traditional EPDs used pedigree data to estimate genetic similarity. In single-step, genomic data more accurately measures relatedness, i.e. genetic similarity. The pedigree and genomic relationship measures are combined.

Since November, AGI has evaluated multi-step vs single-step. They have seen very similar accuracies between the two methods. But, single-step tends to have slightly higher accuracies. Further, there are several advantages to single-step. These advantages include removing the need to recalibrate and using all of the data simultaneously.

Watch for further information from Angus about the switch to single-step as July 7th approaches.

Friday, May 12, 2017

Hair Shedding Update and Reminders


It is the time of year to once again record and report hair shedding scores. This fact sheet on eBEEF.org should come in handy.

Participants in our hair shedding genomic research project should have received an email from Harly Durbin. This email contained an Excel file to report hair shedding scores on enrolled cattle. If not, please get in touch with us as soon as possible. We must receive 2017 data in these Excel files!

It is important that we receive data on our target goal of 8,000 cattle. If your cattle are enrolled in the research program, we should have received DNA cards and 2016 data from you by now. If we have not yet received your data, you are in danger of being removed from the program. If we have not received your data, please get in touch with Harly and I by email or by phone.

We know receiving genomic-enhanced EPDs is very important to hair shedding study participants. This is also a priority to us. We have worked with breed associations and GeneSeek to make this happen.

For IGS breed associations, we are sending genotypes from Mizzou to Mahdi Saatchi, IGS’s genomic scientist. We are still working out how the data will be formatted when we send the data between Mizzou and IGS. For other breed associations, we are sending genotype data directly from GeneSeek to the breed association.

Many participants will start to receive GE-EPDs for their animals in the next few weeks.

Please be patient with us. We are not a service provider. This is our first time sharing research genotypes with breed associations. So, we are forging a new path. Please stick with us as we create tools to select more heat tolerant and sustainable cattle.

Please contact us with any questions or concerns. Or, see our FAQ page.

We appreciate your help and interest in this project!

Game Changers

by Ron Locke
R & J Ranch, Long Lane

All professions require their members to attend periodic continuation training to stay abreast of innovations in their given fields. While some may argue “Cattlemen” or Cow/Calf Producers are not professions, I strongly disagree.  For the sake of argument and space let’s assume I’m right and skip the several paragraphs of justification to that end. We cattlemen need to know how to improve our operations and that requires keeping ourselves informed.
In the past few weeks I have attended several conferences and came to the conclusion there are three “gamechangers” currently available in our industry that are being overlooked by most cattle producers and they are having a significant impact on their bottom lines day in and day out.
The first “gamechanger” is toxic fescue and its insidious drain on cattle performance from birth to death. With years of research at numerous universities and thousands of herds examined and assimilated we know every animal eating toxic K-31 fescue is being affected and more importantly we know there is no silver bullet that will prevent the toxin from lowering conception rates or reducing the weight gain loss we unknowingly experience when animals consume it. There are studies being conducted in genetics which may prove some cattle are better than others on K-31 but it is very doubtful we will find a breed that is immune to the toxin. The only certain way to rid our herds of the losses is to eliminate toxic K-31 from our pastures. The new “toxic friendly” or novel fescues have proven they will perform as well as the old K-31 in harsh conditions and cattle will not incur any of the problems consuming them. The longer you wait to eradicate your toxic fescue the more money you are leaving in the fields.
Bottom Line: You can raise conceptions rates in your herd by 15-20% and increase weight gains on all cattle by over ½ pound per day per animal! It’s impossible to justify, “it’s too costly to eradicate my toxic fescue”, when just the opposite is true.
The second “gamechanger” is fixed time artificial insemination (FTAI). In the past few years we have seen FTAI become more prevalent in the beef industry. Now with a new protocol called Split Time AI we have breeding by appointment with a reduction of drugs used and improved conception rates. Everyone understands a calf born at the beginning of the calving season weighs more than a calf born at the end of the season. At 2 pounds per day that can easily amount to over 100 pounds per calf born early over those late calves and at $1.50 a pound every calf born early puts extra dollars in your pocket. With split time AI you can see over 60% of your calves born in the first 16 days of calving season which I can personally attest to.
Bottom Line: Split Time AI will condense your calving window, significantly improve your herd genetics, and put more pounds on your calves by sale day translating to more money in your pocket!

