Friday, December 16, 2016

Beef Genetics Education Team Announces National Essay Contest: “What does it mean to be a beef breeder in the 21st century?”

Youth participating in 4-H, FFA, or junior beef breed organizations are encouraged to compete in a national essay contest. Essays should respond to the prompt “What does it mean to be a beef breeder in the 21st century?

The winning essay will be published in one of BEEF magazine’s online newsletters (e.g. BEEF Daily or BEEF Cow-Calf Weekly). The 2nd through 5th place essays will be published on A Steak in Genomics blog. We will award $500 for first, $300 for second, and $200 for third place in the contest. The first place winner will also receive 50 GeneMax Focus or PredicGEN tests.
Essays will be judged by beef genetics extension specialists, breed association staff, and trade publication staff.

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


Essays are required to be at least 600 words long but not longer than 3,000 words. Please submit contest entries at https://missouri.qualtrics.com/SE/?SID=SV_9YwBWK2WvM7Tdsh. Entries are due February 15, 2017.


Thanks to our essay sponsors BEEF magazine, Zoetis, and GeneSeek.

This educational program and essay contest are part of the "Identifying Local Adaptation and Creating Region-Specific Genomic Predictions in Beef Cattle" funded by the USDA-NIFA, Grant No. 2016-68004-24827.

Thursday, December 1, 2016

AHA Educational Forum: AHA Creative Services

Sean Jersett, Christy Bengno, Julie Mais, Alison Marx, Caryn Vaught

Number one piece of advise for an advertiser:
Be aware of your sale dates! You need to have the deadlines for dates to go to the printer and when catalogs will be to the customers. You need to have your ducks in a row before the printing date.

How do you handle photography?
Photos need to be high resolution, print quality photos to look good in the catalog. "We need to have the photos identified so we know how to use them," Bengno said. Dropbox or email is a good way to send in the photos. Make sure that email allows for the photos to be sent as high resolution. If you have a lot of photos, Dropbox is much easier. Put the photos in Dropbox and then share the folder with the AHA staff. Make sure you notify the AHA staff that you have added photos to an existing shared photo.

When using phones, make sure your phone has a high quality camera on your phone and that you have your phone setting to the highest resolution possible (largest file size). If you don't change these settings, your phone will not take a high enough quality picture. If you have a 72 DPI photo, it will appear 4 times smaller than it should be in print.

What about breeders using Photoshop?
The Photoshop images are a great way for a producer to share their vision of the picture, but the actual Photoshop and other processing needs to be done by AHA staff to make sure that the requirements for print are meet. Send the raw photo, and the AHA staff will do the edits. Make sure that there is enough background space around the animal.

Advice for preparing an Hereford Journal ad?
Make sure that there is good communication. If the photos are not going to be ready in time, let the AHA staff know. "Too much information is often better than too little information," Marx said.

If an ad is made by a different publication, have the other organization communicate with the AHA staff to make sure the ad is prepared according to AHA specifications.


If preparing an ad, share colors that you don't like. Share items you would like to be included. Photos help a lot! Communication is key. "Some times I like a blank page, but at least tell me what you hate!" Jersett said.

What is the difference between a ride-along and other catalogs?
Figure out your target audience. If you are marketing to juniors showing heifers, including a ride along with the September issue that focuses on the Junior Nationals. If you are focusing on commercial cattlemen, printing in the tabloid publications is a great way to hit commercial ranchers.

The tabloids printed on paper are a cost savings for the AHA. If the commercial producer will fill in a card and send it back to the AHA, this allows them to send out the tabloid at no cost to the commercial producer.

How many clicks are you getting on banner ads?
Working on the back end, AHA staff can give you data on your specific banner ads.


Ag Teachers can request for a free subscription to the Hereford World. But, they need to request a new subscription each year.



Decker's Take Home Message
Progressive beef producers need to make sure they are doing a good job branding and marketing their cattle. To see a full return on investment in best practices and technology, producers need to be aggressively marketing their cattle. Working with the right creative services can really help.

Tuesday, November 29, 2016

Brangus Journal: Understanding Genomic Prediction

Head on over to the Brangus Journal website to see some of my latest writing on genomic prediction.

The Dance Steps of Genomics Part I: Understanding Genomic Prediction

Personally, it is probably my favorite of the articles I have written, so I would encourage you to make the time to read it.

What do you think of the article? As always, your feedback is welcome.

Wednesday, November 23, 2016

AHA Educational Forum: myHERD services

Stacy Sanders and SyAnn Foster
AHA

"When we do things electronically, we are no longer waiting on the postal service," said Stacy Sanders.

He also noted that electronic reporting did not require any handling or processing by the association staff.

The electronic recording also eliminates paper work and automatically uses semen certificates that have been released to the breeder.

In addition to the AHA myHERD.org service, the association also allows you to use Genetic and Economic Management (G.E.M.) and CattleMax. AHA is also working with the smart phone app CALF BOOK. "We want to give you options, we want to give you something that works for you," Sanders said.

The myHERD service is also switching to a different system to enable a faster web interface, which will also work better on smaller screens like tablets and smartphones.

AHA has a goal of 80% of records turned in electronically. Weaning and yearling data is currently above 80% reported electronically, other data points, such as registrations or payments are increasing.

When using a third party software, make sure that you are creating animals in the software, not in myHERD. Once the initial extract is made to go into the third party software, the AHA does not send data to the software. This is a one-way street of the data going from the software into the AHA system.

The easiest way to transfer animals is to make sure you get the buyers member ID. This is the best way to identify a member in myHERD. myHERD is also able to search for nonmembers that are already in the AHA database.

You can also release AI certificates to customers and to see which certificates have been released to you.

myHERD also displays information which producers you have done business with. You are able to download this list to get addresses and other contact information for your customers. This list can also be extend to 5 years. The download is a CSV file which can be easily opened in Microsoft Excel, or other spreadsheet software.

In myHERD you can also update incorrect data, see adjusted weights, and other reports. Breeders can also order DNA tests through myHERD, see the status of currently ongoing tests, and see previous DNA test results.

There is now a new button to get calf crop data. First, go to the TPR Whole Herd Reporting screen. Click on the calf crop you want to retrieve. You can then click on the "Calf Crop" button to download the data on that calf crop. This data includes data records such as weights, chute scores, dam weights, etc. This report also contains EPD and EPD accuracy data. This report will also contain any genetic defect testing.

AHA has held "School of myHERD.org" webinars. They now have 23 myHERD tutorials on the AHA website at http://hereford.org/content/schoolofmyherdtutorials. There are two ways to view myHERD tutorials.
The first method tells you step by step and tells you where on the screen to click.
Second, you can have all steps shown or printed at once.

When ordering DNA tests, it automatically shows you active animals. But, if you need to DNA test a deceased or disposed animal, you can simply click on "All Animals" to show all your animals. After selecting the animal, you click the primary reason for DNA testing the animal. You will then choose the type of test you want to use (parentage, GE-EPD, horn-polled, etc.). When doing parentage, if one of the parents does not have a DNA test on file, it will automatically create a field to order a DNA test for that parent. myHERD will also check for duplicate DNA testing, which saves the association money.

Another new feature in myHERD is to look at the status and results of previously purchased test.

Allflex tag products are now available directly from AHA. Allflex has a Tissue Sampling Unit (TSU) that will take a sample for DNA testing. These ear tags can be various combinations of visual, EID, and TSU Allflex products. The TSU sample can be kept at room temperature for a year, and if kept in a freezer can be kept indefinitely (a long time).
PI testing can also be done with TSU sample. AHA is investigating offering PI testing at the same time as DNA testing. One way to simplify DNA testing and PI testing at the same time is to collect two samples.

Thursday, November 3, 2016

Road Warrior: First Week of November Addition

This weekend I get to cross the state to visit with several producer groups.

Friday November 4th I will be speaking at 3pm at the Joplin Regional Stockyards during the Central States Beefmaster Breeders Association field day. The CSBBA will be having a performance bull sale at the Joplin Regional Stockyards the next day at 1 pm. I will be discussing the how and why of genomics.

Saturday, at 8am I will be speaking as part of the Pearls of Production Program at the University of Missouri South Farm Research Center in Columbia, MO. I will be discussing bull selection, and the South Farm herd bulls will be on display for viewing.

Saturday at 7 pm I will be speaking at the 2016 Beef Producers Seminar in Maryville, MO. The trade show will start at 2pm with demonstrations and presentations to follow.  I will be discussing genomic prediction, and we will have a live animal demonstration with a set of heifers that have commercial heifer genomic predictions.

