Thursday, April 28, 2016

Producers invited to participate in research to identify cows that match their environment

Researchers to use genomics to better understand hair shedding


It’s time to pick a new AI sire. You identify a promising sire, but then you are left with a question. Will his daughters work in your environment and the environment of your customers? A new research project lead by researchers at the University of Missouri, Texas A&M, University of Arkansas and DeltaG will use existing data to look for genetic adaptation to regional beef production environments. Much of this research will look for gene-by-environment interactions. When gene-by-environment interactions exist, some genetic variants have large effects in some environments and small effects in others. This leads to cattle that perform poorly in a certain environment, but well in other conditions. Cattle poorly adapted to their environment result in lost revenue and cause headaches for farmers and ranchers. One of the goals of this research project will be to create region-specific genomic predictions, thus helping farmers and ranchers match cattle genetics to their environment. 

A portion of this project will focus on genome-wide analyses of adaptive traits, such as hair shedding. The research team invites producers of registered cattle to participate in this research. They request that producers commit to participating in the project for 3 years (2016, 2017 and 2018). Of course, cattle will enter and leave herds, but as much as possible, the project would like to have 3 years of hair shedding scores on each animal. In 2016, producers should collect a DNA sample (blood cards preferred) on animals in their herds that are 1-year old or older. Please include farm/ranch name, herd ID, and registration number on each blood card. In May or June of each year, each animal is scored for hair shedding (see Hair Shedding Scores). Each animal must be individually identified, for example with an ear tag, tattoo, or freeze brand. Farmers and ranchers need to collect samples and report data for every animal in their herd older than 1 years of age (whole-herd reporting), and the herd must have a minimum of 10 animals. Cattle must not have Zebu (Brahman) influence and must be registered with a breed association utilizing genomic prediction (Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, Shorthorn, or Simmental). Producers are also required to submit weaning weight data to their breed association on the progeny of cattle used in this project. Producers are encouraged to visit https://missouri.box.com/HairSheddingSummary to learn more about data reporting requirements. Producers from the Gulf Coast and Fescue Belt are encouraged to participate (Missouri, Arkansas, Tennessee, Kentucky, West Virginia, Virginia, North Carolina, South Carolina, Georgia, Alabama, Mississippi, Florida, Texas, Oklahoma, Indiana, Illinois and Ohio). Also, producers from high altitudes who would be willing to report pulmonary arterial pressure (PAP) scores and hair shedding scores are also encouraged to participate (for example, breeders in New Mexico, Colorado, Utah, Wyoming, Idaho and Montana).

In return for participating in this project, the research project will DNA test (genotype) your animals with a panel that contains 200,000 DNA variants (SNPs). Approximately 30,000 of these variants are shared across multiple genotyping panels and can be used to impute missing genotypes (much like i50K or GGP-LD products). Imputation is the process were a smaller number of DNA variants are used to infer the genotypes at a larger number of variants based on patterns of inheritance (see https://youtu.be/mTd7pMN9nQo or http://bit.ly/2064dQm for more information). 
We will provide these genotypes to the producer’s breed association. The breed association will then produce genomic-enhanced EPDs (GE-EPD) for the cattle used in the hair shedding project (see Data Sharing Schematic). Thus, for participating in the project for 3 years, producers will receive GE-EPDs for their animals at a greatly reduced cost. (Producers are responsible for purchasing needles, syringes, and shipping of blood cards. The research project will pay genotyping costs.) All producers are welcome to contribute phenotypic data (hair scores), but genotyping will be limited to approximately 8,000 animals, so the research team may not be able to genotype all submitted animals. Producers are also strongly encouraged to submit hair shedding data on animals that already have GE-EPDs.


Please contact Jared Decker or GeneSeek to order blank blood or hair cards for your animals. Completed cards should be shipped to:
Jared Decker (Hair Shedding Project)
S132B Animal Sciences Center
920 East Campus Drive
Columbia MO 65211


For more information about the project please contact Jared Decker at deckerje@missouri.edu or call 573-882-2504, your local University of Missouri Livestock Specialist or your breed association staff.