Lastly, the third “gamechanger” is Genetic testing. Most registered herd/seed stock breeders have been using genetic testing for many years. Now we can test most all animals, providing informed expected progeny differences, (EPD’s) on our commercial cattle like registered cattle. I’ve heard countless producers tell me they can look at an animal and tell “XYZ”.  I have witnessed many of these same producers put to the test with live animals and DNA testing results proving you can’t.  You simply can’t look at an animal and tell what its next 10-20 calves will weigh at birth or at weaning or how big their ribeye’s will be or nearly anything else for that matter. But EPD’s will with certain degrees of accuracy depending on the trait. If your calves weigh 500 pounds at weaning now and you select a bull with a high weaning weight EPD your calves could easily weigh 550 at weaning next year.  If you are retaining heifers for your herd you may want to focus on heifers that score higher in calving ease maternal (CEM), heifer pregnancy (HP), milk, etc. These traits can be determined the day the heifer calf is born by simply taking a drop of blood from the ear and placing it on a “blood card” and sending it to the appropriate testing lab for your breed/crossbred of cattle. Results are normally back within 30 days, long before you need to market the animals. At weaning time you can select the best heifer calves in your herd to retain and sell the rest.
Bottom Line: For less than $50 with some basic test costing as little as $17 you can determine the value of a calf to your operation about a month after they are born.

I have some experience with each of these topics and would be glad to answer any questions you may have however for more detailed advice I encourage you to contact the specific experts listed below and incorporate these gamechangers into your operation increasing your profitability in the coming years!

Toxic Fescue: Dr. Craig Roberts,  State Forage Ext Specialist & Professor Plant Sciences University of Missouri
 Web profile

Split Time AI:  Dr. David Patterson, State Beef Reproduction Ext Specialist & Professor of Animal Science University of Missouri
Web profile

Genetics: Dr. Jared Decker, State Beef Genetics Ext Specialist & Assistant Professor University of Missouri
Web profile

Thursday, May 11, 2017

Now HIRING! Looking for talented postdoctoral fellow

My group is currently recruiting a postdoctoral fellow.

We are looking for candidates who are passionate about genetics, genomics, and research. Ideal candidates are creative, hard working (while maintaining a work/life balance), and self starters. Our group is strictly computational, so candidates should enjoy working on computers and analyzing data. Candidates should have programming experience (typically in R, Python, Perl, Julia, etc.) and be familiar with the command line. Candidates will need to demonstrate ability to write well and publish research.

We currently have access to over 48,000 genotyped beef cattle with phenotypes and breeding values from breed associations (see Decker, 2015). We are currently negotiating to obtain access to an additional 300,000 genotyped cattle. These samples are in addition to tens of thousands of animals genotyped by the University of Missouri researchers (see Google Scholar profile for examples of data sets). We also have access to whole genome sequencing data from over 2,000 cattle. So, if you like working with lots of data, come join us! Our group uses population genomics to better understand the  history of cattle breeds and to inform future selection decisions. We are interested in local genetic adaption, fertility, inbreeding, and, of course, genomic prediction. We have a large USDA-funded project focusing on local adaption in cattle. With our collaborators, we also enjoy projects looking at the evolution of quail, buffalo, and catfish.

Candidates interested in science communication and extension will also have opportunities to develop these skills.

We hope to fill the position as soon as possible, but hiring the right candidate will be the priority.

Interested candidates should contact Jared Decker, either by email, phone, or Twitter. Please include your CV and references.

As a mentor, my focus is helping you achieve your career goals. I have an open door policy and routinely touch base with my students. We have weekly joint lab meetings with Jerry Taylor's group and Bob Schnabel's group. I have an annual meeting with each mentee to discuss career plans, 5 and 10 year plans, progress, professional development goals, etc. I would be happy to put you in touch with my current graduate students so they can tell you more about my mentorship style and what working in my group is like.

Please contact me if you would like more information about this position.



The University of Missouri is an Equal Opportunity/Affirmative Action employer. To request ADA accommodations, please contact Amber Cheek, JD our Director of ADA Education and Accessibility at 573-884-7278 (V/TTY).

Wednesday, May 10, 2017

Monday, April 17, 2017

eBEEF Monday: Simple Inheritance in Beef Cattle

Managing traits controlled by simple inheritance has economic importance to many beef operations. Understanding simple inheritance can assist producers in breeding cattle that are the phenotype desired, such as polled, or avoid undesirable traits, such as lethal defects. This information sheet explains how simple inheritance works and how it can be managed.