Google says this will be 942 miles on the road for me...

Hope to see you at one of my stops this weekend!

Tuesday, November 1, 2016

Farm Management Program Addresses Tough Times and Tackles Tough Questions in Agriculture

          According to Garry L. Mathes, chair of the 2016 Missouri Livestock Symposium, producers and land owners coming to the Missouri Livestock Symposium to participate in the farm management section can expect the speaker lineup to address some of the toughest questions facing agriculture today. Mathes continues to say that the Missouri Livestock Symposium continually strives to be on the cutting edge of producer education and our Farm Management section is designed to do just that.
Dr. Scott Brown, University of Missouri ag economist, will return for the Saturday program to lead two discussions. The first talk focuses on “Land Values and Cash Rents: How Far Will They Fall” and the second talk concentrates on “Who is Winning the Agricultural Trade Game.” Dr. Brown brings many years of experience dealing with agricultural economics and farm management. Mathes notes Scott is an exceptional speaker and no one will want to miss his presentations. 
Also speaking in the Farm Management Section will be Jennifer Wood, crop insurance agent, discussing the changes and specifics of the Livestock Risk Protection Program as well as additional information on the Pasture Range and Forage insurance program.
Rounding out the Farm Management Section will be three talks on estate planning. Dr. Ron Hanson, University of Nebraska, will address the challenges farming families face when transferring farm ownership to the next generation. Dr. Hanson’s talks include “You Can Buy the Family Farm, But I Still Own It,” “Overcoming Family Challenges to Farm Succession Planning for Success,” and “Keeping Your Farm in the Family for the Next Generation-Is There a Succession Plan.” Mathes continues to say, “We are extremely excited to host Dr. Hanson at this year’s Livestock Symposium. Anyone who owns a farm or ranch will benefit greatly from hearing Dr. Hanson speak about overcoming the family challenges to ownership transfer.”
Mathes notes that there will be a lot more of interest in addition to the Farm Management program. There is a full lineup of nationally acclaimed speakers on beef cattle, horses, sheep, meat goats, stock dogs, backyard poultry and beekeeping. The Symposium also features a free trade show and two free meals—a beef supper on Friday evening at 6 p.m. and a Governor’s Style Luncheon on Saturday at noon.
            The Symposium runs from 4-10 p.m. on Friday, December 2 and 8 a.m. until 5 p.m. on Saturday, December 3. The event will be held at the William Mathew Middle School, 1515 S. Cottage Grove in Kirksville, MO. No pre-registration is needed and there is no cost to attend. Mathes notes, “if there is a better deal anywhere he wants to know about it!”
The Friday night program will also feature a keynote address by Dr. Scott Brown titled “The Financial Challenges and Opportunities Facing Missouri Agriculture.” Dr. Galen Hill of Kirksville, MO will be honored with the 2016 Missouri Livestock Person of the Year.
Additional details about speakers, topics, lodging, meals, trade show, and more can be found at the Missouri Livestock Symposium website at www.missourilivestock.com and our Facebook page; or call Garry Mathes at 660-341-6625 or the Adair County Extension Center at 660-665-9866.

            

University of Missouri Extension provides equal opportunity to all participants in extension programs and activities, and for all employees and applicants for employment on the basis of their demonstrated ability and competence without discrimination on the basis of their race, color, religion, sex, sexual orientation, national origin, age, disability, or status as a protected veteran.

Monday, October 31, 2016

eBEEF Monday: Economically Relevant Traits

Economically relevant traits (ERTs) are those that are directly associated with either a cost or a source of revenue.  Not all Expected Progeny Differences (EPDs) represent traits that are ERTs, and instead represent indicator traits. It is important for producers to know the difference between ERTs and indicator traits when making selection decisions.

For more information, see the eBEEF.org factsheet "Economically Relevant Traits."

Friday, October 28, 2016

Beefmaster Breeders United Convention: EPDs and Selection Indexes

Matt Spangler
University of Nebraska-Lincoln

In the past, the only way we made improvement was through visual appraisal.

Photo from Harlan Ritchie's Beef Review. Difference between 1835 and 1937 champion.
As the picture above shows, we can make a change, but how many of us want to wait 100 years?

Improvement can be accomplished through management and genetics.

In the past we (animal breeding scientist) have probably done a disservice to the industry by producing lots of EPDs, then dumping those in beef producers lap and then expect you all to make meaningful decisions with them. In some situations, this may be as valuable as a free cat.

There are many factors that can influence an animals record, for example a weaning weight. Weaning weight may be affected by age of the calf, age of the dam, how much it was feed, and other environmental factors.

So, we need to compare animals to their contemporaries, Contemporaries are animals of the same sex, raised at the same ranch with the same management. We can calculate a ratio of how different from the contemporary group each animal is. These ratios are helpful for making within herd selection, but it cannot be used to make selection decisions across herds. EPDs allow us to make selection decisions across herds.

What we need to be selecting on is the genetics, because this is inherited from generation and generation and allows us to make genetic progress.

Breeders often misunderstand EPD accuracy. Accuracy is not a measurement of the consistency of the calf crop. Accuracy is a measure of how certain we are of the EPD estimate. Accuracy is really a measure of the possible change we might see in that EPD. The EPD may be 40, but the 68% confidence interval might be between 35 and 45 pounds.

Consider two bulls with a weaning weight EPD of 40. The first bull has an EPD ACC of 0.3, which means a possible change 8.1 pounds. The second bull has an EPD ACC = 0.8, which means a possible change of about 2 pounds.

Another very important tool is percentile rank. If a bull is in the 25th percentile, he is better than 75% of the other bulls in the breed and worse than 24% of the bulls in the breed.

The across-breed EPD adjustment factors are a tool to compare EPDs across different breeds. By adding or subtracting by the adjustment factors.

There is no easily accessible, objective way for breeders, particularly breeders in the beef and sheep industries where ownership is diverse and production environments vary a great deal, to use these predictions [EPDs] intelligently.  -- Bourdon
This is not a question of the intelligence of beef producers. This is commentary on the difficulty of using EPDs. The solution to this is to use economic selection indexes. Profit is of course revenue minus cost. It is quite easy for us to create EPDs for revenue traits. It is harder to create EPDs for the cost side.

Seedstock producers need to discuss the customers needs. Spangler shared the experience of seedstock producers calling him up to sell him bulls to use in the University of Nebraska's cattle herd. They start telling him about the bulls in the sale he should be looking at. These breeders have not asked him about his needs. Seedstock producers need to do a better job of asking their customers about their production. What is the customer's breeding objective? When are they marketing their calves? What is their production environment like?

We need to focus on economically relevant traits, and not indicator traits. Indicator traits are important to measure, record, and report because they help us predict economically relevant traits.
Lets consider pairs of traits. Which one is the economically relevant trait?
BWT vs CE: Birth weight is an indicator of calving ease. Calving ease can cause increased labor costs and leads to problems for cattle rebreeding.
REA vs YG: Ribeye area is a component of Yield Grade. Yield grade is the trait that influences the sale price, thus is the economically relevant trait.
YWT vs CWT: This comparison depends on when cattle are sold. But, for the overall industry, Carcass Weight is the economically relevant trait.
MWT vs DMI: Mature weight is an indicator of the dry matter intake of the cow. The dry matter intake is the economically relevant trait.
RFI vs FI: No one gets paid for residuals. You have to pay the entire feed bill. Feed intake, not residual feed intake, is the economically relevant trait.

There are different traits that are important depending on the production sector of the industry. If you are selecting for cattle

There are three methods for selecting for multiple traits.
First is tandem selection. In this strategy we select for birth weight till it reaches an appropriate level. Then we select for weaning weight. The problem with this strategy is that when we select for increase weaning weight we loose ground on the progress we made for birth weight (birth weight goes up), because the two traits are correlated. This is a very inefficient selection strategy!

Independent culling levels. In this method, you set minimum levels for birth weight, weaning weight, marbling, etc. This method is also inefficient because it fails to recognize bulls that are excellent for several traits but barely misses the cutoff for a trait. This also does not weight traits according to their economic importance.

Selection indices were first developed in 1943. The first selection index in the beef industry was published in 2004. This was a 60 year time lapse.
"This would be similar to corn producers hitching up the mules to plant the corn in the spring," Spangler said. This is a proven technology and needs to be adopted by the beef industry.

