Monday, December 9, 2013

Angus Association Announces Third Recalibration of Zoetis HD 50K Prediction


The American Angus Association announced the 3rd recalibration of the Zoetis HD 50K product. The previous recalibration was based on about 40,000 animals and this recalibration is based on about 51,000 animals.I want to highlight a few points from Crystal Albers' interview with Dr. Kent Andersen of Zoetis and Tonya Amen of Angus Genetics Inc.
First, genomic predictions and genomic-enhanced EPDs are self-improving. Every animal tested can be used for the next round of improvements and recalibration.
Second, genomic predictions reduce the risk and improve the accuracy of purchase decisions for commercial producers.
Third, for the first time the HD 50K product produces genomic-enhanced EPDs for heifer pregnancy.
Fourth, Zoetis recognizes the need for more aggressive marketing of animals with genomic-enhanced EPDs to see a greater return on the investment. They use a website called GenomeXchange where their customers have the opportunity to list information about their operation and advertise cattle that have been tested.

Don't hesitate to contact me if you would like to discuss how genomic technologies could fit into your operation.

*Note: this is not an endorsement of a particular product, simply a discussion of changes in genomic prediction.

Friday, December 6, 2013

My Genetic Ancestry

Congratulations to Eric who only missed my percentage of Neanderthal ancestry by a tenth of a percent! I am 2.9% Neanderthal, which puts me in the in the 83rd percentile (which means I have more Neanderthal DNA than 83% of 23andMe customers).

I also learned other information about my ancestry. I am basically Northern European, most of which is British and Irish.


23andMe has also identified 991 possible relatives. For a handful of these relatives I've been able to identify the ancestor that we have in common.

It has also been interesting to find my risk predictions for certain diseases, my carrier status for several inherited conditions, and predictions for various traits. Unfortunately, 23andMe has runaground of FDA regulations and have stopped offering health predictions to new customers.

As someone interested in population genetics, genealogy, and genomic predictions, I have really enjoyed the information provided by 23andMe. I'm hoping that 23andMe can overcome its difficulties with FDA approval, so that others can benefit from the health predictions provided by genetics.

Thursday, December 5, 2013

Science Fair:
Grey Horse Cancer

Young grey horse
by Jaydot
My second cousin, Elida Miller, is starting her science fair project on grey horse cancer. She is requesting a picture, registered name, age, and breed of horses with cancer. If you know of one please send the pictures and information to ewmsciencefair@gmail.com. 



Would you like to have your science fair project publicized on my blog? Send your information to DeckerJE@missouri.edu.

Tuesday, December 3, 2013

Innovative Genomic Predictions Require Innovative Marketing
Opinion Piece



From discussions with seedstock producers at the recent Hereford Education Forum, I realized producers need to use new marketing strategies when utilizing genomic predictions. If you purchase genomic predictions for your yearling bulls, but continue to market your bulls locally, you are not likely to have a favorable return on your investment. You will need to change one of two things: either your current customers will need to recognize the increased value of animals with genomic-enhanced EPDs or you will need to broaden the scope of your marketing. In the short run, I believe marketing to a wider customer base will be the easier solution. For example, a seedstock producer could market nationally any animals that rank in the top 10th percentile of the breed, while continuing to market his remaining crop locally. To reach this national market the producer will need to advertise in national publications, on their farm's website, through internet sales, or in national consignment sales, just to list a few examples.

The GeneMax™ (GMX) Elite Bred Heifer Sale is an excellent example of combining innovative genomic technology with innovative marketing. The genomic test is an integral part of the marketing program for this sale, so much so that they put it in the name! 

I will be interested to see the results from this sale. I think we will see a premium for heifers that score exceptionally well on the GeneMax test, and we will see average prices for heifers that had GeneMax scores below 50. In the future, I will also be interested to see if consignors are more stringent on GeneMax scores or if they let discerning buyers place a higher value on the heifers with better scores. Because reproduction is a lowly heritable trait (i.e. environment is more important than genetics for reproductive success), it is also important to use best practices, such as those outlined in the Show-Me-Select Replacement Heifer program when developing heifers.

