A Steak in Genomics™

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 ".

Heifer selection is an important aspect of commercial beef operations, but unlike bull selection must be done without the aid of Expected Progeny Differences. This factsheet discusses considerations when making heifer selections, including available genomics tools and the importance of sire selection when replacement heifers are to be retained. For more information, see the eBEEF.org factsheet .

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...

Tom Short Zoetis Can genetic information from a simple DNA sample allow us to reasonable accuracy of the females lifetime performance? We know that our national cow herd inventory decreased to a very low level in 2014. When we rebuilt the cow herd did we keep low quality heifers that should have never been cows? What type of genomic prediction should we be using to select commercial heifers? GeneMax Advantage was produced by a collaboration of Angus Genetics Inc, Certified Angus Beef, and Zoetis. It is applicable to beef females that are at least 75% Black Angus. These predictions are based on the Zoetis HD50K product for Angus. The correlations between the genomic predictions and the breeding value are all quite good, around 75%. The individual traits are combined into three indexes. These are a Cow Advantage Score, Feeder Advantage Score, and Total Advantage Score. The correlation between Total Advantage and the Cow and Feeder indexes are about 70%, but the correlation b...

Breeding objectives indicate value of genomics for beef cattle Dr. Mike MacNeil DeltaG Is genomic testing a good value to seedstock producers? The answer to this question requires several different lines of thought. To answer this we need a system based approach. What makes up a genetic prediction? Information from relatives Molecular breeding value Correlated phenotypes Phenotype No individual animal in a genetic prediction ever has an accuracy of prediction of zero. The information from the calf's relatives brings in substantial amount of information. What are the advantageous of genomic prediction? 1) Increase accuracy of evaluation 2) More exciting is the opportunity to incorporate additional traits costly or difficult to measure measured late in life (after the time of selection decisions) sex-limited 3) Avoid prolonged generation intervals. For many selection decisions in beef cattle, we make many selection decisions around a year of age. 4)...

Guest Post Written by David Hoffman, MU Extension Livestock Specialist/County Program Director Spring is quickly approaching.  That means warmer weather and green grass are on the way.  For the cow/calf producers, it means that calving is in full swing (or about over for some) and the breeding season is just around the corner. Decisions are being made that will impact the cattle operation for several years, such as the next herd bull to purchase or the sires to breed cows and heifers through artificial insemination.  Some producers spend many hours in selecting the right bull for their operation, looking over pedigrees, EPDs, performance data, etc.  There is a tremendous amount of data available on purebred cattle, but limited genetic data on commercial cattle. In the past, selection for our commercial replacements has been on individual performance, structural soundness, body phenotype and possibly genetic information about sire(s) and/or dam. There has be...

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 !

My group is currently recruiting people to fill two graduate student positions. We will also be recruiting a researcher to fill a postdoctoral position in the coming year. We are looking for candidates who are passionate about genetics, genomics, and research. Ideal candidates are creative, hard working (while maintaining a work/life balance), and self starters. Our group is strictly computational, so candidates should enjoy working on computers and analyzing data. Candidates should be willing to learn programming (typically in R or Python), or already have some programming experience. We will soon have access to over 200,000 genotyped beef cattle with phenotypes and breeding values. We also have access to whole genome sequencing data from over 2,000 cattle. So, if you like working with lots of data, come join us! Our group uses population genomics to better understand the  history of cattle breeds and to inform future selection decisions. We are interested in local genetic ada...

Dorian Garrick Iowa State University The Pre-Genomic Era In the Pan-American Evaluation there are four countries, US, Canada, Uruguay and Argentina. Agricultural Business Research Institute (ABRI) collects the pedigree and trait data. Then the Animal Genetics & Breeding Unit uses BREEDPLAN to estimate EPDs. To put the number of records turned in to the AHA data in context, we can compare them to other breeds. The 11 breed associations in International Genetic Solutions add 340,000 new animals in each of 2012 and 2013. AGI adds about 300,000 per year. Herefords add a little less than 100,000 animals per year. The Early-Genomic Era Cattle have 30 pairs of chromosomes. There are about 100 million base pairs per chromosome and about 2.6 billion base pairs in the entire DNA (genome). Most errors in chromosome replication are fixed. But, some slip through and are passed down through generations. The EPD of a bull is a sum of the average gene effects he carries. Until the g...

Based on input and requests from breeders, we’ve been working on some updates to the information displayed on the Animal Search feature on Angus.org. These new features went live this morning [10 November 2015] , and I want to take a minute to highlight and explain these enhancements. Genomic Progeny  EPD percentile ranks Progeny  For complete post, please visit Angus Genetics Inc blog , and read the post by Dr. Tonya Amen. Decker's Take Home: I always love to see breed associations changing and innovating. I think these changes will allow producers to more quickly evaluate an animal's genetic merit. Plus, I'm sure breeders appreciate AGI responding to requests. Loading...

