A Steak in Genomics™

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 t...

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...

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 .

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 consignmen...

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 acro...

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 .

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 ...

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 ...

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!

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.

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 sem...

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?

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 kee...

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...

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.

Come see me tomorrow at the Missouri State Fair!

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!

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."

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...

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,...

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.

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.

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 a...

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."

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 preferr...

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 dis...

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.

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.

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....

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 .

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 w...

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 selectin...