When designing a selection index we are trying to make improvement for traits in our breeding objective. The breeding objective may contain things like calf survival, weaning weight, fertility, etc. The more closely the traits for which there are EPDs match the traits in the breeding objective, the better the selection index works. When the breeding objective trait is not predicted, we need to use an indicator trait.

Why do we use the past five years of economic data and not the current prices and spreads? We are selecting cattle to use in the future, not today. A five year average is going to give us a better prediction of future prices than current prices will.

For the Beefmaster Terminal Economic Index, carcass weight is the most impactful trait, followed by feed intake and third by marbling.

For Beefmaster Maternal Economic Index, smaller mature weight is the most important trait, while increased weaning weight and increased maternal effect on growth (milk) are the second and third most importnat traits. This index selects bulls that will producer daughters that are smaller cows that wean heavier calves.

As Spangler and his group developed these indexes, they looked at how sensitive their indexes are to the assumed genetic correlations and the assumed economic values. Whether or not the calves were all calf feeds or yearling slaughter, had no effect on the index.
They found that the indexes were very robust (insensitive) to changes to genetic correlations or economic assumptions.

Lets look at two bulls, one with an index of 100 and the second with an index of 76. Lets assume that over 4 years, these two bulls are exposed to 120 cows.
120 exposure X ($100 - $76) = $2880 in profit difference between the two bulls.

Improvement in current indices can be made by increasing the number of economically relevant traits that have EPD predictions.

  • Input traits
  • Fertility


Enterprise level profitability should move closer to industry level profitability. Cow-calf producers don't get paid for tenderness, but tenderness is a big driver of consumer demand.

Seedstock producers should focus on the indexes that influence their customer's profitability. If a seedstock producer's customers retain ownership, then the seedstock producer should focus on the terminal index. If the majority of the customers retain females and sell at weaning, then the seedstock producer should focus on the maternal index.

Progeny receive half of their genetic material from each parent.
Breeding Value = 1/2 Sire Breeding Value + 1/2 Dam Breeding Value + Theta.
What is theta? Theta is the Mendelian sampling term. This accounts for the random sample of genes a calf inherited from its sire and dam. Even really good bulls can produce bad calves due to this random shuffle of genes (see fact sheet).

Seedstock producers are not truly cattle producers, they are genetic providers. Genetic improvement, driven by accuracy, selection intensity, and generation interval, should be the focus of seedstock producers. Seedstock producers need to realize that using younger sires can decrease their generation interval and increase their genetic progress.

Keep in mind, that a genomic test increases accuracy. The accuracy will always increase, but the EPD estimate can go up or down. But, the incrase in accuracy can allow us to use younger bulls with more confidence.

GE-EPDs allow commercial producers more confidence that they are picking the right bull.

In the past, we have seen producers only testing what they thought were their top bulls. This is not optimum.
At UNL, they have space to put 90 bulls on feed. At weaning they genomically test every bull calf. With the genomic test, they now have EPDs on every trait. Before they were picking bulls somewhat blind. Now they have data and information behind which bulls go on feed.

"Genomics helps breeds the most that already have very sound databases," Spangler said.

One of the things that breed associations do poorly is collectively bargain for the price of technology. In Ireland they negotiated to genotyped all of the cattle in the country. Because they were able to buy one million SNP chips, the cost per tested animal was less than $20.


Wednesday, October 26, 2016

NBCEC Brown Bagger: Implementation of single step methodologies at Angus Genetics, Inc.

Steve Miller
AGI

Angus Genetic Services provides evaluations for AAA, CAA, and Charolais breed associations.

"The ship has sailed on using genomics. Breeders are using it now, and seeing the benefits of it," said Miller.

Previously at AGI, they have been using a two-step approach. In this method, a genomic prediction is created and then is used as an indicator trait for EPD estimation. The calibration data set size has increased dramatically as Angus breeders have used genomic-enhanced EPDs.

The orgininal method of incorporting genomic predictions as correlated trait.

In the future, we will stop referring to genomic-enhanced EPDs. We don't refer to EPDs as pedigree-enhanced or performance-enhanced, we simply refer to them as EPDs. In the future use of genomic data in genetic prediction will become so routine that we will simply call them EPDs.

Is the Animal Model Obsolute?


In single-step genomic prediction, we combine the measures of relatedness from pedigree data with the measures of relatedness from the genomic data. In comparison to pedigree data, genomic data captures more variation is relationships.

Consider 6 full sibs. Their pedigree relationship is 0.59 (slightly higher than 0.5 due to inbreeding in the pedigree). But with genomic data the relationships vary from 0.49 to 0.65.

Single-step
 eliminates the need for periodic calibration.
utilizes all available data

The migration to single-step genomic evaluation is not unique to beef cattle. This has happened in multiple breeds and species on multiple continents.

One of the keys that makes single-step genomic evaluation is APY.

The Angus association has 7.6 million birth weight records and 254,000 genotyped animals.

The move to single-step required more computing power at AGI; they have purchased 4 new servers.

Between the previous correlated evaluation and single-step evaluation, for  200 proven sires the correlation between the current and new EPDs were 0.99.

AGI is currently in the process of changing horses on the fly. They are currently running two genetic evaluations, the current two-step correlated genetic evaluation and the new single-step evaluation. They are looking at the consistency of these predictions over weekly runs.

Right now, when we recalibrate a genomic prediction, we can see big jumps in EPDs. But, with weekly evaluations as data is added, AGI sees  incremental changes in EPDs as phenotype data is added.

Single-step BLUP will allow progressive breeders to leverage all of their data. Phenotype and genotype information will be utilized together in a single step.

Angus Association has also started a sire progeny testing program to get carcass data on proven, popular sires.

The Angus Association has not yet identified a time to completely switch to single-step BLUP. They are evaluating single-step, and when they are confident that the program is ready, they will switch.

NBCEC Brown Bagger: Implementation of single step methodologies at International Genetic Solutions

Dr. Mahdi Saatchi
International Genetic Solutions

IGS performs genetic evaluations for 12 breed associations from North America.
IGS has over 16 million animals in their database and is adding over 400,000 animals per yer.
IGS has 84,197 animals with genotypes. Simmental makes up about 40,000 of these genotypes.

Currently at IGS they blend the molecular breeding value (MBV, the genomic prediction) with the multi-breed international cattle evaluation. This is more like the blending that occurs with selection indexes.

Single-step genomic prediction allows information from genotyped animals to be spread to related animals in the data set.
Also, multiple-step genomic predictions were often trained on breeding values, and any errors in the estimation of the breeding values influenced the genomic prediction.

There are two approaches to single-step genetic evaluation. Single-step BLUP uses a breeding value model. Single-step Bayesian Regression uses a marker effects model.

In Single-step Bayesian Regression does not requiring inverting the relatedness matrix.
Also, in single-step Bayesian regression allows us to give different importance to DNA markers used (i.e. variable selection). In the dairy industry, they observe little benefit from Bayesian regression models. But, in the beef industry, we see genomic regions (i.e. QTLs) that have large effects in multiple breeds. Bayesian regression allows us to fit large effects to certain DNA markers used in the genetic prediction.

In the single-step Bayesian regression model, we infer (in other words predicting or imputing) the genotypes for all animals in the data set, even those animals that have not been genotyped.

Researchers at Iowa State, lead by Rohan Fernando, have created what they call a hybrid model which estimates marker effects for genotyped animals and breeding values for animals without genotypes.

With Simmental data, Bruce Golden see extra improvement in the precision when using a single-step Bayesian regression with different weights for DNA variants. This approach nearly cuts in half the uncertainty of EPDs compared with pedigree estimates.

This approach appears to be a major step forward in the precision of EPD estimation.


Monday, October 24, 2016

eBEEF Monday: How to Get Started with DNA Testing

This fact sheet goes through the fundamentals of how and when producers might use DNA testing in beef cattle production.  It covers the different types of tests that are available, how to submit samples and to whom, and what to do with the results.

For more information, see the eBEEF.org factsheet "How to Get Started with DNA Testing".