See Fact Sheet for more information on Simple Inheritance in Beef Cattle.

Monday, April 10, 2017

eBEEF Monday: Parentage Testing

Parentage testing can be a valuable tool for both seedstock breeders and commercial producers.  This fact sheet covers how parentage testing works and tips for using parentage testing successfully. Parentage testing is often thought of as a tool that is only applicable to seedstock producers, but in fact, there are benefits to commercial producers as well. Parentage testing not only ensures correct pedigree, but can provide information to make important management decisions for commercial producers. Knowing some of the basics of parentage testing and how it works can help a producer understand the benefits of testing.

See Fact Sheet for more information about Parentage Testing.

Friday, April 7, 2017

Answering Genomic Prediction Questions

I received the following comments and questions from a beef breeder.

1. From a producer perspective I experienced the implementation of NCE [National Cattle Evaluation] from the beginning to the Genomically Enhanced phase we are experiencing.  I saw line breeders with lifetimes of work begin to outcross in order to keep up.  From the stuff I have read from Dr. Wilhelm two things stuck me.  Maybe my understanding of these is out of context but he felt one of the positives of numerical breeding was going to be the elimination of line breeding.  The second was his statement that creating some kind of index or indices with the merging the individual traits would be a mistake. ARE THE UNINTEDED CONSEQUENSES OF ELIMINATION OR DEVALUING OF LEGACY GENETICS AND LEGACY BREEDING METHODS SOMETHING TO WORRY ABOUT or conversely are the consequences of a narrowing toward what is bigger and better something to worry about?

Expected progeny differences (EPDs) from NCE are simply a tool. The breeder makes the decision about which direction to move the bell curve, either towards “bigger and better” or in the opposite direction.

The purpose of linebreeding is to increase the frequency of favorable DNA variants. EPDs accomplish this same purpose. However, linebreeding has some serious shortcomings, namely that while the frequency (and homozygosity) of favorable alleles are increased, the frequency (and homozygosity) of many unfavorable alleles are also increased. This leads to inbreeding depression, or the reduced fitness of inbred animals. The growth rates and, most costly, the fertility of linebred cattle is reduced. Linebreeding requires very strict culling, and in most cases, cattle operations cannot deal with the economic losses of such high culling levels and decreased performance. Of the more than 10 inbreeding lines started at the USDA research center in Miles City, Montana, only 1 has survived the effects of inbreeding depression. EPDs accomplish these same goals, without the negative consequences.

Selection decisions from pedigree-based EPDs typically resulted in between family selection, i.e. the same sire families were selected again and again. If left unchecked, this leads to narrowing the gene pool. However, genomic prediction allows us to practice within family selection and identify the genetic merit differences between close relatives, such as full or half siblings. If the narrowing of genetic diversity is a concern, then genomic prediction and GE-EPDs are actually a tool to help avoid losing genetic diversity (pick the best animals from many different families).

Personally, I am not concerned about the “loss” of legacy genetics. First, we have a cryopreserved genetic bank in Fort Collins, Colorado that has over 60 years of genetic material (mostly semen). Second, we have lots of genetic and phenotypic diversity available within breeds, we have tools to manage and correct consequences of the narrowing of the gene pool, and at the end of the day, we have crossbreeding to restore genetic variability.

The theory behind selection indexes is even older than that behind EPDs. Selection indexes are simply the most effective way to make progress for multiple traits. What is the most important trait? What trait should be optimized or maximized? In my mind, the answer is quite simple: Profit. Just as a weaning weight EPD describes progeny performance differences in pounds, economic selection indexes describe profit differences in dollars.

2. It is obvious I blame associations, animal science, Genomic companies for being in such a hurry to introduce this technology very little thought was given to the effects of training biases.  Was the merging of EPDs and Genomics more about getting ahead than getting it right?

“If you build it, they will come.”
– Cheesy, but applicable line from Field of Dreams

If you ask breed association leadership, all of them will attest that increased DNA testing and producing the data needed to create genomic predictions does not increase until there is a genomic-enhanced EPD available. I don’t know and won’t speculate on the psychology behind this, but time and time again, the rate of genomic testing did not increase until after a genomic-enhanced EPD was released.