Watch for a frequently asked questions section in a future post.

Thursday, March 31, 2016

Angus Announces Routine Calibration of GE-EPDs

Genomic-enhanced selection tools to undergo scheduled upgrade

American Angus Association® and Angus Genetics Inc. (AGI), the organization’s genetic services subsidiary, will soon release newly calibrated genomic-enhanced expected progeny differences (GE-EPDs).

On March 21, AGI announced plans to release the latest calibration of its genomic-enhanced selection tools in mid-April.

The process is the fifth of its kind since introducing GE-EPDs in 2010, and further refines how DNA test results are incorporated with pedigree, performance measures and progeny data into the selection tools released through the Association’s weekly National Cattle Evaluation (NCE).

AGI President Dan Moser says the extensive process of calibrating GE-EPDs results in further accuracy on more animals in the Association’s growing database, but with generally less incremental change with each consecutive calibration.

“This latest calibration represents a fine-tuning of the genomic-enhanced EPDs provided through AGI,” Moser says. “When this process was first introduced, we had fewer animals with which to train the equations used to generate GE-EPDs. As that process has evolved and we successively gain additional genomic and phenotypic measures, we’re able to refine those equations, allowing for more powerful genetic predictions on more animals.”

AGI and research partner Zoetis began work in June 2015 to train genomic equations using animals within the current population with both DNA information and performance measures like weights and carcass characteristics. Total animals used in the training population numbered more than 108,000 head, a nearly 88% increase from the 57,550 animals used in the last calibration released September 2014 (Fig. 1).
Figure 1. Increase in Data over Five Calibrations.

“When GE-EPDs were first developed, they were based on a training population of just more than 2,200 animals, given the novelty of the technology. In comparison, we sometimes process more than that in just one day at AGI,” Moser says. “That’s how quickly we’ve advanced in the past six years. More people than ever are DNA-testing their animals.”

The effort is paying off. Larger test populations provide stronger correlations and explain a greater percentage of genetic variation among traits — but Moser says that percentage jump from one calibration to the next has leveled with time thanks to increasing accuracy with each release.

“For the vast majority of animals, producers won’t notice any significant shifts in GE-EPD values after Calibration 5 is released,” Moser assures. “Heifer pregnancy (HP EPD) may show slightly more change than other traits, and the numbers for young animals with DNA information and little or no progeny, or those with newly incorporated progeny information are perhaps more apt to adjust.” (Table 1.)

Table 1. Genomic Weighting between 2014 and 2016 recalibrations. Expressed as correlations between molecular breeding value (MBV) and phenotypic data.
Trait
Sept 2014
Apr 2016
Difference
CED
0.62
0.67
0.05
BW
0.68
0.69
0.01
WWT
0.56
0.56
0.00
YWT
0.66
0.68
0.02
DMI
0.74
0.73
-0.01
YHT
0.74
0.75
0.01
SC
0.78
0.80
0.02
DOC
0.71
0.68
-0.03
HP
0.45
0.62
0.17
MILK
0.36
0.37
0.01
MWT
0.68
0.74
0.06
MHT
0.68
0.71
0.03
CWT
0.60
0.60
0.00
MARB
0.67
0.65
-0.02
REA
0.69
0.68
-0.01
FAT
0.65
0.65
0.00

In all cases, GE-EPDs will be more accurate than the values they replace thanks to the calibration, a process that normally takes about nine to 10 months. Luckily, computer technology has kept pace with a larger volume of samples, Moser says.

Both phenotypic data and the accuracies built through the calibration process work to better characterize the genetic merit of registered Angus cattle — and set the stage for further advancements in the science of genetic selection.