Monday, October 17, 2016

eBEEF Monday: Recent Developments in Genetic Evaluations and Genomic Testing

The application of genomics to improve the accuracy of EPDs is a rapidly developing field. There are ongoing improvements in genotyping and sequencing technologies, statistical methods to increase the correlation between genomic predictions and true genetic merit, and the computing systems to handle the large datasets associated with animal breeding. One thing still remains true in the genomic age and that is the need to collect accurate phenotypic records. It is essential to ensure performance data, pedigree, and DNA information are recorded and reported accurately. Genomic predictions will only be as reliable as the data upon which they are based.  Although it might seem like the genomics era could signal the end of performance recording, the opposite is true. Now more than ever, it is important that producers accurately report data, and ensure that animals which are genotyped are correctly identified so that their information can contribute towards improving the accuracy of the genomic predictions of the future.

For more information see the eBEEF.org factsheet "Recent Developments in Genetic Evaluations and Genomic Testing".

eBEEF Monday: Recent Developments in Genetic Evaluations and Genomic Testing

The application of genomics to improve the accuracy of EPDs is a rapidly developing field. There are ongoing improvements in genotyping and sequencing technologies, statistical methods to increase the correlation between genomic predictions and true genetic merit, and the computing systems to handle the large datasets associated with animal breeding. One thing still remains true in the genomic age and that is the need to collect accurate phenotypic records. It is essential to ensure performance data, pedigree, and DNA information are recorded and reported accurately. Genomic predictions will only be as reliable as the data upon which they are based.  Although it might seem like the genomics era could signal the end of performance recording, the opposite is true. Now more than ever, it is important that producers accurately report data, and ensure that animals which are genotyped are correctly identified so that their information can contribute towards improving the accuracy of the genomic predictions of the future.

For more information see the eBEEF.org factsheet "Recent Developments in Genetic Evaluations and Genomic Testing".

eBEEF Monday: Recent Developments in Genetic Evaluations and Genomic Testing

The application of genomics to improve the accuracy of EPDs is a rapidly developing field. There are ongoing improvements in genotyping and sequencing technologies, statistical methods to increase the correlation between genomic predictions and true genetic merit, and the computing systems to handle the large datasets associated with animal breeding. One thing still remains true in the genomic age and that is the need to collect accurate phenotypic records. It is essential to ensure performance data, pedigree, and DNA information are recorded and reported accurately. Genomic predictions will only be as reliable as the data upon which they are based.  Although it might seem like the genomics era could signal the end of performance recording, the opposite is true. Now more than ever, it is important that producers accurately report data, and ensure that animals which are genotyped are correctly identified so that their information can contribute towards improving the accuracy of the genomic predictions of the future.

For more information see the eBEEF.org factsheet "Recent Developments in Genetic Evaluations and Genomic Testing".

Monday, October 10, 2016

eBEEF Monday: Commercial Replacement Heifer Selection

Heifer selection is an important aspect of commercial beef operations, but unlike bull selection must be done without the aid of Expected Progeny Differences. This factsheet discusses considerations when making heifer selections, including available genomics tools and the importance of sire selection when replacement heifers are to be retained.

For more information, see the eBEEF.org factsheet.

Wednesday, October 5, 2016

NCBEC Brown Bagger: Potential impacts of functional variants on national cattle evaluation

Larry Kuehn
USDA-MARC

When we go from less than a thousand animals to several thousands of animals, genomic predictions can explain about 50% of the genetic variance for important traits. Genomic prediction is working and providing tremendous benefits to seedstock and commercial producers.

But, we still struggle with genomic predictions with very little data recording and genomic predictions that work well across breeds.

Two methods are used to use genomics in national cattle evaluation. With the genomic pedigree method you track genetic effects more accurately than with pedigree data. With the second method you are relying on linkage on chromosomes between the DNA markers and the variants responsible for the differences (causal mutations).

The linkage signal between DNA markers and causal variants breaks down over generations due to recombination (switching) between paternal and maternal chromosomes. Because this linkage breaks down over time is part of the reason genomic predicitons don't work well across breeds.

When we train a prediction in Angus and use the predictions in Red Angus, the predictive ability of the genomic prediction goes down significantly.

Table 1. Correlations from genomic predictions trained in Angus and used in Angus or Red Angus.
Breed Weaning Weight Yearling Weight
Train in Angus, Predict in Angus 0.36 0.51
Train in Angus, Predict in Red Angus 0.16 0.08

As we have additional whole genome (entire DNA) sequencing data, we will discover more DNA variants that affect the composition (sequence) or length of proteins. Many of these broken genes will likely affect fertility.

As we discover variants that appear to affect the function of proteins or are causal variants, we will need to use different methods to fully utilize this information. These DNA variants will need to be weighted differently in the genomic prediction, or genomic predictions will need to fit multiple classes of variants.

USDA has started a selection experiment in which they are selecting against variants that cause the protein coded by the gene not to function properly. The first calves from this experiment will be born in the spring.

Kuehn highlighted several research needs including:

  • Continued annotation (identification of genes and regulatory elements) of the reference genome
  • New sequence assemblies
  • Improvement of functional variant panels (DNA tests)
  • Improved imputation method and strategies (infer DNA variants not testing using the patterns of genotyped variants)
  • Continued detail oriented phenotyping
  • Improved methods to incorporate into national cattle evaluation
  • Gene expression difference (the amount of RNA produced by the same gene in different animals)
  • Evaluating cellular expression


Kuehn and coworkers believe that functional variants offers new opportunities for national cattle evaluation.

Monday, October 3, 2016

eBEEF.org Monday: The Genetics of Horned, Polled and Scurred Cattle

The condition of horned, polled or scurred in cattle has important economic and welfare considerations, but is poorly understood. This factsheet explores the genetic aspects of these conditions, their relationships with each other and how to manage them in your breeding program.

For more information see the factsheet "The Genetics of Horned, Polled and Scurred Cattle" on eBEEF.org.

Monday, September 26, 2016

eBEEF.org Monday: Genetic Correlations and Antagonisms

Knowledge of which traits are antagonistic can be utilized to manage the impact of selection decisions on other correlated traits.  However, it is important to remember that although genetic correlations can sometimes create the need to exercise more care in selection to alleviate unintended consequences, these correlations can sometimes be utilized to our benefit.  Understanding the magnitude and direction of genetic correlations can assist in selection decisions.  Utilizing balanced selection for multiple EPDs in a breeding objective or using an appropriate selection index will ensure that genetic antagonisms don’t become a limiting factor for genetic progress.

See the eBEEF.org factsheet for more information.

Saturday, September 24, 2016

Thompson Research Center Field Day: Modified Genes: Science or Supper?

Rod Geisert

In the 1950s, artificial insemination was developed. In 1978, the first human born from in vitro fertilization was born. Both of these technologies were criticized at the time, but now they are widely accepted.

When you fabricate something in science, you are going to get caught! When someone makes a claim in the literature, others try to replicate it. There was a fraudulent report of cloning in mice, and although this was not a true success, it got people thinking about and trying to clone animals.

A clone is simply an identical twin born on a different day.

Dolly the clone was named after Dolly Parton, because the cell from the donor sheep was from a mammary cell. Cloning animals did not immediately change how we raise livestock. But, cloning allows us to do additional things, like gene editing.

Who is going to feed the world? You are! Technology revolutions, like the green revolution and industrial revolution, have allowed the human population and food supply to continue to grow.

We can use the cow’s mammory gland (udder) as a factory to make milk containing pharmaceuticals. But, they could also delete the gene responsible for coding the prion protein (the protein messed up in Mad Cow disease). This way, we can confidently use the protein made in the milk without the worry of getting Creutzfeldt–Jakob disease.

Wouldn’t it be great if we could breed a cow that would never get mastitis? We can, by introducing a gene from bacteria that destroys the cell wall of the bacteria responsible for mastitis.

PRRS disease in swine causes hundreds of millions of dollars in lost revenue for the swine industry. Researchers at the University of Missouri removed a gene that was necessary for PRRS to replicate within swine cells. Twenty-five percent of the embryos treated with the CRISPR-Cas9 system contain the gene edit. Gene edited pigs could snort tons of the virus and never get sick (see http://munews.missouri.edu/news-releases/2015/1208-pigs-that-are-resistant-to-incurable-disease-developed-at-university-of-missouri/ for more information).

Gene edited animals are not transgenic. They are simply animals in which we have edited the DNA using a very precise technology (CRISPR-Cas9). Would you eat a cloned animal? Would you eat a twin animal? Eating a cloned animal is no different from eating a twin.

This is not technology that will impact the beef industry 100 years from now, 50 years from now; the use of this technology in the beef industry is right around the corner.