To see a significant return on investment, early adopters of genomic prediction will need to employ similar marketing strategies. 

*Note: this is not an endorsement of the GeneMax™ test or the Elite Bred Heifer Sale. 

Wednesday, November 27, 2013

Beef Genetic Prediction Workshop to be held at Kansas City, Dec. 12-13

by Duane Dailey

As animal scientists and farmers learn more about beef cattle genetics, this knowledge will be used to make predictions and select breeding stock.
A Genetic Prediction Workshop will be held in Kansas City, Dec. 12-13, to share the latest information and experiences.
“We’re at a stage where beef breeders, especially seed-stock producers, can learn and add to the discussion,” says Jared Decker, University of Missouri Extension geneticist, Columbia.
The conference brings together academic, beef industry, breed association and cattle producer leaders.
“Ways to use genomics in cattle selection will be a major focus,” Decker said.
The conference is hosted by the Beef Improvement Federation, a national group.
The speakers will share their progress. An aim will be to work on ways to use the genome to enhance EPDs (expected progeny differences). Commercial cattle producers can use those EPDs to select breeding stock.
The meeting will include plans for making across-breed EPDs. Research on that project is underway at the U.S. Meat Animal Research Center, Clay Center, Neb. A USDA working group, NCERA, is pursuing that development.
The conference will be at the Holiday Inn KCI, 11728 NW Ambassador Drive, Kansas City, Mo.  The registration fee covers meals during the conference.
Program and registration details are available at http://www.ksubeef.org under “Upcoming Beef Events.” Pre-registration closes Dec. 1. Motel accommodations are at a special rate.

Friday, November 8, 2013

Presentation on broken genes in beef cattle
National Beef Cattle Evaluation Consortium Brown Bagger seminar

One of the focuses of my extension program is helping farmers and ranchers understand how to manage genetic defects in their herds and how science is changing how we identify these broken genes. I recently gave a webinar during the NCBEC Brown Bagger series, which can be viewed here.

I know each producers is going to have different opinions about managing defects. The point I strive to make is that we need to use optimal strategies to manage these loss-of-function mutations.

Monday, October 28, 2013

Beef Improvement Federation to Host Genetic Prediction Workshop
Dec. 12-13, in Kansas City, Missouri

The Beef Improvement Federation (BIF) will host a Genetic Prediction Workshop in Kansas City, MO on December 12-13, 2013 at the Holiday Inn KCI Airport and KCI Expo Center, 11728 NW Ambassador Drive.

The conference is designed to give academic, allied industry, breed association staff and cattle producers a forum to learn about and discuss the latest developments in beef cattle genetic evaluation strategies. The implementation of genomics technologies in national cattle evaluation systems will be the focus of discussion.  Speakers will highlight the experiences and current status of technology deployment at several major US breed associations, experiences developing genomic predictions of genetic merit and alternate strategies for computation of genomically enabled EPDs. The conference will also feature discussion of planned modifications to the system used to compute the Across Breed EPD adjustment factors at the US Meat Animal Research Center.

A USDA multi-state project (NCERA-225) focused on implementation and strategies for national beef cattle genetic evaluation will meet prior to the Genetic Prediction Workshop. This meeting will feature station reports and research updates from a number of committee members.
Registration for the BIF Genetic Prediction Workshop is $100 and includes a buffet breakfast, lunch, dinner and breaks during the conference. For NCERA committee members, an additional registration of $25 is required and includes a breakfast and break for this portion of agenda. Attendees must preregister for the events by December 1, 2013. Online registration and full agenda is available at http://www.ksubeef.org in the ‘Upcoming Beef Events’ section.

LODGING: A room block is available through November 8, 2013 at the Holiday Inn KCI Airport. Room rates are $92 plus applicable tax and are available the nights of December 11 and 12.  Conference attendees should call the hotel reservations department directly at 1-800-957-4654 and identify themselves with the NCERA-225 & BIF Genetic Prediction Workshop block.  Reservations made after 11/8/2013 are accepted based on room type and group rate availability. 

