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Showing posts from 2014

GE-EPDs and Genetic Selection
Breed Improvement Session
Angus Means Business National Convention

There was standing room only for the Breed Improvement Session of the Angus Means Business National Convention on November 4th, 2014.

Genomic Recalibration
Dan Moser, Angus Genetics Incorporated
Performance data reported to the American Angus Association has become more important than ever. Not only is this data necessary to get highly precise estimates from sires, but it is the foundation of developing genomic predictions for genomic-enhanced EPDs. In the training or recalibration of genomic predictions, basically an EPD effect is estimated for every DNA variant included in the genomic prediction test. The genomic prediction (also called the Molecular Breeding Value, MBV) is the sum of every EPD effect for approximately 50,000 DNA variants evenly spread throughout the cattle chromosomes.

Initial GE-EPDs in 2010 were based on 2,253 animals. In 2012 the training set increased to  11,756, by 2013 the training set was larger than 38,000 animals, and now in 2014 has reached over 57,000 an…

Feed Intake, $F, $B and You

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In October, we reported that Angus Genetics Inc would be including feed intake data into $F and $B indexes. On December 5th, 2014 those changes took effect. In our October poll, 91% of the respondents indicated that they considered including feed intake data as an improvement to the $B index. And, the data backs this up (see here for more about our data-driven philosophy). Since 2004 the American Angus Association has seen an increasing genetic trend for feed intake. This means Angus producers have been indirectly selecting for increased feed intake, which is a negative when we are striving for more efficient cattle.

One of the best examples of moderating one trait while improving others is the relationship between birth weight and other production traits. Since the mid-1980s Angus producers have been decreasing birth weight and the associated calving problems while increasing correlated traits such as weaning weight and carcass weight. This is perhaps one of the great accomplishment…

Data-Driven Extension Education and Research

As you know, I started in my current position at the University of Missouri Beef Genetics Extension Specialist in March of 2013. Check out the first A Steak in Genomics video to see how I describe my approach to extension education and research. (Excuse the ums and uhs, I was a little more nervous than usual as it was a job interview!)

Have you ever wondered why polls started appearing at the bottom of these blog posts? It is an effort to have a data-driven extension program in which we measure and respond to feedback from you, the Steakholders.

In order for us to really make progress in using genomic technologies and animal breeding best practices in beef production, there needs to be an open and honest conversation about these topics. If you ever are concerned there is an inaccuracy in my writings or presentations, please bring it to my attention as a comment on the blog, in an email, or a phone call. But please bring the data! Don't bring fallacies or antidotes to a data-drive…

Piecing the Puzzle
Story By Rebecca Mettler for Cattlemen’s News

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Rebecca Mettler wrote a story for the Joplin Regional Stockyards Cattlemens News. Mettler talked to Dr. Megan Rolf of Oklahoma State University and me about the use of DNA testing in the beef industry with a focus on commercial operations. Check out the article on page 18 of the November issue!

Food Babe Visits University of Florida


Post at Illumination Blog

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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. 

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 Geneti…

Angus Association Refines Genetic Evaluation
Expect Changes in $B Index Rankings

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*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 Z…

American Gelbvieh Association Releases Genomic-Enhanced EPDs

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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 …

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

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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 International 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…

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.

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

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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... ☺

Applying new technologies to investigate ancestry in cattle


Article from Fall 2011 "Lincoln Letter"
Newsletter of the North American Lincoln Red Assocition

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Jared E. Decker and Jeremy F. Taylor

Animal breeding can be viewed from the perspective of three basic categories: recording matings, predicting the outcome of matings, and planning future matings.  Thus, ancestry is a central and integral part of animal breeding, and breeders have had an inherent interest in ancestry since at least the time of Robert Bakewell (1725-1795).  Until recently, we could only trace ancestry as far back as we had pedigree records.  But, with the advent of DNA technologies we are now able to infer the extent of relationships among individuals separated by hundreds, thousands, and even millions of years – i.e., the individuals are from different species.
In 2009, we published research that describes the relationships between 48 different breeds of cattle and the relationships between cattle and other ruminant species. We used a recently developed DNA analysis kit, called the Illumina BovineSNP50 BeadChip, to survey approximately 50,000 sites among the entire 3…