Friday, September 23, 2016

Thompson Research Center Field Day: Economic Opportunities for Missouri Cattle Producers Facing Lower Cattle Prices

“Supply and Demand works!” said Scott Brown at the Thompson Research Center Field Day. We have seen huge increases in meat production in the last two years. In 2014, we saw record cattle prices. Beef producers saw high prices, so they produced more beef. This of course lead to lower cattle prices.
The strengthening dollar has also lead to fewer beef exports. Lots of beef production but very little exports. We may not be done with lower cattle prices. A $1.10 looked a lot better on the way up than on the way down.
“Scott, where is the bottom at? Guys, if I knew where the bottom was at I’d be rich by now” Brown said.
If you had bought LRP or futures in the spring, you would be much happier right now.

When comparing 2008 to 2016 cattle inventory, it looks like Texas, Oklahoma, and Missouri still have a lot of room left to grow.

If you look at cattle return for 2016, it is the 8th or 9th highest all time. In 2015, cow-calf producers were still in charge. Now, the cow-calf producer is only seeing 65% of the value, compared to 90% in 2015.

We may be starting to find the bottom. Fundamentals suggest we might see higher prices, but there is still considerable down turn risk.

Do you have a marketing plan? Doing the same thing year after year is a plan, but it sure isn’t responsive to the market.

Is it a strategy to reduce risk to focus on cattle that grade higher? Prime has stayed strong over time.
There is a lot of volatility in the Choice-Select spread. CAB-Select spread continues to be a premium, but the Prime-Select spread continues to be the strongest premium. New products for consumers also provide premiums, especially for early adopters. It pays in the long haul to focus on what consumers want.

Prime boxed beef prices has remained flat in 2016, while Choice and Select boxed beef prices have declined all year.

Supply is not very responsive to negative returns due to fixed costs.


Thursday, September 22, 2016

Decker Extension Evaluation Survey

When I was hired as a beef genetics state extension specialist in University of Missouri Extension, I said I would strive to have a data-driven extension program. It is now time to more fully evaluate my extension program. I would sincerely appreciate if you would take a few minutes to complete the survey below:

Decker Extension Evaluation Survey

All responses are anonymous. The survey will be open till Friday October 21, 2016. Please one survey per person.

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

Wednesday, September 21, 2016

Thompson Research Center Field Day: Overview of reproductive research at the Th ompson Research Center

Dave Patterson

Patterson's research focus seeks to answer the question "Can we overcome the resistance to adopt AI with the development of fixed timed AI protocols?"

The Thompson Research Center has been involved with AI research since 1997 when the FDA was evaluating the use of CIDRs using cattle at the farm. In 1998, Patterson started using the center for his research and many students have been trained while working on projects at the research center.

The Show-Me-Select Program is designed to help producers understand the importance of heifer development based on reproductive success. There have been 271 veterinarians involved in the program and 123,091 heifers have been enrolled in the program. There have been $44,565,350 in gross sales through Show-Me-Select heifer sales. Ninety-five percent of the counties in Missouri have enrolled heifers in the Show-Me-Select program. Heifers from the Show-Me-Select program have been sold into 19 states. Heifers are classified as Tier II if they are sired by a proven AI sire. Tier II with an AI pregnancy see a $292 premium at sale. When the cattle market prices are high, there is smaller difference in premiums between the different classification of heifers in the sale. But, as the cattle market prices decrease, we once again see larger premiums for AI sired and AI bred heifers.

Reproductive tract scores help cattle producers know if a heifer is mature enough to bred. Reproductive tract scores can be collected by a veterinarian and help producers know which heifers to keep and bred and which heifers need to be culled. Heifers that have reached puberty earlier tend to do better in fixed-time AI protocols.

In 2010, 68% of heifers were bred at least one time by AI. In 2015, 90% of the heifers were bred at least one time by AI. Ultrasound pregnancy diagnosis has also increased drastically in the program.

Managing two-year-old cows presents a unique challenge in managing a beef herd, because they face many obstacles to re-bred. Patterson’s group is researching how to best synchronize these females for improved fertility rates. Protocols that use CIDRs help cycling two-year-olds get breed and help non-cycling cows start to cycle and get bred as well. With either a 14-day CIDR or 7-day CoSync + CIDR protocol, 88% of the two-year-old cows were pregnant in the first 30 days of the breeding season.

Can we improve pregnancy rates if we manage the cows differently in the AI synchronization protocol? Patterson's group is looking at split-time AI to improve pregnancy rates. In heifers, we can improve pregnancy rates by 15% using a split-time AI protocol. But, we don’t see any improvement in cow pregnancy rates. See "Split-Time AI: Using Estrus Detection Aids to Optimize Timed Artificial Insemination" for more information about split-time AI.

The 14-day CIDR-PG protocol for heifers with split-time AI.
The 7-day CO-Synch + CIDR protocol for cows with split-time AI.


The only heifers or cows that need a GnRH injection are only those that have not expressed estrus (heat). This means fewer shots and reduced costs.

Patterson’s group is also working on the development of a 9-day CIDR protocol. Preliminary results suggest that the 9-day protocol is having a much tighter grouping of the estrus response of the cows. On the 9-day protocol, there was a 17 percentage point improvement in pregnancy rates (77% vs 60%) compared with the 14-day protocol. In follow up projects, the 9-day protocol had a 10 point advantage.

Patterson urged producers to make sure that you are using the current years AI protocols sheets.

In the last 10 years, we have doubled the amount of semen that is sold. Fixed-timed AI protocols have made artificial insemination easier to accomplish.

As the market turns down, how can you distinguish your cattle from the rest of the market? Using reproductive technologies is a great way to differentiate your cattle.

Next year’s Applied Reproductive Strategies in Beef Cattle meeting will be in Manhattan, Kansas. Previous years proceedings may be seen on their website, http://beefrepro.unl.edu/proceedings.html.

Decker's Take Home Message
Artificial insemination allows beef breeders access to much better bulls than a typical natural service bull. Fixed timed AI protocols have made it much easier to implement an AI program.

Monday, September 19, 2016

eBEEF Monday: What is Gene Editing?

Gene editing is a category of new methods that can be used to precisely edit or change the genetic code. As the name “gene editing” suggests, these technologies enable researchers to add, delete, or replace letters in the genetic code. In the same way that spell check identifies and corrects single letter errors in a word or grammar errors in a sentence, gene editing can be used to identify and change the letters that make up the genetic code (i.e. DNA) within an individual. This factsheet explores the many possible uses of gene editing.

For more information see the factsheet at eBEEF.org.

Thursday, September 8, 2016

Profitability in focus at Red Angus Commercial Cattlemen’s Symposium in Oklahoma City

Oklahoma City – Cattlemen from around the country gathered in Oklahoma City to attend “Dollars in Your Pocket,” the Commercial Cattlemen’s Symposium held in conjunction with the National Red Angus Convention. A full slate of speakers addressed 200 cattlemen and women on overall profitability in the industry, present economic conditions, nutritional changes to improve cowherd efficiency, and calf crop marketing methods. Dr. Clint Rusk, head of the animal science department at Oklahoma State University, served as emcee for the day.

Darrell Peel, Oklahoma State University Extension Ag Economist, opened the session with a market forecast. “Cattle slaughter is up, carcass weight is up resulting in a 4.7 percent increase in beef production. Total meat supplies will be up, with beef leading the way,” Peel noted. “It should be noted that there is only a 1.5 percent increase in beef consumption.”

He also stated that beef demand continues to be strong. He expects it to rise further as beef prices come back down in the meat case and consumers return making additional purchases. “Beef demand will come back in line with people who were priced out of the market a year ago,” Peel forecasted.

Peel shared with cattlemen and women that volatility has been an issue in recent years and predicted he expects fewer larger swings in the market. “Looking ahead, we have a lot more potential for stability. While cattle prices may erode a bit more in the future, for the most part, we are looking for more stability. The biggest unknown in the future will be on the demand side. Demand could go a long way to offset the supply pressure,” Peel added.

Tom Brink, Red Angus Association of America CEO, brought the keynote address to the conference and encouraged the cattle raisers in attendance to strive for progress in his presentation, “The Curse of Being Average.”

Brink challenged beef business owners to look at their cost of production and the available data in their businesses in order to be better than average in one, two, three or even four areas of profit-driving categories to survive and thrive.

“There is over a $300-per-head advantage by beating the average,” Brink said. “Average won’t take anyone very far in the cow-calf business. You have to know your numbers.”