“We’re continuously looking for ways to streamline the processes involved in providing the industry’s most advanced genomic-enhanced selection tools,” says Moser. “AGI is committed to keeping Angus breeders at the forefront of this technology and ultimately reducing the risks inherent in managing their individual cow herds while also driving efficiency.”

Members may access the complete NCE, released each Friday, at www.angus.org and through the Association’s online record keeping system AAA Login.

ANGUS MEANS BUSINESS. The American Angus Association® is the nation’s largest beef breed organization, serving more than 25,000 members across the United States, Canada and several other countries. It’s home to an extensive breed registry that grows by nearly 300,000 animals each year. The Association also provides programs and services to farmers, ranchers and others who rely on Angus to produce quality genetics for the beef industry and quality beef for consumers.

For more information about Angus cattle and the American Angus Association, visit www.angus.org.

Decker's Take Home Message:
The largest jump in correlation between genomic prediction and phenotype was seen in Heifer Pregnancy (HP). This increase was due to a larger number of heifer pregnancy phenotypic records, thus highlighting the need to report data. Improvements like this are also why the AAA is trying to increase enrollment in MaternalPlus.
On average the correlations increased, with a few traits having slight, basically meaningless decreases.
Recalibration has the benefit of ensuring the genomic prediction matches the current generation. 



Angus Convention 2015: Maternal Plus

During the 2015 Angus Convention, there was a producer panel discussing the American Angus Association's MaternalPlus program. Matt Perrier of Dalebanks Angus and Richard Tokach of Tokach Angus discussed a producer's perspective on the program. In this post I share some of their thoughts on the program. (Unfortunately, I didn't have the names of the panelists prior to taking notes, so I can't assign quotes to individual panelists.)

Fertility is the number one driver of profitability. No matter how well they grow, how well they grade, if she can't reproducer herself, she can't be profitable.
We could have both animals that are great in terms of performance and carcass quality, as well as fertility.

MaternalPlus provides us an opportunity to record reproductive data and to produce estimates of fertility.
The graphs through the program are also very helpful.

MaternalPlus is a tool the association gives you. You can choose to use it or not. But, MaternalPlus can give a breeder and their commercial customers a competitive advantage.

MaternalPlus has made us more of a system thinker. It allows our ranch to find the cows that aren't working, but more importantly it allows us to report that data to the association.

We don't have to put a disposal code on every cow. We just have to get it cleaned up. The association will work with you on this. This is the first big step; getting your cow inventory cleaned up. Sending data into the association has always taken time, whether it was reporting weaning weights of 1984 or more recent tasks. But reporting this information is what has made Angus bulls valuable for commercial customers.

We have learned to value having a scale on our operation. We need to learn to value MaternalPlus.

We need to celebrate each time we have a new tool.
"Decide and make the mindset that this will be worth the effort."
Choose a time that is best for your annual enrollment. Avoid breeding season, calving season, and your annual bull sale.

Keep track of all of the cows you ship. Keep the records as you are shipping the cows to the sale barn. Keep track of why she is on the truck to the sale barn.

It is as simple as enrolling, and then everything remains the same. If you used AIMS, you continue to use AIMS. If you have used AAALogin, you continue to use AAALogin.

If a cow is removed from your inventory, you can still look up her data from Production Reports (she won't be in your inventory list).

Angus has a prototype productive life EPD. Allows cows to receive credit for each month of life in production. Also uses disposal codes to weed out cows that left the herd for reasons that weren't her fault (e.g. drought).

We have got to characterize reproductive performance.

The Milk EPD has a heritability of 14%. This is exactly the same as heifer pregnancy EPD.

"Other breeds have done it. They have used whole herd reporting to estimate longevity and other reproduction EPDs. They find heritabilities around 15%, which is plenty of genetic variation to find differences between sire groups," affirmed Moser.

"We don't want to disposal code ourselves to death. Just getting a disposal code that she is open is great!" said Amen.