For more information about the BIF Genetic Prediction Workshop or the NCERA-225 meeting please contact Dr. Bob Weaber at 785-532-1460 or bweaber@k-state.edu or Lois Schreiner at 785-532-1267 or lschrein@ksu.edu.



Story by: Bob Weaber

For more information:

Dr. Bob Weaber – 785-532-1460 or bweaber@ksu.edu

Monday, October 21, 2013

Genomics, Ancestry, and a Contest!

In addition to DNA variants' utility in predicting EPDs, disease risk, and other traits, they are also very useful in predicting an individual's ancestry. The most common use of this in livestock is parentage verification or testing. But DNA variants can also be used to look at relationships over much longer time scales. For example, my coauthors and I have used SNPs to look at relationships among ruminant species and breeds of cattle.


Last week I sent 10 mL of my saliva to 23andMe to for processing and DNA testing. This is the human equivalent of genomic-enhanced EPDs (although 23andMe uses different statistical methods). In addition to finding out if I carry specific genetic disorders and my risk for common diseases, I will also find out about my ancestry.

One of the interesting things we have learned from sequencing ancient genomes is that most humans from Europe or Asia have Neanderthal ancestry. So, as part of my 23andMe results I will learn what percent of Neanderthal ancestry I have.

So, here is the contest. Whoever has the closest guess to my percentile rank for the amount of Neanderthal ancestry will win a $20 gift certificate to Texas Roadhouse, or another steak house of their choosing. Your guess must be a number between 0 and 100. A guess of 0 would mean I have no Neanderthal DNA and I am likely from Africa. A guess of 100 would mean I have the most Neanderthal DNA of any living human. A guess of 50 would mean that I have an average amount of Neanderthal DNA. Guesses must be made in the comment section of this blog, guesses on any other social networking site will not be accepted. Contest will run till November 5th, 2013. Ties will be broken by whoever posted their guess first. Extra points will be given for the funniest jokes!
reconstruction: John Gurche; photograph: Tim Evanson
Guess away!

*NOTE: There were glitches with the comments section of this blog. Because of that I opened the contest up to people who also made comments on social media sites. Edited 19 November 2013.

Wednesday, August 28, 2013

Thompson Farm Field Day

I will be speaking at the Thompson Farm Field Day on Tuesday September 17th about increasing the precision of purchasing, mating, and culling decisions. Hope to see you there!


Friday, August 23, 2013

BEEF Cow-Calf Weekly
The Truth: Every Living Thing Is A Genetic Defect Carrier

Pills 014 Here is a link to my article in the BEEF Cow-Calf Weekly. I know there may be some questions (and disagreement) about my article. Please comment with questions or contact me by email.
Luckily, we now have the tools to manage these broken genes.

Gereedschapsrek monument dieselgemaal Papekop aan het Kromwijkerpad te Woerden

Thursday, August 22, 2013

North American Limousin Foundation updates parentage testing

I received news that NALF is switching to SNP genotyping for parentage verification. Quote from their e-Partners newsletter:
 Performance Committee 
SNP Parentage Transition
Within the past 12 months, members have experienced problems with parentage verification due to new lab contracts and GeneSeek Inc.'s acquisition of long time NALF official parentage DNA lab Scidera. In order to alleviate verification issues and extended turn around times, the NALF board has decided to transition all parentage testing to SNP technology starting with calves born January 1, 2013. Members with active AI sires and donor dams will be receiving a letter in the next week requesting samples on their AI sires and donor dams which GeneSeek and NALF will run historical profiles on in order to verify their progeny via SNP free of charge. These historical animals will not be rerun for parentage verification. New samples are requested if at all possible. Please read your letter in regards to semen samples. If you have any questions, please contact Brittany or Joe in the NALF office.    
I would be happy to answer any questions breeders may have about this change.