In encouraging producers to get serious about improvement, Brink pointed out the opportunity to use DNA tools in selecting commercial heifers.  “They don’t tell us everything, but they are a powerful, powerful tool,” he Brink.

During the afternoon session, Dr. John Arthington, the University of Florida, director of the Range Cattle Research and Education Center, shared the importance of mineral supplementation and the effective use of products to improve beef cattle performance.

Darrell Busby, livestock specialist and manager of the Tri-County Steer Carcass Futurity, explained and assisted members in gaining a greater understanding of retaining ownership of beef calves for additional profit opportunities. This subject was of particular interest in the current market environment to garner the most profit per head.

The Commercial Cattlemen’s Symposium was the opening session of the 2016 National Red Angus Convention, held September 7 - 9 in Oklahoma City.

The Red Angus Association of America serves the beef industry by enhancing and promoting the competitive advantages of Red Angus and Red Angus-influenced cattle. RAAA provides commercial producers with the most objectively described cattle in the industry by seeking and implementing new innovative technologies based on sound scientific principles that measure traits of economic importance. For more information, visit redangus.org.

Friday, August 26, 2016

ASA Fall Focus: Taking Technology Home to the Farm and Ranch

Here are videos from the American Simmental Association's Facebook livestream of my presentation titled "Taking Technology Home to the Farm and Ranch."

Tradition

Intuition

Legacy

Seedstock Producers as Educators

Decker's Rants

EPDs and Environment 

Q&A


Saturday, August 20, 2016

ASA Fall Focus: Information Learned from the IGS Genomics and Genetic Evaluation

Dorian Garrick
Iowa State University

Garrick started working on animal models applied to sheep and goats in 1982 (the year I was born ☺).

In the old system, each breed has their own data silo. This is combined together to have a joint pedigree and performance data.

Genomics has changed this.

EPDs are determined by the collective action of many genes. Selection increases the frequency of favorable gene effects and decreases the frequency of unfavorable gene effects. This allows producers to breed better cattle year after year. Genomics allows us to increase the accuracy of genetic prediction, especially for young animals with little or no data.

In human medicine, researchers are looking for individual DNA variants that are predictive of a person's risk for developing a disease. In beef cattle genomics, we don't use this conservative approach; we use all of the DNA variants simultaneously. Using all of the DNA variants gives much better predictions.

The hoped outcome is data to information to knowledge. The genetic prediction methods really can be a black box for producers.

Right now, the major problem is merging the data from the multiple breed associations and doing so in a repeatable and efficient manner.

The Irish Cattle Breeding Federation has negotiated a deal that they can genotype an animal for $20, because they bought 1,000,000 SNP assays at once (a bulk deal). United States breed associations need to consider more stringent DNA testing requirements, such as genotyping all parents, which would lead to bulk deals.

We can continue to improve predictions by:

  • Better marker panels - fewer better features used
  • More animals genotyped
  • More phenotypes collected (particularly for carcass, reproduction, and disease)
  • Improved quality control of all data
  • Better models and analytical methods

The purpose of collecting pedigree, performance and genomic data is to make better selection decisions.
The information systems used to input, store, and analyze data need ongoing development.


ASA Fall Focus: BOLT

Bruce Golden
Theta Solutions LLC

Historically, Simmental has been one of the leaders in the development of genetic prediction.

There has been evolution of statistical models used to predict genetic merit (EPDs). Each time the EPDs got better and better. To predict EPDs, you do two things; first you build the problem on the computer then you solve the problem.

What drove the evolution of the methods used to predict genetic merit?
Knowledge of the model? All of these models were well known by 1970.
New methods? Maybe a little.
Data? Yes, there has been the creation of genomic data and more phenotypic records.

But, the main driver has been to improve the accuracy of prediction. Striving to reduce the prediction error variance. Try to make sure that we are making better solutions and increasing the rate of genetic gain.

Improvements in computing power has also helped in the development of genetic predictions.

Another change is going to be better DNA markers that are closer to the genes and causal variants.

Computer gaming required really fast and affordable computer processors. Theta Solutions is using these improvements in computing to increase the speed of genetic prediction.

Theta Solutions is taking the data, new hardware, and new computer programs to do genetic analysis of large genomic data.

"It is not enough to take the old software and run it on this new gaming hardware. It requires rethinking and rewriting the software." Golden said.

Not only are they trying to compute EPDs more quickly, is implementing models that are more complex and specific.

Why would one use a Bayesian sampler for mixed models?

  • No accuracy approximation bias (better way to calculate EPD accuracy)
  • Can get the prediction error covariance (Instead of just comparing a bull's accuracy to zero, you can compare the accuracy differences between bulls or between groups of bulls. This will also allow a highly reliable accuracy measure for economic selection indexes.)
  • Marker selection methods
  • Prior knowledge
The IGS analysis feels they have:
  • Superior Marker Effects Model
  • Superior accuracy computation
  • New stayability approach - Random regressions
  • New breed effects model (using USDA MARC differences and year trends)
  • Carcass traits are being solved together with birth weight (birth weight is included to acount for a selected subset of the animals having carcass data)
Also has a method for including external EPD


New stayability model can now differentiate between unknown or missing data versus data saying a cow did not calve.

Theta Solutions is going to start working on final production acceptance testing in two weeks.

ASA Fall Focus: Application of Genomic Technology to Optimize Herd Replacement and Produce Elite Breeding Stock

Mahdi Saatchi
Lead Genomicist
International Genetic Solutions

Imagine a sire who is heterozygous (one A variant and one B variant) for a DNA position. At that same position a dam  is also heterozygous.
If we consider two progeny of this pair of sire and dam, they can be 0% related to 100% related at this position.

Calf 1 Calf 2 Relationship
A/A A/A 100%
A/A A/B 50%
A/A B/B 0%
A/B A/A 50%
A/B A/B 100%
A/B B/B 50%
B/B A/A 0%
B/B A/B 50%
B/B B/B 100%

If we apply this to the entire genome, we expect full siblings to share 50% of their DNA. But, just as the relationships can vary at a single locus, the relationships can vary for the entire genome. In chicken data, researchers see that the relationship between siblings ranges from 0.2 to 0.7.

Fig. 2 from Lourenco et al. 2015  http://gsejournal.biomedcentral.com/articles/10.1186/s12711-015-0137-1#Fig2
By more precisely measuring the relationship between animals, genomics allows us to more precisely predict an animal's genetic merit.

Genomics allows us to improve several parts of the key equation for genetic change. Genomics allows us to have more accurate selection decisions, increase the selection intensity and decrease the generation interval.

Genomic predictions have previously been shown to be accurate for Simmental cattle (Saatchi et al. 2012).

Genomic predictions are reliably predicting yearling weight. Genomic predictions are explaining real differences in yearling weight. Based only on the genomic prediction (molecular breeding value), there is a 100 pound difference between animals in the top 25% and bottom 25% of animals based on the genomic prediction.

Genomic information can be used for more than just producing genomic-enhanced EPDs. Saatchi points out that strings of DNA variants (called haplotypes) are sometimes never observed in two copies in an animal. If these haplotypes are never seen it two copies it likely means that they carry a variant that is responsible for the loss of pregnancies.

ASA Fall Focus: Nuts and Bolts of Animal Breeding

Wade Shafer

What is the science of animal breeding? Shafer cited Wikipedia, saying, "The scientific theory of animal breeding incorporates population genetics, quantitative genetics, statistics, and recently molecular genomics and is based on the pioneering work of Sewall Wright, Jay Lush, and Charles Henderson."
He highlighted the work of Sewell Wright, Jay Lush, and Henderson, and Lenoy Hazel. Not only is animal breeding about the genetic value of animals, it is also about the economic value of those animals.

Animal breeding is where the rubber meets the road. "It is one of the most practical sciences."

Simmental has the slogan of "Visual analysis tells you what an animal appears to be, his pedigree tells you what he should be, his performance and progeny tells you what he actually is."

In 1971, Vaniman used Paul Miller, a dairy genetics at ABS, to produce the first sire summary using Boeing Airlines computers.  The foreword said that sire summaries would revolutionize beef breeding.

In 1982, ASA signed a long term contract with John Pollack and Dick Quass at Cornell University to deliver and advance genetic evaluation. This was the largest BLUP evaluation at the time. Best Linear Unbiased Prediction, BLUP, was developed in the 1950s and 1960s, but wasn't able to be deployed at a large scale till the 1980s when computer technology caught up. The contract with Cornell was exclusive, mean Cornell only did genetic evaluation for Simmental.

