Wednesday, October 22, 2014

Food Babe Visits University of Florida


Post at Illumination Blog

For those that have experienced the clarity and beauty of viewing the world through the lens of science, interacting with those who choose opinion and fear over facts and evidence can be very frustrating. But Kevin Folta, at the University of Florida didn't even get to interact with or question Ms. Hari about the misinformation she shares to a large audience. Head over to the Illumination blog to read Kevin Folta's thoughts. 

Wednesday, October 8, 2014

Brown Bagger EPD Updates

Jack Ward, Wade Shafer, and John Genho presented during todays NBCEC Brown Bagger seminar. They gave updates about how their breeds are utilizing genomic information.

Jack Ward
The American Hereford Association will release an Udder EPD in the Spring 2015 update, which is typically published in late December. They are also working on a Feed Efficiency EPD which could be released in December, but will more likely be in the Summer of 2015. In the Summer of 2015 the AHA will also publish a Sustained Cow Fertility EPD (similar to other breed's longevity EPDs) and a Heifer Calving Rate EPD (a measure of heifer fertility).

Ward also presented a nice analysis of price differences between bulls with and without genomic-enhanced EPDs. He set an upper limit of $15,000 to avoid high priced bulls that would skew the numbers. Bulls with traditional, low accuracy EPDs averaged $5,325. Bulls with genomic-enhanced EPDs averaged $7,475 at sale. More results can be seen in Ward's Hereford Genetic Summit presentation.

Wade Shafer
For the first training of Simmental genomic predictions, there were 2,800 animals with genotypes (DNA information) and phenotypes (trait measurements) available. This resulted in genomic predictions that gave the same amount of information as 1 to 9 progeny; which depends on the correlation between the genomic prediction and the trait, and the heritability of the trait. To avoid confusion, Shafer emphasized that they do not provide the genomic predictions to the producer only the genomic-enhanced EPD, which combines the genomic prediction and the traditional EPD. This is done to avoid confusion.

The American Simmental Association has created a collaborative genetic prediction service called International Genetic Solutions, which computes EPDs for 11 breed associations. The database contains records for over 15 million animals. During their last round of genomic prediction training they used 5,240 Simmental, 2,164 Angus, 1,604 Red Angus, 999 American Gelbvieh, 571 Maine-Anjou, and 85 Canadian Gelbvieh. For every trait the correlations stayed the same or increased. Progeny equivalents ranged from 1 to 28 progeny, Simmental specific weaning weight genomic predictions gave the same information as 5 progeny. The multiple-breed genomic predictions gave the same information as 8 progeny. For marbling, Simmental-specific genomic predictions gave the same information as 4 progeny, multiple-breed predictions gave the same information as 8 progeny.

In the current round of retraining they are using 56,116 animals from Simmental, Angus, Gelbvieh, Limousin, Red Angus, Maine-Anjou, and Shorthorn. They are currently looking at different ways to approach this training.

Researchers at Iowa State University have created a new approach to combine DNA genotypes and pedigree information in a single step. International Genetic Solutions is planning on using this method in the Spring of 2016. They are working with Bruce Golden and Dorian Garrick to completely rebuild the software used for EPD estimation. This software will use the new single-step method to incorporate DNA information, more robust accuracy estimates, and utilize modern computer hardware which allows multiple processes and faster calculations.

John Genho
Genho discussed the use of single-step  BLUP which simultaneously combines DNA genotypes and pedigree information. Every animal receives half of its chromosomes from its sire and half from its dam. On average an animal receives a quarter for it chromosomes from each grandparent, but these fractions can be quite different from a quarter in individual animals. Single-step BLUP uses DNA information to more precisely calculate relationships between animals rather than simply relying on averages. Genho's company Livestock Genetic Services, LLC uses this method for the Santa Gertrudis Association and several herd-specific genetic evaluations.

Monday, October 6, 2014

Angus Association Refines Genetic Evaluation


Expect Changes in $B Index Rankings

thompson research center_0265
*UPDATED 7 October 2014

I had a brief meeting with Dan Moser of Angus Genetics Inc today in which he informed me of several updates to the American Angus Association's genetic evaluations.

First of all, heifer pregnancy EPDs, which were not estimated this summer, are once again being successfully estimated. When the dataset became large the analysis would no longer run properly. Previously, the heifer's service sire was fit as a fixed effect in the EPD equations. This means sires were forced to have the same conception rate in every herd. In the new model, the service sire's conception rate is fit as a random effect, meaning that we do not perfectly measure the conception rate and allow for factors that influence conception, such as differences in semen handling, to vary between herds. The base year of the heifer pregnancy EPD was also changed from 2000 to 2005 due to 2005 being the earliest year with a large amount of pregnancy data.

Second, the fourth recalibration of Zoetis' genomic predictions was completed this summer. Very few changes were seen. The only trait that saw some movement was carcass weight. With over 60,000 animals genotyped most of the diversity within U.S. Angus has likely been sampled. Further, the effects of the approximately 50,000 SNPs have likely been accurately estimated.

