Dorian Garrick Theta Solutions LLC The Theta Solutions LLC is made up of Dr. Bruce Golden, Dr. Dorian Garrick, and Dr. Daniel Garrick. They have developed the BOLT software for genetic and genomic evaluations. The American Hereford Association formed an advisory committee to check the new genetic evaluation system. The advisory committee looked at the process during development. The advisory committee included: Joe Ellis Jack Holder Lee Haygood Paul Bennett Mitch Abrahamsen Suppose we had 100 progeny (i.e. offspring) on 1 bull. You might look at that bull and decide you like him or you don’t like him. But, that bull is just an envelop that carries genetic information. What the bull looks like really doesn’t matter, what matters is what his progeny look like. The way to look at the genetic value, or breeding value, of the bull is to look at his offspring. But, there are lots of environmental effects that influence the performance of the offspring. One example is the age ...

Daniela Lourenco The University of Georgia Before genomics, we were fairly happy with genetic prediction. Traditional evaluation combined pedigree, individual performance and progeny information. This was equal to summing all of an animal's genetics effects and dividing by 2. SNPs are used as markers for genes, or regions of the genome that impact production. The color of a banana peel (green vs. yellow) is a marker for banana ripeness. SNP markers are used in the same way. Marker assisted selection did not work. Why? Most traits are polygenic, meaning they are controlled by hundreds or thousands of genes. Trying to predict quantitative traits with a small number of DNA markers doesn't work well. What is 100,000 times cheaper now than in 2001? Airline flights are 2 times cheaper. Computers are 5 times cheaper. DNA sequencing is 100,000 times cheaper now than in 2001. A Holstein bull named Freddy was the best bull according to genomic predictions in 2009. In 2012, ...

Head over to the Brangus website to read my article, " Gene Editing: What Beef Producers Need to Know. " For more information, see Alison Van Eenennaam's blog post titled " FDA seeks public comments on regulation of genetically altered animals ." Importantly, the open period for commenting on the draft regulations has been extended until June 19th. Draft guidance:  https://www.fda.gov/downloads/AnimalVeterinary/GuidanceComplianceEnforcement/GuidanceforIndustry/UCM113903.pdf Commenting Website: https://www.regulations.gov/document?D=FDA-2008-D-0394-0279 ). Loading...

Denton, Texas — Cattlemen and women frequently ask if DNA scores are truly predictive of phenotypic results. A recent study completed by the Red Angus Association gathered DNA data on a set of Red Angus calves and followed the cattle through harvest, collecting phenotypic data. The results illustrated the Igenity® DNA scores accurately predicted carcass weight, marbling score and overall carcass value. The cattle were raised and owned by Bob and Elaine Yackley of Onida, South Dakota, and fed at a custom feed yard. A total of 91 head of 2015-born steers comprised the group that was DNA tested with Igenity Silver and followed through harvest to obtain carcass data on each individual animal. The top 25 head with the highest DNA scores for Average Daily Gain (ADG) and marbling were compared to the bottom 25 head, which exhibited the lowest combined DNA scores for the same two traits. Summarized results for the two groups are shown in the table. This comparative analysis reveals that ...

Hat tip to Dr. John Cole, USDA, and Jesse Hoff for bringing this to my attention on Twitter . I need to make an important point: I am not a patent lawyer. I do not have a deep understanding of patent law and nothing in this post should be considered legal advice or council. On November 8, 2016 Canada issued a patent to Ben Hayes and Michael Goddard for genomic prediction. Genomic prediction is estimating an animal's breeding value (i.e. genetic merit) using DNA variants. See the Canadian Intellectual Property Office website for more detailed information about the patent. Meuwissen, Hayes and Goddard first published their work on genomic prediction in 2001. Hayes and Goddard filed for a patent of the method on December 21, 2007 with the United States Patent and Trademark Office. About 23 days later, the Illumina BovineSNP50 Beadchip, a DNA test that can test 54,000 DNA variants quickly and cheaply for cattle, was released at the Plant and Animal Genome Conference. This 50K ...

This fact sheet goes through the fundamentals of how and when producers might use DNA testing in beef cattle production.  It covers the different types of tests that are available, how to submit samples and to whom, and what to do with the results. For more information, see the eBEEF.org factsheet " How to Get Started with DNA Testing ".

Tonya Amen Consultant for Illumina, Inc. One dairy operation was making $35 per year progress for net merit. After using genomics in late 2009, they were making $50 per year in progress for net merit. After they started testing females, this rate increased to nearly $80. This dairy herd is now seeing $340 more in life time production by using genomics. From 2005 to 2008, $B was increasing by $3.77 per year. From 2009 to 2015, $B increased by $5.62 per year. From 2013 to 2015, $B increased by $9.31 per year. A 146% increase in genetic trend. We have seen more rapid genetic improvement in Angus, Hereford and Simmental, all of which line up nicely with the deployment of GE-EPDs. Thus, it is possible (likely?) that this improved genetic improvement is due to the benefit of genomics. In the dairy industry, genomics is equivalent to 25 production records, 25 conformation records, and 140 fertility records. Genomics is saving the Canadian dairy industry $111 million dollars ann...