Simmental has also benefited from a close relationship with Montana State University and the cattle industry in the state of Montana.

Shafer pointed out stalwarts in the breed. He pointed out gathers such as Jerry Lipsey and Ropp. Steve McGuire has been the shepherd of the data.

Glimpse of the future, through the past. Shafer highlighted the career development of Dorian Garrick at Cornell. Red Angus is a partner of the Simmental Association. Red Angus worked with Colorado State University, with Bourdan and Brinks leading the way. They had a productive graduate student, especially with computers, named Bruce Golden.

In 1997, the Simmental Association and Cornell University teamed up to produce the first multi-breed genetic evaluation. Originally, this was deveoped to do a better job of predicting cattle, such as half bloods, that were being used in the grading up process.

In 2001, the National Beef Cattle Evaluation Consortium was federally funded through an earmark to support genetic evaluation.

In 2007, six breeds tried to join together to start a joint genetic prediction. This never materialized. In 2010, the Red Angus Association of America and the ASA created a joint genetic prediction. This ultimately lead to the creation of International Genetic Solutions. "An unprecedented collaboration between progressive breed associationss to enhance beef industry profitability." IGS now contains 12 breed associations, with 17 million animals, with 340,000 new records each year.

Theta Solutions is a company created by Dorian Garrick and Bruce Golden to advance the technology of genetic prediction. Theta Solutions software is called BOLT for Biometric Open Language Tools.

Lauren Hyde and Jackie Atkins

What are our selection decisions? How many bulls should I use? Should I use old bulls or young bulls? Which replacement females should I keep?

The speed of genetic change (hopefully progress) is
Directly proportional to:

  • Accuracy of selection
  • Selection intensity
  • Genetic variation

Inversely related to:

This is called the key equation. 

Accuracy of selection is the strength of the relationship between the ture breeding values and their predictions for the trait under selection. Accuracy increases when we use EPDs from BLUP. If using phenotypes, the accuracy is based on the heritability of the trait (which is much lower that using EPDs). 

If the BIF accuracy is 0.1, the change in weaning weight is 8 pounds. If the BIF accuracy is 0.25, the improvement in weaning weight is 12 pounds. 

Selection intensity is how choosy we are when we are selecting animals. Are we keeping everything or selecting at random or are we choosing the very top animals? Selection intensity is the difference between the average and the selected parents, divided by the variability (standard deviation) in the trait.

It is hard to change amount of genetic variation in a herd.

Generation interval is the average age of the parents when the progeny are born, In cattle this tends to vary between 4 to 6 years.

Trade-offs
Accuracy vs. generation interval
Decrease in generation interval causes decrease in accuracy and vice versa.
Quick turnover of herd sires mean we have fewer progeny per sire and less accurate predictions.

Selection intensity vs risk
Selection risk is that the true genetic merit of replacements is significantly worse than expected. With fewer sires we increase the intensity but increase our risk. With more sires we decrease our risk but we also decrease our selection intensity.

Male selection can be more important than female selection. We can be more choosy when selecting bulls and we have more progeny per bull.

You are not supposed to do single trait selection. But, selecting on an index is not single trait selection. ASA recommends that producers use indexes to select for increased profit.


Wednesday, August 17, 2016

17th Annual Missouri Livestock Symposium December 2nd and 3rd

The Missouri Livestock Symposium committee is currently planning their 17th annual Symposium in Kirksville, MO for December 2nd and 3rd. The Missouri Livestock Symposium (MLS) committee works year-round to find the best speakers on timely topics that benefit producers in their respective enterprises.
The MLS began in 1998 with a simple conversation between then University of Missouri Extension Livestock Specialist Bruce Lane (retired) and local Adair County livestock producer and current MLS chair, Garry Mathes. Since those humble beginnings the MLS has grown exponentially and recently had attendees covering a majority of Missouri’s 114 counties plus 16 states, with over 2,000 in attendance.
Attendees have an opportunity to attend the largest agricultural-based trade show in the Midwest, featuring many local, state, and national agricultural businesses. Comments regularly heard include, “my favorite show,” “something for everyone in the field of agriculture,” and “we were made to feel very welcome and were well taken care of.”
The Symposium kicks off Friday afternoon December 2nd at the William Mathew Middle School. Visitors can peruse the sold out trade show before the free beef meal at 6 pm. The evening program begins in the auditorium at 7 pm when the MLS committee will recognize the 2016 Agriculture Educator of the Year and the Livestock Person of the Year. The Friday evening program concludes with a keynote speaker. This year Dr. Scott Brown, University of Missouri extension agricultural economist, will address current domestic and global farm and ranch financial pressures.
The Saturday program is unique and is what has branded the MLS for the last 16 years. Instead of focusing on one particular species of livestock, the MLS holds programs on beef cattle, horses, sheep, meat goats, forages, stock dogs, estate planning and farm management; as well as timely nutrition/food topics, saving the honeybees and backyard poultry production. The MLS features eight different educational tracks and contracts over 30 speakers from across the nation representing universities, governmental agencies, and private industry. Speakers address the timeliest information for producers to take home and improve their operations. A Governor’s Style Luncheon is provided on Saturday and is free to attendees. The meal is sponsored by Missouri’s commodity groups.
Highlights of speakers and topics for 2016 include Richard Winters, Winter’s Horsemanship and Kim Lindsey, AQHA ranching director in the horse section. The beef section will focus on the impending effects of the Veterinary Feed Directive (VFD), highlight some of the latest advances in beef cattle genomics, and feature a panel discussing capturing value when marketing your calf crop.
Additional highlights include Dr. Michael Neary, Purdue University, featured in the sheep and stock dog sections and Dr. Ron Hanson, University of Nebraska, conducting a 3-session estate planning course. Other topic highpoints include land prices, beef economy outlook and climate trends affecting agriculture.
Since the beginning, the MLS remains deeply connected to University of Missouri Extension and their mission of improving the lives of citizens through education. MLS chair, Garry Mathes and current Livestock Specialist Zac Erwin believe this will be the best program to date. Anyone seeking further information on the MLS are encouraged to visit our website at http://www.missourilivestock.com, Like us on Facebook, call the Adair County Extension Center at 660-665-9866 or MLS chair, Garry Mathes at 660-341-6625.

Decker's Take Home Message
I will be speaking at the meeting in Kirksville, and hope to see you there!

Thursday, June 30, 2016

The Next Generation

The beef industry values sustainability. We value successful operations that are passed on to generation after generation. That is why beef producers support  youth programs.

Those of you who know me personally, know I am way too busy for my own good.  I've learned to say no and am making strides in simplifying. When the beef project leader in my kid's 4-H club came open, I should have kept my mouth shut. Instead, I volunteered to be the leader, because I value educating youth. I wanted to pay it forward and help kids fall in love with cattle the way I did.

On Friday July 8th will be our Sturgeon Beef Show. I hope those of you in mid-Missouri will come out and enjoy the successes of our youth.

If you are interested in sponsoring a breed champion, please let me know. Thanks to those who have already sponsored.

Watch the blog for pictures of my little ones falling in love with cattle. If you time driving by my house just right,  you might even catch a glimpse of a computational geneticist trying to catch a calf out in the pasture. :)

Sincerely,
Jared

Saturday, June 25, 2016

BIF 2016: Genomics, return on investment - fact or fiction?

Tonya Amen
Consultant for Illumina, Inc.

One dairy operation was making $35 per year progress for net merit. After using genomics in late 2009, they were making $50 per year in progress for net merit. After they started testing females, this rate increased to nearly $80.
This dairy herd is now seeing $340 more in life time production by using genomics.

From 2005 to 2008, $B was increasing by $3.77 per year.
From 2009 to 2015, $B increased by $5.62 per year.

From 2013 to 2015, $B increased by $9.31 per year.
A 146% increase in genetic trend.

We have seen more rapid genetic improvement in Angus, Hereford and Simmental, all of which line up nicely with the deployment of GE-EPDs. Thus, it is possible (likely?) that this improved genetic improvement is due to the benefit of genomics.

In the dairy industry, genomics is equivalent to 25 production records, 25 conformation records, and 140 fertility records.
Genomics is saving the Canadian dairy industry $111 million dollars annually.
Genomics is saving the New Zealand Farming Coop $4.2 million annually. The genetic gain is increasing despite the cost saving.

A genomic test for Angus gives a breeder the same amount of information as 17 progeny with records for dry matter intake. A $47 test is much cheaper than doing a feeding trial on 17 progeny.