Monday, August 19, 2013

Cattlemen can avoid passing on broken genes

Radio Free Strawberry
by Alan Levine
I had a great conversation with Tom Steever at the Missouri State Fair Simmental Event.

Listen to the interview. Then, post your thoughts in the comments section.

In the future, how will your operation approach genetic defects?

Most important innovation?

BEEF Magazine is running a poll asking the question, What’s The Most Important Innovation In Genetics?

Artificial insemination and EPDs (national databases) are currently the most popular answers. But, these two innovations relied on one another to be successes!
Artificial insemination would not be as beneficial if we could not identify the outstanding sires that deserve to be used in herds across the country. EPD evaluations would not be nearly as accurate if we didn't have huge numbers of progeny for popular sires. Plus, these progeny are born in very different environments across the country, so we are able to accurately account for environmental effects in EPD predictions. These two technologies rely on each other and work together. So, my answer is both!

As DOC HARRIS said, the important word in the poll question is "was". If the question used "will be" I think the answers would be different. As new challenges arise in the beef industry, I will be keeping an eye on the solutions offered by genomics.

Thursday, August 15, 2013

Reaching the Peak

Peak
By Gürkan Sengün [Public domain], via Wikimedia Commons
A member of the Ranchers.net's Ranch Talk Forum, graybull, made an interesting comment about my blog. 
Very interesting thoughts about DNA testing and related.  And you are exactly correct...........more tools will get you where you are going.
Cavet is that "if you are driving on the wrong road........going faster will only get you there quicker."
I realize that this is a common misconception from the examples and explanations I have been using to describe genomic selection and genomic-enhanced EPDs. Let's see if I can fix that.

Two thoughts.
First, these tools can be used to reach an optimum rather than an extreme. In fact, as you get closer to the optimum, you need to make small, precise steps, rather than large steps of varying precision. As you approach the apex of the peak, if you continue to take large steps, it is possible you could go past the optimum. But, decreasingly small, precise steps in the right direction will help you reach the optimum. Genomic-enhanced EPDs provide more precise estimates of the animal's genetic worth earlier in the life of the animal, especially when compared to parent average EPDs. Genomic-enhanced EPDs provide the most bang for the buck when young animals are tested for which there is little data. By making breeding and culling decisions using more reliable genomic-enhanced EPDs, a breeder will be able to reach an optimum easier.

Assume the grid below represents two traits, birth weight from left to right and milk from front to back. If birth weight is too small, calves are under-developed and struggle after birth. If birth weight is too large, we end up with calving problems. If milk is too low, the dam does not provide enough milk and the calf is light when we take it to market. If milk is too high, the dam does not have the energy resources to be fertile and rebred. For these two traits we are trying to reach the optimum in the middle. Genomic-enhanced EPDs can help us reach that peak, as we make better decisions when we cull heifers or buy a clean-up bull.
Mexican hat potential polar
By RupertMillard (Own work by uploader, with gnuplot) [Public domain], via Wikimedia Commons

Second, as a caveat, there is an idea floating around that if you are going to fail, fail fast. This is a data-driven philosophy where you try a new approach, gather lots of data, then quickly evaluate the outcome. If the new approach is working, continue to use it. If the new approach fails, cut your loses and move on. This idea is usually associated with tech start-ups, and I make no claims about how appropriate it is to livestock production.

Please share your thoughts in the comments about reaching an optimum or failing fast.

Wednesday, August 14, 2013

Cherry Picking and Cattle

From Wikimedia Commons, the free media repository
There is a great post about picking cherries and raising cattle at the Black Ink blog. I really like how the husband and mother-in-law had different attitudes toward change. It is also interesting how the source of new information influenced the response.
What traditions in livestock genetics need to be questioned?
Do you have an example of how your operation questioned tradition and found an improved practice?
I would love to see your examples in the comments section.