Further, this question assumes that breed associations and research partners got it wrong. I can firmly reject this assumption. The scientists involved in this process were very careful and conscientious. Further, the theory behind genomic prediction has been in place since 2001. Although the method was not used in the beef industry till 2010, the idea was already 9 years old by this time.

3. I think you all have acted more like cheerleaders/salesmen than responsibly educating commercial and seed stock producers about the limitations of the technology.  This isn’t a personal you it is for everyone pushing the technology.

The stated goal of my extension program is “Communication for Rural Innovation” borrowed from the book by the same name. Encouraging technology adoption, whether that be 40-year-old EPDs or newer (but validated) genomic predictions, has been a goal of mine from the first day on the job. I do not and will not apologize for that.

Why?

Because from my vantage point, the beef industry must more fully embrace technology to remain competitive. I discuss embracing technology here, here, and here. The chicken and pork industries are vertically integrated and a small number of decision makers control the genetic selection of those production systems. These selection decisions are data-driven and scientifically based. These industries have seen significant genetic progress and profit improvement. I think one of the beauties of the beef industry is the lack of vertical integration, but I fear if there is not sufficient technology adoption, integration may become inevitable.

Further, I am a proponent of sustainability as defined by NCBA. Sustainability is increased profitability, decreased environmental impact, and improved social acceptance. In a different definition, the UN Food and Agriculture Organization (FAO) defines sustainable practices as environmentally non-degrading, technologically appropriate, economically viable, and socially acceptable. The adoption of technology, including genomic technologies, allows beef producers to keep doing what good producers have always done- raise beef in a sustainable manner. Every time we adopt technology, agriculture becomes more sustainable.

In my opinion, technology adoption is an American tradition. I am proud to encourage the survival of this tradition, but I try to help beef producers think through the decision processes required to make sure the technology matches their operation.

Does the technology have limitations? Yes it does. I discuss those in my article that appeared in the Brangus Journal, “The Dance Steps of Genomics Part I: Understanding Genomic Prediction.”  

4. Is there re evaluation- retraining and third party validation work that could be done to address some of the concerns?

Over the last 7 years, a person has been hard pressed to attend an educational event organized by a breed association that did not discuss training, retraining, and validation of genomic predictions. I have been to various presentations by Dorian Garrick, Bruce Golden, Mahdi Saatchi, Kent Anderson, Dan Moser, Ignacy Mistal and others that have discussed in detail these processes. There have been minor hiccups along the way, but these were corrected in a matter of weeks, not months or years. Further, the switch to single-step genomic prediction will better integrate pedigree and genomic data, and will remove the need to re-calibrate genomic predictions.


Taking Angus for example, employees of Zoetis have trained genomic predictions. Independently, Angus Genetics Incorportated staff have validated these predictions. In Simmental, Dorian Garrick and Bruce Golden have trained genomic predictions and Simmental staff then validate these predictions. No genomic prediction can be used, unless it is first validated. 

I realize that this blog post may not persuade the author of the questions and comments, although I hope it does. Regardless, I hope this post will inform the broader beef community. 

Additional questions or comments? Feel free to contact me

Thursday, April 6, 2017

Spring 2017 Decker Extension Evaluation Survey

I am conducting a follow up serve to the one completed last fall. I would sincerely appreciate if you would take a few minutes to complete the survey below:

Decker Extension Evaluation Spring 2017

All responses are anonymous. The survey will be open till Thursday April 20, 2017. Please one survey per person.

Don't hesitate to contact me with questions or concerns.

Friday, March 31, 2017

2017 Cattle Raisers Convention How to Create Highly-Valued Feeder Calves

Tom Brinks
CEO Red Angus Association of America

What does it take to create Valuable Feeder Cattle?

1. Starts with the right mindset.
We can have cattle that excel for both maternal and carcass traits.

2. Understand the key value attributes for cattle going through the supply chain, then breed and manage your cattle accordingly.

Cattle that stay healthy, grow and grade are winners!

If it takes more than two sentences to describe the breed make-up of your cattle, it shows that you don't have a plan for your cattle. If you don't have a plan for your cattle, you can expect to receive discounts on your cattle. If you can briefly describe your cattle, e.g. 100% Char-Angus, 100% Red Angus on Santa Gertrudis, 100% SimAngus, etc.