Three benefits:
1) Identify future problems
2) Identify current problems
3) Gives representative proxies for genetic merit of steer mates

There is also value in avoiding inbreeding. Inbreeding decreases performance, thus avoiding inbreeding helps us to avoid decreased performance. In dairy cattle, there is a $20 lost revenue per year for a 1% increase in inbreeding.

Selecting cattle for placement in a feedlot can be worth up to $38 per head. If we are just trying to use this information for different management, the value is less than $1 per head.

CLARIFIDE plus now can directly predict disease risk in Holstein cattle. As discussed previously, we see large reductions in feed efficiency due to health problems.

Amen's is pointing out that we see a $204 premium for heifers with genomics tests in the Show-Me-Plus program. This leads to a return on investment of 167% to 700%.

Friday, June 24, 2016

BIF 2016: Using genomic tools in commercial beef cattle: taking heifer selection to the next level

Tom Short
Zoetis

Can genetic information from a simple DNA sample allow us to reasonable accuracy of the females lifetime performance?

We know that our national cow herd inventory decreased to a very low level in 2014.

When we rebuilt the cow herd did we keep low quality heifers that should have never been cows?

What type of genomic prediction should we be using to select commercial heifers?

GeneMax Advantage was produced by a collaboration of Angus Genetics Inc, Certified Angus Beef, and Zoetis. It is applicable to beef females that are at least 75% Black Angus. These predictions are based on the Zoetis HD50K product for Angus. The correlations between the genomic predictions and the breeding value are all quite good, around 75%.

The individual traits are combined into three indexes. These are a Cow Advantage Score, Feeder Advantage Score, and Total Advantage Score. The correlation between Total Advantage and the Cow and Feeder indexes are about 70%, but the correlation between Cow Advantage and Feeder Advantage is about 50%. So, if in doubt about your breeding objective, use the Total Advantage Score.

The Cow Advantage is 13% Cow Cost, 66% number of calves, and 21% weight of calves. Carcass Advantage is a combination of feedlot and carcass traits.

Maximum genetic economic improvement is made by selecting on indexes.

Check out Bob Weaber's fact sheet on eBEEF.org for more information about indexes. http://articles.extension.org/pages/73372/beef-cattle-economic-selection-indices

By selecting on GeneMax Total Advantage, we see about 0.5 standard deviation improvement in Calving Ease Direct. We see about 0.9 SD improvement in weaning weight, 0.4 for marbling, calving ease maternal abour 0.6 SD. If we selected only on weaning weight, we would see unfavorable changes in mature weight, mature height, and decreased improvement for calving ease and other economically important traits.

In Short's model, value of the test is measured over a 10 year period based on the performance of the cow's progeny, grand progeny, and great grand progeny.

The heifers that you test and retain have to pay for the heifers that you test and cull. By 7 years, we see a net revenue of $300 per tested heifer. Break-even occurs between years 3 and 4. The value of the future generations is about 1.5X that of tested females. Keep in mind, investments in genetics is a long term investment!

146 heifers tested in SD herd.
By visual apprasial, the top 100 heifers averaged a 56 Total Advantage Score
By index rank, the top 100 heifers averaged a 65 Total Advantage Score.

A $39 test cost is approximately only $15 more than recommended health protocols to first calving for a first heifer.

Also consider other value considerations.
Value added marketing programs, the average of the heifers matches the average of the steers. Could use this information in marketing steers through TopDollar Angus or Reputation Feeder Cattle.

Also a great shout out to Missouri's Show-Me-Plus program!

This tool is also a unique value to commercial producers because historically they do not have access to genetics predictions for commercial heifers.

See bifconference.com for more information.

Thursday, June 23, 2016

BIF 2016: Can Beef Seedstock Producers Afford Genomics?

Breeding objectives indicate value of genomics for beef cattle

Dr. Mike MacNeil
DeltaG

Is genomic testing a good value to seedstock producers? The answer to this question requires several different lines of thought. To answer this we need a system based approach.

What makes up a genetic prediction?

  • Information from relatives
  • Molecular breeding value
  • Correlated phenotypes
  • Phenotype
No individual animal in a genetic prediction ever has an accuracy of prediction of zero. The information from the calf's relatives brings in substantial amount of information.

What are the advantageous of genomic prediction?
1) Increase accuracy of evaluation
2) More exciting is the opportunity to incorporate additional traits
  • costly or difficult to measure
  • measured late in life (after the time of selection decisions)
  • sex-limited
3) Avoid prolonged generation intervals. For many selection decisions in beef cattle, we make many selection decisions around a year of age.
4) Reputation. This is hard to quantify in dollars and cents!

What is improvement???
MacNeil's definition is making cattle that are more profitable in the next generation.
This can be boiled down to income minus expense.

MacNeil uses a computer model to estimate the effect of changing one trait by a unit of measure and seeing how that influences profit.
This model:

  • Is an abstraction of any actual beef production system.
  • Captures sources of income and expense
  • Has economic parameters which reflect future expectation
  • May be discount income and expense streams 
  • Has data-driven biological parameters 

For these models, MacNeil simulates many animals.

For feed efficiency simulations, MacNeil used 5 scenarios.
Scenario 1: Phenotypes only (accuracy = 2√h2)
Scenario 2: Phenotypes + low accuracy genomic prediction
Scenario 3: Phenotypes + higher accuracy genomic prediction
Scenario 4: (Phenotypes + siblings) + low accuracy genomic prediction
Scenario 5: (Phenotypes + siblings) + higher accuracy genomic prediction  

Going from phenotype to genomics has a fairy substantial jump. Going from a low accuracy genomic prediction to a high accuracy genomic prediction also has a big jump. When we have pedigree predictions with lots of phenotypes, there is no benefit from adding genomics.

"If you have a bull with 200 progeny records, don't waste your money on genomics," MacNeil said.

How many breeding objectives (economic selection indexes) should we have? MacNeil did an analysis. In South Africa, you receive discounts when the carcass weighs 500 pounds.
The correlation between the South African index and United States index was 0.68. The breeding objective in South Africa would work fairly well in the United States. The differences in breeding objectives across the United States are minuscule across environments in the United States. In other words, use indexes! They work!

Genomics only helps birth weight predictions by 9%. Genomics helps dry matter feed intake by 41%, because there are many fewer feed intake records.

For a maternal objective, fitness drives the bus. The cow needs to stay in the herd. This accounted for 50% of the value in the breeding objective.

For stayability in beef cattle, adding genomics had a 76% improvement in the accuracy of genetic prediction. This is because this trait is measured later in life and there are fewer phenotypic records.

In a terminal objective, we increase accuracy by 27%. 

If we generate 60 harvested progeny per sire, we earn $169 per genomic tests.
If we generate 15 replacement heifers on a bull, we earn $159 per genomic tests.

"You are on the order of 4 times the cost for return, based on the cost of the test." MacNeil said.

What are the take home messages:
Breeding objectives greatly facilitate multiple-trait selection
Genomic predictions for component traits add substaintal accuracy to prediction of breeding objectives
Genomic technology has greatest promise for traits that are infrequently recorded or recorded after the selection decision point
With reasonable transfer of economic benefits from commercial to seedstock sector, it indeed does appear that seedstock producers can afford genomics, provided they use rational breeding objectives.


"I started this exercise believing the answer was no." MacNeil said. "I believed it was a shell game about the perception of the value of the technology." 

MacNeil proved to himself that he was wrong.

Multi-trait breeding objectives keep you from going too far down the wrong path. They put the right amount of emphasis on each trait.
Tandem selection and independent culling levels are both less effective than breeding objectives through economic selection indexes.
 If we chase one trait, then run into a problem, select for a second trait, run into a new problem, so chase a third trait- this is tandem selection.

MacNeil stated, "I am troubled by the Angus $B index, as it is an incomplete objective" (i.e. it only takes part of the production system into account, not from conception to slaughter). But, using $B is MUCH better than using the individual component traits.

See bifconference.com for PowerPoint and Proceedings.

Decker's Take Home Thoughts
While many of the cattle that are on our farm or ranch are selected at a year of age, the ages of AI sires can vary greatly. Thus, AI sires may be a potential opportunity to decrease the generation interval. While commercial producers should likely use proven AI sires, this may not be the case for most seedstock producers. Using younger AI sires may be low hanging fruit for many seedstock herds.
Use genomics and use economic selection indexes so that your breeding decisions are rational.