Friday, August 2, 2013

Judging Contest with a GeneMAX twist


Certified Angus Beef is have an intersting contest on their Facebook page where people are asked to visually appraise and rank a set of 4 heifers. But, the official placings are based upon their GeneMAX scores. GeneMAX is a genetic test marketed by Zoetis to identify cattle that grow well in the feedlot and produce a highly marbled carcass. Post your placings on Certified Angus Beef's Facebook page for a chance to win. Post the reasons for your placing in the comments section below!

Friday, July 5, 2013

DNA future inspires action now


Cody Jorgensen talked with Angus VNR about the reasons he uses genomic technologies. In addition to collecting more information earlier, Jorgensen also discusses the impact genomics may have in the future.

If you are a smaller producer with limited resources, what can you do now to prepare to use genomic technology? The first step is to collect tissue samples, either hair bulbs or blood on FTA cards, on all of your animals for future use. The next step would be to test influential animals in your herd. This is typically going to be your herd bulls, as they produce the most progeny each year.

We don't know if genomic technologies will be rapidly or slowly implemented, but we do know they are here to stay. As Jack Ward said at the BIF Convention, "The boat has left. You can either get on it or be left behind."

Wednesday, June 12, 2013

Comparison of updated Angus GE-EPD tests

As you may know, both Zoetis and GeneSEEK have updated their genomic tests.

Zoetis still uses about 50,000 SNPs, but have now trained their data set with more animal records and genotypes. The genetic correlations for the Zoetis test range from 0.38 to 0.73. See this Angus Journal article for more information.

GeneSeek now use about 80,000 SNPs in its genomic test. The genetic correlations for the GeneSeek test range from 0.60 to 0.70 for most traits, except milk which is at about 0.4 and calving ease direct which is at 0.34. See this explanation from the American Angus Association.

So, the accuracy differences appear to be pretty small.

Both tests cost $75. If you add genetic abnormality tests, such as AM, NH, or CA, to the Zoetis test, you pay $23.00 per test. If you add an the same genetic abnormality tests to the GeneSeek test, you pay $8.00 per test. See the Angus Genetics Inc. website or https://www.angusonline.org/AGI/AgiDnaPricing.aspx for more details.

Tuesday, June 11, 2013

Scientific Hype Cycle

File:Gartner Hype Cycle.svg
Gartner Research's Hype Cycle diagram, by Jeremy Kemp.
27 December 2007. Used under a CC-BY-SA license.
 

I was recently told that I was being over exuberant in my promotion of genomic technologies. If I have slipped into hyperbole, it has been for two reasons:
a) An unintentional mistake.
b) Push back against the disillusionment of a valid technology.

In previous decades new DNA technologies, such as microsatellites, AFLP markers, etc, lead to a lot of hype about how the beef industry was going to be radically changed by these DNA technologies. These were the "Technology Trigger" and "Peak of Inflated Expectations" in the diagram above. I've previously described that these single gene DNA tests completely under-performed compared to expectations. Consequentially, the "Peak of Inflated Expectations" was followed by the "Trough of Disillusionment". In this period of disillusionment, two important things happened. First, Meuwissen, Hayes, and Goddard proposed a new way to use DNA markers to predict genetic merit. Rather than looking at individual genes, they suggested we use markers throughout the genome to account for 100% of the animal's DNA in these genomic predictions. Unfortunately, in 2001 the technology and capability to simultaneously test enough markers was not available. But, in 2007 a group of universities and the USDA developed a DNA panel that was release by Illumina in 2008 as the BovineSNP50 BeadChip. With this technology we could now simultaneously test over 50,000 markers evenly spaced throughout the genome. Genomic selection was implemented within the dairy industry in 2009, and later several beef breed associations followed suit.

Genomic prediction works, as the dairy industry has shown.
From Brian Van Doormaal, 2012. Increased Rates of Genetic Gain with Genomics. Canadian Dairy Network.
The rate of genetic change visually increased with the start of genomic selection in 2009. I would guess that the dairy industry is somewhere between the "Slope of Enlightenment" and the "Plateau of Productivity". Hopefully, the beef industry will leave the "Trough of Disillusionment" and start the trek up the "Slope of Enlightenment". To do this, we need to have genomic tests at price points that allow broad application within the industry, genomic tests which explain a large portion of the genetic variance, and explanations to help producers understand when and how to use these technologies.