"Before the speaker [Ken Schmidt] rode a Harley, first he rode a bike with training wheels." MaternalPlus is the training wheels program for Angus breeders.

For more reporting on this session see "MaternalPlus®: What’s it Worth?" by Nicole Lane.


Tuesday, March 15, 2016

A new tool for selecting commercial beef heifers: genomics

Guest Post
Written by David Hoffman, MU Extension Livestock Specialist/County Program Director

Spring is quickly approaching.  That means warmer weather and green grass are on the way.  For the cow/calf producers, it means that calving is in full swing (or about over for some) and the breeding season is just around the corner.
Decisions are being made that will impact the cattle operation for several years, such as the next herd bull to purchase or the sires to breed cows and heifers through artificial insemination.  Some producers spend many hours in selecting the right bull for their operation, looking over pedigrees, EPDs, performance data, etc.  There is a tremendous amount of data available on purebred cattle, but limited genetic data on commercial cattle.
In the past, selection for our commercial replacements has been on individual performance, structural soundness, body phenotype and possibly genetic information about sire(s) and/or dam. There has been little to no measure of genetic potential of commercial replacement heifers.  However, that is rapidly changing with the use of genomic testing.
Genomic predictions are being developed and available for commercial cattle producers to utilize in their operation.  Commercial cattle often do not have EPDs, which provide a predictive measure of the animal’s genetic potential like purebred cattle.  These genetic predictions can be used to select replacement heifers, market feeder calves, and/or make mating decisions.
Through genomic testing, producers are able to make more informed decision that could impact their operation for many years.  Depending on the test utilized for genomic testing, producers can gain valuable information on maternal traits, performance traits and carcass traits. Some of the genomic tests are breed specific, such as Angus (>75%) or Gelbvieh; whereas others are non-breed specific.
Selection decisions can be made by retaining the higher ranking animals that meet your production goals and culling the animals that are below average.  In addition, genetic predictions can be utilized in making mating decisions.  If you have low scoring heifers for carcass traits, you could mate your heifers to higher carcass value bulls and increase performance.
Majority of the tests cost between $20-50 per head, depending on the number of traits being evaluated.  The greater the number of traits being measured, the higher the price tag for the test.
In addition, the genomic tests offer sire parentage testing.  Think of the opportunity to measure performance differences of multi-sired groups of heifers.   One could gain tremendous information on their herd bulls and make decisions accordingly to your specific goals of your operation.
With the genetic information on commercial cattle, producers can make management and marketing decisions that could potentially be very powerful.  I would not recommend making selection or management decisions solely on the results of genomic testing.  Genomic testing is another tool in the tool box.  Will it be utilized by every producer?  No, but those that choose to take advantage of this new technology could increase their rate of progress in their herd dramatically.

Friday, February 26, 2016

Main Point: Embrace Science and Tech

Today, an article I wrote appeared in BEEF Magazine's Cow-Calf Weekly.
Do we HAVE to cull genetic defect cattle? Science says no
In this article, I used genetic defects as a case study for what happens when we don't embrace the new opportunities science provides. Science now allows us to manage genetic defects differently than we did 50 years ago.

But, I fear with all of the baggage genetic defects bring, that my main point will be lost. My main point is simple.
Embrace science.
Embrace technology.
Embrace new approaches.

I love that Burke Teichert encourages us to be a constant learner searching for better practices. I have also tried to encourage people to embrace science.

In conclusion, I am not a genetic defects zealot. Manage them how you see fit. But, I am a science zealot! Please look for ways science and technology can benefit your operation. For different production systems and breeding objectives, how science is used will look differently. Science can improve all beef production systems.