3. Plug in to a value-added marketing program.
You need to use some sort of value added program. These programs verify

  • Health
  • Genetics
  • Natural
  • Nutrition
  • Source


What makes your calf crop unique? What is noteworthy about your calves? Providing these to prospective buyers shows that your are serious about your cattle.

You need to be intentional about marketing your cattle.

We are very discriminating buyers when we are purchasing a bull. Unfortunately, we all too often sell our calf crops as a commodity. We need to rethink this attitude and practice.

When we create valuable cattle, we need to put a label on it so that buyers know they are valuable.

What will it take to EARN a premium from feedyards?

  • Need to document genetic superiority
  • Solid health program with vaccine history on calves
  • High growth and marbling genetics are required
  • Historical feedlot and carcass data can help
  • Load lot groups will always receive more. Are there options to partner with a neighbor? 


High genomic steers outperformed low genomic score steers for every trait, and the high genomic scoring steers were $50 more profitable.

2017 Cattle Raisers Convention Common Traits of Successful Ranches

Dr. Rick Machen
King Ranch Institute

Successful Ranches share 1 common trait, and 5 components of that trait. 
Succesful Ranches are Stewards of the Resources
  1. People 
  2. Resources 
    • Natural (soil and water, plants)
    • Animals
  3. Financial
  4. Customers


1. People
*raise
*hire
  • Integrity
  • Work ethic
  • Motivated
  • Competent

A strong work ethic is not inherent, it is learned. The younger the learner,  the stronger the ethic.
People who are successful ranchers are life long learners.
It is easy to be passionate on easy, happy days. Are we passionate on the bad days, such as the people suffering from fires in Kansas, Texas and Oklahoma?

2. Resources
How does that energy from the sun taste? Cattle convert the grass growing from the energy from the sun into high quality protein.
Good Stewarts realize they can't control how much they get, but they can manage what they have. Gracing management is huge, must have a grazing plan.
Have to manage invading species.
In Texas if you remove the juniper canopy, the native grasses come back from the existing seed bank.
They match the production of the cow to the production of the environment.
Performance Measures:
  • Conception rates
    • Cowherd
    • 2nd calf cows
    • 1st calf heifers
  • Calving ease (short season with calving ease service bulls)
  • % calves born in first 30 days
  • % calf crop weaned
  • Pounds of calf per acre

Example ranch that is very successful:
  • 97% calf crop weaned 
  • 350 day calving interval
  • $280 cow cost

Cattlemen have been practicing sustainability for decades. Matching the cow to her production environment.
Diversification will be important as we move forward. Oil, multiple species, recreation, etc.

3. Financial
Hay, supplement fee, depreciation...
Avoid fed feed costs. Has feeding hay become a habit? What can you do to reduce feeding hay?
What is your cost of production? If I make a small change here what is the revenue outcome?
Smart ranches invest wisely, save when possible, expect and prepare for the tough times.
There are certain items we need to have to operate. Too many ranches suffer from  "hardware disease", i.e. lots of equipment, trailers, and other unnecessary purchases.
Never buy what you can lease, never lease what you can borrow.

4. Customers
Have to make sure we are meeting the concerns of today's customers.

5. People (again)
Need to look at generational transfer. Involve them when they are young.
Use teamwork.
"Keep the ranch in the family and the family in the ranch. " -Donnell Brown

2017 Cattle Raisers Convention: Making the Cow Herd More Efficient by 2037

Dr. Clay Mathias
King Ranch Institute

After adjusting for inflation, there was an 18% increase in calf value from 1990 to 2015.

The big cost categories are Depreciation, Feed, and Labor. The drivers of these are corn, oil, ag land and minimum wage.

  • Corn cost increased 24%.
  • Oil increased 284%.
  • Ag land increased by 134%.
  • Labor only increased by 9%.

"Like calf prices, all of these increased more than inflation." Mathias said.

We have seen a 30 to 50 lb increase in weaning weight over the past 20 years in the seedstock sector. We have data-driven tools for selection decisions such as genomic-enhanced EPDs.

In Texas, New Mexico, and Oklahoma:
Pregnancy rate from 1993 to 1995 was 89%. In 2013 to 2015 it was 90%.
Weaning rate from 1993 to 1995 was 84%. In 2013 to 2015 it was 84%.
Weaning weight from 1993 to 1995 was 525 lbs. In 2013 to 2015 it was 525 lbs.
Pounds of calf weaned/cow exposed was 439 lbs. It was 438 lbs. in 2013 to 2015.