Bottom line. Genomic selection works. And that is no hyperbole.




p.s. For those of you needing some entertainment and encouragement. Enjoy.



Monday, May 27, 2013

Angus Report: Identifying the Stars

Today on the Angus Report, Jena Thompson and I discuss using genomics to distinguish differences between full siblings and identify the superior animals at an earlier age.



Jena also mentions a new project at the University of Missouri in which we will sequence the genomes of approximately 150 bulls from 9 different breeds. From this research we will identify variants that reduce fertility and lead to cows not getting bred earlier in the breeding season.

How Risk Adverse Are You?

I just came across a great post by Allie Janson Hazell about risk tolerance and genetic testing on The Genoscape blog.

In several posts (such as this and most recently this) I've argued that livestock producers should use genomic-enhanced EPDs to reduce their risks. Rather than the risk of finding out about health issues, which is discussed on The Genoscape, in livestock production we are interested in financial risk. So how risk adverse are you?

To find out, head over to the Rutgers Cooperative Extension website and take their Investment Risk Tolerance Quiz.

In future posts I plan to discuss reasons other than risk management why genomic-enhanced EPDs are valuable.

Thursday, May 23, 2013

You Would be Crazy Not to Test!


I am in the process of purchasing a new house. In this process I am collecting as much information as possible to make an informed decision and reduce my risk. I've had the home inspected, which included looking at the roof, exterior, basement, crawl space, kitchen, bathrooms, electrical, heating, air conditioning, plumbing, and vegetation. I've also paid for a radon inspection and a pest inspection. I've done all of this because this is a large investment and I want to avoid future headaches.

This winter and spring we have seen several bulls in various breeds sell for prices with six figures. Whenever I look at these bulls on the respective breed association websites, I am shocked that most of these bulls have parent average EPDs. These bulls have no production, progeny, or genomic information. Why does this surprise me?

If we think back a few years, we can identify a bull that sold for six figures at a national sale. At the time this bull was marketed, his parent average EPDs put him in the top 25% of his breed for an important trait. But, several calf crops later and a much more reliable estimate of his EPDs, this bull is now in the bottom 25% for that important trait. Genomic selection alleviates this problem!

Genomic selection and genomic-enhanced EPDs provide the same amount of information as about 10 to 20 progeny. The buyers of these six figure bulls could have collected much more data and significantly reduced their risk of making a poor purchasing decision. They could have demanded that the bull be tested with a genomic panel prior to the purchase. If the seller is getting six figures for a bull, I'm sure he can scrape up $85 for a genomic test.

When we purchase a house, we are making a decision that will affect us for years to come. When we purchase a bull, we are making a decision that will affect our herds for years to come. By purchasing bulls with genomic-enhanced EPDs buyers are getting a clearer picture of what they are actually purchasing. In my opinion, you would be crazy not to test!

Monday, May 13, 2013

Commercial Agriculture Profile

I was featured in the Spring 2013 issue of the MU Commercial Agriculture newsletter.
My favorite line from the interview:
"We are at a point where the technology used to analyze DNA is rapidly changing. The tools we use in animal breeding are also changing. My main focus will be to educate beef producers on how to utilize the new technologies to increase their profits."