Thursday, February 18, 2016

Genomic ROI: Early Returns Suggest Premium for Show-Me-Plus Heifers

Anyone familiar with the Missouri beef industry, knows the Show-Me-Select™ Heifer Program. In 2015, we started a new heifer classification in the Show-Me-Select™ Heifer Program, called Show-Me-Plus. A Show-Me-Plus heifer simply has a genomic prediction, either reported as genomic-enhanced EPDs for registered heifers or genomic tests for commercial heifers. At the most recent board meeting, the board approved 5 additional products; now heifers qualify for Show-Me-Plus with breed association GE-EPDs, GeneMax Focus, GeneMax Advantage, Gelbvieh Maternal Edge, Red Angus Herd Navigator, Igenity Gold, Igenity Silver, Igenity Gold Angus, Igenity Silver Angus, Method Choice, and Method Commercial tests.

In the Southeast, West Central, and North Central sales, there were 33 lots of 86 heifers that carried the Show-Me-Plus label.
Below are the summary statistics for the 2015 Fall Sales, breaking heifers out by Tier II (sire identified heifer out of a proven AI sire), pregnancy, and Show-Me-Plus classifications.

Table 1. Summary statistics from Show-Me-Select sales in Southeast, West Central, and North Central regions.
Year
Tier
Pregnancy
SMP
Count
Median
Mean
Premium
Show-Me-Plus Premium
2014
 I
NS
No
81
$2,700
$2,785
Base
2014
 I
MX
No
4
$3,100
$3,069
$283
2014
 I
AI
No
106
$2,900
$2,958
$172
2014
 II
NS
No
5
$2,875
$2,790
$5
2014
 II
AI
No
11
$3,400
$3,189
$403
2015
 I
NS
No
66
$2,250
$2,223
Base
2015
 I
NS
Yes
3
$2,700
$2,683
$461
$461
2015
 I
MX
No
3
$2,200
$2,133
-$89
2015
 I
AI
No
76
$2,350
$2,354
$131
2015
 I
AI
Yes
20
$2,538
$2,696
$474
$343
2015
 II
NS
No
3
$2,100
$2,100
-$123
2015
 II
MX
No
1
$2,400
$2,400
$177
2015
 II
AI
No
4
$2,550
$2,538
$315
2015
 II
AI
Yes
10
$2,500
$2,598
$375
$60
Tier II heifers are sire identified out of a proven AI sire
NS = Natural Service
AI = Artificial Insemination
MX = Mixed lot of Natural Service and Artificial Insemination bred heifers
SMP = Show-Me-Plus

As can be expected from the beef market trends, the average price was lower in 2015 compared to 2014. In 2014 there was a premium placed on Tier II heifers, meaning buyers valued information on the genetic potential of the heifer, i.e. knowing who her sire is. We also see a premium placed on AI pregnancies. In 2015, we again see premiums for heifers carrying AI pregnancies and Tier II heifers. But, we also see strong premiums for Show-Me-Plus heifers, ranging from $60 to $461.

However, some of the premiums associated with Show-Me-Plus heifers could be due to the reputation of the consignor. To remove the effect of heifer consignor we fit a statistical model in which we adjusted for the effect of consignor, along with weight, number of head in the lot, pregnancy type, Tier I vs Tier II, region and buyer. In this analysis, Show-Me-Plus classification was fit as a random effect in which we predict its effect on price per heifer. (Estimated breeding values and EPDs are examples of random effects common to beef producers; random effects are simply predictions in which we account for uncertainty.) Below are the predictions from that statistical analysis.

UPDATE:
I have been analyzing (i.e. fighting with) this data for about a month, trying to make sure I understand it and analyze it appropriately. Over the weekend I had additional ideas about how to look at the data. Previously, if consignor and Show-Me-Plus status were fit separately, all of the variation in price went to consignor. So, in the previous analysis, consignor interacted with Show-Me-Plus status. Early this week I fit a different statistical model, that I think is more appropriate. In this model Show-Me-Plus status and consignor are fit independently. But, consignor has a main effect and an interaction effect with year (year is nested within consignor). This gives more conservative, and I believe more realistic, predictions for the effect of Show-Me-Plus status. I also fit the data from all three regions and only those regions in which Show-Me-Plus consignors had sold heifers in 2014 and 2015. The prediction only using consignors who sold in 2014 and 2015 was more conservative (by $100), so that is the data I report here.

