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%.