Lastly, feed intake data will be incorporated into the $B (dollar beef) economic index this December. This is done to account for feed efficiency differences between animals. The cost of feed is a major driver of profit in the feed yard. The Angus Association now has sufficient data to include this important economically relevant trait in the $B index. Many sires that previously ranked high for the $B index will continue to rank high because they have excellent feed efficiency. But, many sires that have excellent growth, marbling, and yield, yet because their progeny inefficiently use feed will rank lower for the $B index. So, if your favorite $B sire drops in the rankings come December you now know why. This knowledge will allow you to make corrective matings in the future to increase the feed efficiency of your herd.

*My apologies to AGI staff for inaccuracies that appeared in the first version of this post.

Saturday, October 4, 2014

American Gelbvieh Association Releases Genomic-Enhanced EPDs

The American Gelbvieh Association (AGA) has released genomic-enhanced EPDs with the fall 2014 international cattle evaluation. Genomic-enhanced EPDs (GE EPDs) combine pedigree, individual performance and genomic information to save time and money, reduce risk, and accelerate the rate of genetic progress.

GE EPDs provide more precise EPDs based on a combination of both phenotype and DNA. One major benefit of these EPDs is risk reduction through increased accuracies. These increased accuracies save time when assessing young breeding stock as well as deliver commercial customer confidence when buying seedstock. Herd improvement is accelerated when breeders can more accurately identify young individuals with the best genetics.

GE EPDs also give the chance to collect data on economically important traits, which are expensive or difficult to measure.

The information from the genomic data can be as informative as a bull's first calf crop or a cow's lifetime production record. Since the genomic data is incorporated directly into the EPDs, cattle producers will not have to learn how to interpret the new data.

Development of GE EPDs for Gelbvieh and Balancer® animals has been in progress at the AGA since 2012, starting with the Genomic Pioneers project. This project helped to build a diverse panel of Gelbvieh and Balancer genetics to be the foundation genetics for the calculation of the GE EPDs.

"The AGA has been working closely with the scientific community over the past couple years to build the training population for developing GE EPDs for the Gelbvieh breed," says Susan Willmon, director of breed improvement at the AGA. "Implementing genomic-enhanced EPDs is a high-priority goal in the AGA's strategic plan and we are excited to be able to offer this tool to our breeders and their commercial customers."

EPDs that are genomically-enhanced will show up on the new American Gelbvieh Association Registry Service as highlighted in yellow. All animals with these enhanced EPDs will also have the AGA GE EPDs logo on their registration certificate.

For more information on GE EPDs visit Gelbvieh.org or contact Susan Willmon at susanw@gelbvieh.org or call 303-465-2333.

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Be sure to click on the links for more A Steak in Genomics content!

Wednesday, September 24, 2014

North American Limousin Foundation and American Shorthorn Association Move Genetic Evaluations to International Genetic Solutions

Cavans Waterloo Serene S171
Photo by Robert Scarth
Stier
Photo by LID
In a blog post by Kris Ringwall I became aware that the American Shorthorn Association has moved its genetic evaluations to International Genetic Solutions, the genetic evaluation arm of the American Simmental Association. The North American Limousin Foundation (NALF) has also announced that it is  joining a growing group of breeds that use Interenational Genetic Solutions (IGS) as their service provider for the estimation of EPDs. NALF joins Red Angus Association of America, American Maine-Anjou Association, American Chianina Association, American Simmental Association, American Gelbvieh Association, Canadian Simmental Association, Canadian Angus Association, Candadian Gelbvieh Association, and most recently American Shorthorn Association. The new Shorthorn evaluations were released this fall; the first release of Limousin IGS evaluations will be released in the Spring of 2015.
As Kris Ringwall points out, this is good news for commercial cattlemen as EPDs from these evaluations will be directly comparable across the partner breeds. This also provides a larger quantity of data backing these genetic evaluations. And, in the prediction of EPDs data is the name of the game.

Thursday, September 11, 2014

BEEF Editor's Blog:
Will Quality Beef Be The Industry’s Nirvana?

Learn More at Thompson Research Center Field Day

Burt Rutherford recently reported on a presentation by Mizzou's Scott Brown. Dr. Brown challenged beef producers to identify a strategy to remain profitable when beef prices come down in the next decade. Brown's solution is to target more cattle that grade Prime on the rail. He presented data from the Thompson Research Center, where 30% of the steer calves consistently receive a Prime grade. The genetics used at Thompson Research Center has allowed the herd to meet those levels.

To here more about the genetics and changes that have occurred at the Thompson Reseach Center, watch this blog or attend the 2014 Thompson Research Center Field Day where both Scott Brown and I (among others) will be speaking.

Wednesday, August 27, 2014

Smithsonian's Genome Unlocking Life's Code exhibit coming to St. Louis, Mo.

For a little over a year, the Smithsonian has housed the Genome: Unlocking Life's Code exhibit at the National Museum of Natural History. This fall, that will change as the exhibit makes a cross country tour visiting several U.S. cities. The exhibit will be housed at The Saint Louis Science Center from May 15 to September 10, 2015.

The exhibit was designed to celebrate the 60th anniversary of Watson and Cricks discovery of the structure of DNA. The exhibit allows visitors to learn about the human genome and genomics, and how DNA codes for the diversity of life on Earth.

I wonder if the exhibit discusses cattle... ☺