The International Brangus Breeders Association Selects New DNA Testing Provider

SAN ANTONIO, TX- The International Brangus Breeders Association (IBBA) has selected GeneSeek, a division of Neogen Corporation, as the association’s new DNA services provider. The partnership will allow Brangus breeders to submit DNA samples to GeneSeek for parentage determination and lay a foundation for Genomic-Enhanced EPDs for the breed association. “IBBA’s agreement with GeneSeek moves us closer to conducting all Brangus parentage testing using Single Nucleotide Polymorphism (SNP) genetic markers versus previously used technologies,” said Dr. Tommy Perkins, IBBA Executive Vice President. Samples will be tested with the GeneSeek®Genomic Profiler™ GGP HD 80K (tests approximately 80,000 DNA variants) and the GeneSeek®Genomic Profiler™ GGP LD 30K (tests approximately 30,000 DNA variants) for eventual incorporation into genomic-enhanced EPDs for the Brangus breed. The GGP 80K is finding a role as a premium genomic profiler, while the GGP LD 30K is a highly accurate, affordable option …

Charolais Association Reaches Genotyping Milestone

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In their efforts to develop genomic predictions and genomic-enhanced EPDs, the American-International Charolais Association announced today that they have surpassed the 1,000 samples suggested to develop genomic predictions. Now that this level has been reached the association can prepare to release a commercially available genomic prediction test. As we have seen in other breed associations, once the genomic prediction test is commercially available, the amount of data available for retraining can grow. As new animals are tested they can also be used in future rounds of retraining (also called recalibration).

This is an exciting day for the AICA. Congratulations Charolais breeders! Now, what will you do with genomics?
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"Vache de race charolaise avec son veau" by Forum concoursvaches.fr - http://www.concoursvaches.fr. Licensed under CC BY-SA 3.0 via Wikimedia Commons.

Eureka Genomics Receives USDA Grant For Bovine Genotyping Project

Management aims to raise additional capital to commercialize range of high-value targeted genotyping assays for clinical, animal health, and agriculture.

HERCULES, CA, August 18, 2014 — Eureka Genomics, a leader in Next Generation Genotyping (NGG), announced that it has been awarded a $450,000 grant from The National Institute of Food and Agriculture. The Institute is an agency of the U.S. Department of Agriculture (USDA). Eureka Genomics was awarded this grant to commercialize a second generation NGG assay focused on bovine genotyping known as the Sparse Genome Scan (SGS).

Eureka Genomics’ SGS is a technology platform that produces commercially relevant data, currently generated from micro arrays, at less than half the cost.

This most recent USDA grant awarded to Eureka Genomics follows an ongoing cooperative research and development agreement with the USDA’s Meat Animal Research Center.

"The USDA’s financial and research support is part of Eureka Genomics’ strategy to accelerat…

Dan Moser to Lead Angus Genetics Inc.

Angus announces new AGI president and director of performance programs.

The American Angus Association® welcomes Dr. Dan Moser as its new president of Angus Genetics Inc. (AGI) and Association director of performance programs.

A unanimous selection of the AGI board of directors, Moser brings more than 15 years experience in genetic research and education to the Association’s 25,000-plus members and their commercial partners.
“We are excited for Dr. Moser to join our team of talented professionals and for what he represents to the future of genetic evaluation for the Angus breed,” says Kevin Yon, chairman of AGI and Angus breeder from Ridge Spring, S.C. “Dan not only is one of the industry’s most respected geneticists, but also possesses a common touch, a rare ability to communicate complex concepts into actionable and beneficial information for producers. Along with our talented team of scientists and customer service providers, we are looking forward to him taking our genetic evaluat…

Improving Feed Efficiency: Feed Efficiency Project Releases Decision Support Tool

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The Beef Feed Efficiency Project has released a new decision support tool. The tool is an Excel spreadsheet in which producers can enter data on a group of cattle with growth and feed intake data. Click here to download the Excel file.

The spreadsheet is pre-loaded with some example data. Depending on how you define efficiency, the animals rank quite differently. Let's consider the example data in the "Many Wts +fatRFI" tab. (See the "notes" tab for further explanation about the traits reported or this factsheet released by the project.)

If we look at Feed:Gain ratio (F:G) Ear Tag 3 is top ranking animal.

Ear Tag ADG Met.Mid Wt. DMI Fat F:G 3 5.24 207 21.0 0.30 4.01 5 5.06 205 23.0 0.25 4.54 1 4.62 179 22.0 0.20 4.76 6 4.52 213 23.0