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.