Friday, May 10, 2013

New Price for Hereford GE-EPDs

Previously I discussed companies lowering prices for Angus genomic-enhanced EPD tests and a cost-sharing program for the American Hereford Association.
Now the American Hereford Association has decreased the cost for all animals to $85. From the Hereford eNews:

Price Change for DNA Testing

The American Hereford Association (AHA) has worked closely with GeneSeek Inc. and the National Beef Cattle Evaluation Consortium (NBCEC) to adopt a new pricing structure for genomic-enhanced expected progeny difference (GE-EPD), parentage and abnormality testing.
The new cost will be $85 and will be inclusive of all of testing except horned/polled (H/P), that cost will still be an additional $48.
This $15 savings will allow breeders the opportunity to do more comprehensive herd testing. The basic panel for parentage and abnormality testing is still available for $30 or $20 if you do 50 animals or more. The procedure is still the same and hair follicles from the tail are still the preferred method of DNA. You can find an instructional video for proper hair collection on the Hereford YouTube Channel.
For more about Hereford DNA testing download the DNA Testing Procedures Fact Sheet. To request DNA kits or for more information, contact Toni Shapiro at 816-842-3757 ortshapiro@hereford.org.
If you've not had a chance to check out the Hereford educational videos take time to visit the Hereford YouTube channel or Hereford.org and see what's available.

Monday, May 6, 2013

Diagnostic for Disease Susceptibility in Sheep

Here is an article about the discovery and utilization of genetic markers to reduce the susceptibility of sheep to ovine progressive pneumonia virus.
From Viral Infection in Sheep Linked to Gene:

"Producers could use the marker we’ve made available to make a flock genetically less susceptible to disease, and therefore, decrease the risk of animals becoming infected again over time," Leymaster says. 
The ultimate goal is to give producers tools that allow them to choose breeding stock that do not have genetic risk factors, he says, so they can reduce the prevalence of OPPV and eventually eradicate it from flocks. 
 "We don’t want to oversell these findings, but at the same time, we want producers to consider how they might use this to their advantage," Leymaster says. "We’re continuing our research and will be able to contribute additional information in the future. I’m optimistic that the industry will be able to successfully address this major disease problem." 
This is a great example of using genomics to meet a need of the industry and improve animal welfare.

Thursday, April 25, 2013

Happy DNA Day!
Welcome to the genomic revolution

Happy DNA Day! Today we celebrate the publishing of the double helix structure of DNA by Watson and Crick, but we also celebrate the genomic revolution which is upon us. The genome is the collection of all the DNA in your body, or in your livestock's body, or any other living organism for that matter. Richard Resnick gave a great TED talk about the genomic revolution. While the decline in the cost of sequencing has slowed, scientists, including those in agriculture, continue to push the genomic revolution forward.










For those of you who worry this video is all about humans, steak is mentioned at 6:30 into the video and food production is mentioned at 7:00.

The genomic revolution will continue to impact the way we produce and consume our food. Astute livestock producers will put their "typewriters" in the closet and embrace the "computers and Ethernet" of genomic technologies.

Tuesday, April 16, 2013

Angus Report: $W Index

Tonya Amen from Angus Genetics Inc. discusses the weaned calf value, or $W, selection index. As breed associations continue to collect data and conduct research, they will calculate additional EPDs. It will become increasingly difficult for cattle producers to practice multiple trait selection as they are inundated with trait EPDs.

Fortunately, this is were selection indexes come to the rescue. These combine multiple EPDs into one value, weighting each EPD by its economic importance.

Friday, April 5, 2013

Beef Improvement Federation 2013


Missouri producers interested in quality beef and genetic improvement can attend a nearby national meeting. But, they need to sign up before April 15th to get the early-bird rate.
The Beef Improvement Federation (BIF) meets in Oklahoma City, June 12-15. It’s where researchers, producers and industry leaders meet to discuss discoveries in beef production.
The theme is “Where Profit and Progress Intersect.” A major topic will be the crossbreeding vs. straight-breeding debate.
New genetic tools are available that aid production of quality beef. Producers will hear various sides of all issues.
MU beef reproduction specialist Dave Patterson will present results of research on breeding protocols. Those were developed and tested at the MU Thompson Farm, Spickard Missouri.
It’s a chance to hear the latest in beef cattle breeding and genetics.
The main program is June 13-14. Other events and ranch tours surround the meeting at the Renaissance Hotel and Convention Center in Oklahoma City.
There will be more than serious science. The group visits the National Cowboy & Western Heritage Museum the evening of June 13. Entertainment includes the Bunkhouse Band.
Producers can sign up at the BIF website. Hotel links are included.
There is one fee for all four days. However, various combinations down to one-day tickets are available. The early-fee deadline is April 15.