Table 2. Predicted premiums for classifications in the Show-Me-Select Heifer Program.
Classification
Premium/Discount
2014 Sire Identified, Proven Sire
$64 $0
2015 Sire Identified, Proven Sire
-$78 $0
Artificial Insemination Pregnancy
$126 $130
Show-Me-Plus
$406 $204

Again, in 2014, we see a premium for Tier II heifers. But in 2015, the premiums associated with being sire identified appear to have shifted to Show-Me-Plus classification. Regardless of year, we predict a $130 premium for AI pregnancies (consistent regardless of the way data are analyzed). Heifers with a Show-Me-Plus classification received a $406 $204 premium in 2015. Because random effects are predictions, I would predict in 2016 that we see about a $400 $200 premium for Show-Me-Plus heifers.

If we only look at the Southeast and West Central regions, consignors who had Show-Me-Plus heifers in 2015 sold heifers at $133 and $165 above average (affect of Show-Me Plus status removed). They had the 1st and 3rd highest consignor effects. If we look at all three regions, the Show-Me-Plus consignors sold $30, $90, and $126 above average (the 3rd, 5th, and 12th largest consignor effects). If we do not include Show-Me-Plus status in the analysis, consignors of Show-Me-Plus heifers sold at $305, $244, and $218 above average (the 1st, 3rd, and 4th largest consignor effects.

I believe if we looked at data from additional years (2013, 2012, 2011, etc.) we would see a larger effect of Tier II heifers. However, in the 2014 and 2015 data, being sire identified basically had no effect. In the current model, I did not adjust for buyer.

We did not collect genomic prediction scores for the Show-Me-Plus heifers. Thus, the premiums are simply an effect of whether or not the heifer was tested. We would expect higher scoring heifers to sell for more money, but we have not collect the data to look at this in the Show-Me-Select program.

Here is the part you need to be aware of as a beef producer, especially if you sell bred heifers. The return on investment (ROI) for a heifer with a high density genomic-enhanced EPD is 433% 167%. But, we know we should be testing our heifers with the low density panels, thus the ROI for a heifer with GE-EPDs is 789% 326%. Commercial heifers tested with available commercial heifer products have ROI around 900% to 1500% 400% to 700%. Let's say my estimate is off by $300, with a $100 premium and a $40 test, the ROI is 150%.

Obviously, this is preliminary data based on a small number of heifers (86 Show-Me-Plus heifers out of 544 heifers sold in 2015). However, the results are very promising, and I look forward to gathering more data in 2016.

So, once again I say, "You Would be Crazy Not to Test!"

Thanks to Erin Larimore, David Hoffman, Zac Erwin, and Judy Burton for providing sale data and Jerry Taylor, Tonya Amen, and Michael Bishop for feedback on the analysis.

*Note: Updated text in blue, old results struck through.

Friday, January 22, 2016

Making a Positive Genetic Impact on Your Herd: NCBA's Cattlemen's Webinar Series


Technology in the beef industry is constantly improving, which can make it hard to keep up. Plus, we want to ensure that we are using all of the available practices to produce beef in a profitable, efficient, and conscientious manner. With this in mind, National Cattlemen's Beef Association hosts an annual webinar series, and this year I am excited to be involved!

On February 16th at 7PM CST, Bob Weaber and I will present during the NBCA Cattlemen's Webinar Series. Dr. Weaber will discuss the positive effects crossbreeding has on your cow herd and how new research is allowing us to better understand why crossbreeding works. I will discuss where we have been and where we are going with DNA and genomic technologies. There will be a question and answer period, so please bring questions.

Register today at www.beefusa.org!