Producers may wish to collect DNA samples on animals for a variety of reasons including parentage testing, quantitative trait testing, testing for genetic defects, or archival purposes.  This fact sheet discusses the current methods of DNA sampling.  Please see the fact sheet for more information.  http://www.extension.org/pages/73198/dna-sample-collection#

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 provide...

Technology in the beef industry is constantly improving, which can make it hard to keep up. Plus, we want to ensure that we are using all of the available practices to produce beef in a profitable, efficient, and conscientious manner. With this in mind, National Cattlemen's Beef Association hosts an annual webinar series, and this year I am excited to be involved! On February 16th at 7PM CST, Bob Weaber and I will present during the NBCA Cattlemen's Webinar Series. Dr. Weaber will discuss the positive effects crossbreeding has on your cow herd and how new research is allowing us to better understand why crossbreeding works. I will discuss where we have been and where we are going with DNA and genomic technologies. There will be a question and answer period, so please bring questions. Register today at www.beefusa.org !

Angus Convention 2015 Richard Resnick CEO of GenomeQuest One can not impede scientific progress. - Mahmoud Ahmadinejad   Resnick gave a series of examples of how genomics is changing society. Resnick put a nice spin on the typical sequencing cost figure . He overlays Illumina's ( $ILMN ) stock price on top of the figure. He went on to explain that the only real differences between humans, cattle, corn, and other species is the proteins they make. The amino acids, the building block of proteins, are actually the same between species. Resnick used cystic fibrosis as an example of a disease in which genetics has been very important. One DNA variant that causes the disease is called ΔF508. When a person has this variant, the gene produces the protein, but a check and balance in the cell recognizes the protein as not correct and destroys it. A different variant, G551D, is not so severe that the protein is destroyed, but the protein does not function properly. A drug call...

And where are we going next? Data via  http://www.genome.gov/sequencingcosts/ . Code for generating the plot at  https://missouri.box.com/SequencingCost . This graph never ceases to amaze me. On the horizontal axis we have dates from September 2001 to July 2015. On the vertical axis we have the cost to sequence a million base pairs of DNA, with the axis having a logarithmic scale  (each tick mark is multiplied by 10, e.g. change from 10 to 100 to 1000). The blue line describes what is called Moore's Law  which describes the increase in purchasing power as computer costs come down. The rate of improvement in DNA sequencing easily outpaces the improvement in computing. Since September 2001, the price of DNA sequencing has dropped 6 orders of magnitude  from $5,292.39 to $0.015. From more than $5,000 to less than 2 cents!!! Same data as above by with the vertical cost axis  on a normal scale, not logarithmic. What caused the drop in sequencing f...

The American Angus Association® and Angus Genetics Inc. (AGI) will host the first-ever International Genomics Symposium as part of the 2015 Angus Means Business National Convention and Trade Show. The event takes place Nov. 3 in Overland Park, Kan., and will provide cattle producers with cutting-edge information about advancements in genomics technology – and how these advances impact their businesses. The symposium is sponsored by GeneSeek, a leading provider of comprehensive genomics solutions to the cattle industry, including the GeneSeek Genomic Profiler (GGP-HD). “We are excited about the symposium and what it will mean for the cattle business,” says Dan Moser, AGI president. “Genomics is rapidly reshaping the way we produce livestock, and providing producers with the best information available will not only help us improve quality and consistency, but also make our industry more competitive.” Genomics researcher and entrepreneur Richard Resnick (previously featured on this blog) ...

DNA sampling Tonya Amen, AGI During the second portion of the Breed Improvement session, Dr. Amen answered the question "How can we avoid sample failure when DNA testing animals?" She gave four points: Have proper collectors on hand. Blood samples are preferred, as the process can be automated. Blood samples can also be archived, whereas tissue samples cannot be. Contact your DNA service provide or see the Angus website. Have samples properly identified. "You cannot invent your own collection system!" said Amen. A business card, airline barf bag, and other home-remedies won't work! Practice good sampling technique. Make sure you have a nickel sized spot that has soaked completely through the card. Do not send wet samples-mold will grow like crazy! Make sure samples dry overnight in a safe place (not the dash of your truck!). Package well. Padded envelopes work well. Consider shipping method. How long will the sample be in transit? Staff at AGI have a...

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 !

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 recor...

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... ☺

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, affordabl...

Duane Dailey ,  Writer,  University of Missouri Extension COLUMBIA, Mo. – Selecting breeding animals on how they look, by phenotype, worked for centuries. Progress in improving cattle was made just on appearance. Now genotype pushes phenotype back to horse-and-buggy days. It’s data and what’s inside that counts. Arrival of huge computers and sequencing of the bovine genome changed all. “There’s a better way of selecting,” said Jared Decker, University of Missouri geneticist, at a Cattlemen’s Boot Camp, July 14 in Columbia. Training by MU scientists was sponsored by the American Angus Association with MU. The Cattlemen’s Boot Camp is a national program. Things changed in the 1970s with statistical models that predicted EPDs (expected progeny differences). Then software was developed to combine many EPDs into a single economic index number. Indexes help herd owners search a sire catalog to match a bull’s traits needed to improve a farmer’s cow herd profits. “We ...