Read more at University of Missouri Extension news.

Friday, March 15, 2013

Genomic Sweepstakes!?!?

Pfizer Animal Health (I thought we were supposed to call them Zoetis?) is having an online sweepstakes to gain more information about producers' use of and attitude towards genomic testing.

This contest only pertains to Angus-influenced cattle, as the HD 50K product is designed for registered Angus cattle and the Genemax product is designed for commercial cattle with a high percentage (>75%) Angus ancestry.

Here is a link to enter the sweepstakes. Here are the official rules.

Monday, March 4, 2013

Beef Genetics Extension
My new career in science communication and translational research

I am excited to announce that I have accepted a tenure-track faculty position in the Division of Animal Sciences at the University of Missouri focusing on beef cattle genetics extension and research. While my basic research efforts will continue, such as reassembling the bovine reference genome sequence, a much larger part of my efforts will focus on my extension program.

My Extension Program

My extension program will be a mix of science communication and collaborative translational research, concentrated on using genomic technology in beef cattle breeding and production. I will work with beef breeders to help them understand and use new genomic technologies in their operations. I will collaborate with breed associations to assist in developing and deploying genomic selection programs. I have adopted Cees Leeuwis' redefinition of extension education as communication for rural innovation.

My Motivation

When I was 9 years old I exhibited a heifer at my county fair. I was dead last in a class of about a dozen heifers. Due to my competitive nature, I did not enjoy that experience! This motivated me to learn as much as possible about genetic improvement and animal breeding. The Hereford World became one of my favorite magazines. My final year in 4-H I bred and exhibited the champion heifer at my county fair.
Goldie, my champion show heifer from the 2001 show season.

It was while reading the Hereford World that I first became aware of and interested in DNA technologies. Obtaining a PhD in Genetics was a perfect fit for my life-long interest in science, evolution, selection, and animal agriculture. Becoming a professor and using genomic information to improve animal breeding is a youthful aspiration come true. Thanks to everyone who has made this a reality. Now, let's deliver on the promise of genomics!

Thursday, January 31, 2013

Data-Driven Bull Buying

There are lots of ways to make a decision. We can act on our impressions or intuitions. Or, we can gather data and let the evidence guide our decisions. I call this a data-driven philosophy.

This week, Amanda Radke and Kris Ringwall gave their perspectives on a data-driven bull purchase. Both are great articles that I encourage you to check out.

Here is my take—we need to make our decisions on a single metric that takes all available information into consideration. These metrics are expected progeny differences (EPDs) and economic indexes. EPDs combine performance records, information from relatives, information from correlated traits, and—in the case of genomic-enhanced EPDs—results from DNA tests. EPDs are the most accurate measure for a particular trait of the bull's merit as a sire. Economic indexes combine multiple EPDs and economic values of each trait to create a single measure of the bull's merit for increasing a producer's profit. We should not be selecting on performance data, because these measures are confounded with the environment in which that bull was raised. Economic indexes, because they combine various forms of data, should be the main source of information when making selection decisions.

One of the traits that beef breed associations do not estimate EPDs for is structural correctness. Currently, beef producers must visually inspect animals to make sure they are structurally sound. Sam Comstock gave a presentation during the NBCEC Brown Bagger series about how the dairy industry estimates  genetic merits for structural soundness.

Bull buyers that would like to take less risk when purchasing a bull should look for producers who provide genomic-enhanced EPDs for their sale offerings. Genomic-enhanced EPDs are more accurate than pedigree-based EPDs because more information was used when estimating the EPD. The more reliable the EPD (i.e. accuracy), the less that value is going to change over time. When the EPD accuracy is higher, the producer can be more confident that the bull will meet his expectations.

Let's continue to strive for data-driven decision making in animal agriculture.