Identical trends are seen in the northern plains. However, this is looking at averages, and some individual ranches have seen improved performance.

Why is there no change in the commercial cow-calf level? Not limited by growth potential.
Why has reproductive performance not improved? Perhaps we have reached a maximum level.

What is more important, genetics or management?
Good genetics must be accompanied by great management.

How much improvement can we see in pregnancy rate and weaning rate? To do this in a cost effective manner, might have limited opportunity to make improvement if pregnancy rates are above 90%. If rates are below 90%, can probably make improvement in a cost effective manner.

If we look going forward, in the next 20 years we can expect the cost of oil, land, feed, and labor to all increase.

"There are opportunities going forward, we need to know how to capitalize on it," Mathias said.

A manager cannot control commodity prices, grazing land prices, compensation rate for labor, and others.

We can control labor (number of employees), feed, depreciation, technology, and genetic decisions. We need to think through these and identify the right decisions.

One of the laws of system dynamics and thinking, is that the harder we push the harder the system pushes back. An example of this could be asking each employee to work an extra hour each day. There is likely to be push back to this as employees value time with family, etc.

The greatest opportunity and leverage for cost effective performance are at the ranch level.

Crossbreeding is always high leverage. It improves fertility, calf age at weaning, calf weaning weight, and cow longevity. This is not a new concept, but remains underutilized. If you improve fertility, age at weaning, weaning weight and cow longevity you improve pounds weaned per acre.

Calving heifers can be high labor, and thus high expense.

Feeding hay is also an issue. Depreciation of equipment and storage facilities.

Labor is a high leverage factor. Can you operate your herd with one less employee?
Are the children of current employees also planning on being ranch employees? In most cases, probably not.

Where do we focus?
There is no silver bullet. Ranches are different in many ways, so there is no single answer. However, there are several factors in common.

Management should focus on high-leverage interventions at the production system level (ranch level).

  • Maintain or improve genetics of the cowherd.
  • Optimize labor, purchased feed, and depreciation to minimize unit cost of production.
  • Employ proven technology with positive ROI.
  • Marketing calves and cull cows to their highest value.


Question from the audience: Why do we see higher performance in the upper plains vs Texas?

  • They have higher quality dormant forages.
  • They have a less challenging environment, especially in terms of heat stress.
  • They have genetics with higher performance potential.


Decker's Take Home

I appreciate Mathias singing the praises of crossbreeding. However, I continue to doubt that genetic selection decisions have been optimized in the last 20 years of the beef industry. When we look at BEEF Magazine survey data, producers are using phenotypes (actual birth weight) as their top selection criteria. This indicates to me that producers are not fulling using genetic selection tools.

How can we change this?
First, if we are focusing on profit, we should be using economic selection indexes to make and drive our selection decisions. Here, we are putting all of our emphasis on profit and each trait is being incrementally changed according to its economic importance. This is the optimal way to use these selection tools.

Second, I think there are opportunities to better match the cow's genetics to her environment. We are working to create these tools.

I believe if we use these two tools (economic indexes and environment-specific genetic selection) this will allow the commercial sector to see genetic and performance improvement.

I always enjoy hearing Mathias speak because I learn more about systematic decision making focused on profitability.

Thursday, March 2, 2017

Second Youth Leadership Academy seeks applications

COLUMBIA, Mo. – Applications are being accepted for the second annual University of Missouri Division of Animal Sciences Youth Leadership Academy.
Twenty high school students with an interest in agriculture and the livestock industry will attend the May 31-June 3 event at MU’s Animal Science Research Center.
“The intensive four-day event focuses on increasing knowledge of Missouri’s diverse and dynamic livestock industry, as well as building participants’ leadership and communication skills,” says Marcia Carlson Shannon, MU Extension swine specialist.
Students receive personalized instruction and interaction with counselors, professors and livestock industry leaders. They learn leadership skills, tour leading agricultural operations and businesses, and discuss current issues regarding livestock production, Shannon says.
Applications are available at MU Extension centers in each county and from FFA advisers. MU Extension, MU Division of Animal Sciences and Friends of the MU Animal Science Youth Leadership Academy sponsor the event.
Contact MU Extension livestock specialist David Hoffman at hoffmand@missouri.edu or Shannon at carlsonm@missouri.edu for more information.