Duane Dailey Senior Writer, University of Missouri SPICKARD, Mo. - It has happened before, but always surprises. The biggest, best-looking beef cows had the worst genetic scores. At the University of Missouri Thompson Farm Field Day, eight cows were sorted out for study by farm visitors. Four cows were top of the herd. Four were on the bottom. They were sorted on genetic value scores from DNA testing. Cows that looked the best to visitors who didn't know the scores were large frame in good condition, but their calves at side were light-muscled and less fleshy. Jared Decker, MU Extension geneticist, said the bottom-scoring cows were ready to "go on down the road." They will be replaced by heifers from high-scoring younger cows. The soon-to-be cull cows had not produced prime-grade calves like the high-scoring cows, Decker said. Farm manager Jon Schreffler agreed with results from the GeneMax Advantage tests. The high-scoring cows also had high scores in herd ...

The Thompson Research Center Field Day will be held on Tuesday September 15, 2015 at the research center in Spickard. I will be discussing the use of genomics predictions in registered and commercial heifers. In addition to my talk and demonstration, there will be information on reproduction, nutrition and forages, antibiotic labeling, economics, and timber sales. In the survey below, let me know what topics or questions you would like addressed in my presentation. For those of you in Northwest Missouri, I would love to see you there. Loading...

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) ...

On January 27th I spoke with Scott Brown during the evening portion of the Southwest Missouri MU Extension Beef Cattle Conference organized by Patrick Davis, Andy McCorkill, and Eldon Cole. I discussed the facts about EPDs working to change a herd and how genomic testing can improve the precision and reliability of EPDs. Genomic testing is allowing us to select for traits that were previously not under selection, such as feed efficiency , bovine respiratory disease resistance, embryonic loss, and tenderness. You can download my slides from my extension website . But, in this post, I want to focus on Scott Brown's comments. For those of you who don't know Dr. Brown, he is a leading agriculture economist who has been influential in the formation of agricultural policy on the state and national level. On Tuesday night he gave a projection on the future of beef cattle economics. As we all know, beef prices are at record highs, but this is driven by historically low cattle num...

For those of you who follow my Twitter feed , you know I have been a little disgruntled about a paper that appeared in PNAS earlier this week. I think this paper may be the motivation behind a new documentary called " Cowspiracy " that Amanda Radke reported about on Monday. Jude Capper (a.k.a Bovidiva ) really takes this paper to tasks and points out some serious flaws in the analysis. In addition to ignoring beef's benefits as a source of nutrients such as iron and B vitamins, the habitat that ranches create for livestock, and the ability to turn arid rangeland into food, the authors also miss that cattlemen can be an ally to conservationists. But, Jude Capper and other have sufficiently defended the beef industry. In this post, I want to take this opportunity for us as a beef industry to collectively take a look in the mirror. What do we need to learn from this research? Despite errors in the analysis, should the beef industry decrease its use of feed grains? P...

Dorian Garrick Henderson originally described breeding values (EPDs) as sums of gene effects. Meuwissen, Hayes, Goddard re-expressed this as sums of effects estimated for genotyped DNA variants.   In current selection we have two models for genetic prediction, one for genotyped animals and a separate model for animals not genotyped. You can combine a pedigree based relationship matrix with a genomic based relationship, we call this single-step BLUP or HBLUP ( Aguilar et al., 2010 ). There is a second approach which Garrick refers to as a hybrid approach. Now breeding values for nongenotyped animals are expressed as the part explained by genotyped relatives and the part not explained by genotyped relatives. This is similar to the animal model where we have the breeding value explained by relatives and the breeding value due to the random shuffle of genes across generations. This model is in press and should be out later this summer (Fernando, Dekkers and Garrick 2014 GSE). I...

Several of the breed associations gave reports on their progress to implement genomic-enhanced EPDs. When a breed is small it is difficult to obtain genotypes of animals with reliable EPD estimates. More on this later. The American Gelbvieh Association has implemented and released genomic-enhanced EPDs. See page 30 of the April 2014 Gelbvieh World  for more information. Gelbvieh has implemented a solution unique to beef breeds in which a beef producer can either purchase a low density or high density SNP test. The SNPs not genotyped on the low density tests are implemented based on inheritance patterns in the populations. This process is referred to as imputation . This September, the American Hereford Association will be adding a low-density SNP test that will be marketed at half the cost of the complete SNP test. The SNPs not genotyped on this assay will be imputed from the genotyped DNA variants, the same as the Gelbvieh strategy. When first introduced, AHA genomic predicti...

I talked about use of high-throughput DNA sequencing to improve fertility by removing DNA variants from a breed that cause embryonic losses during pregnancy. Here is a  link  (Managing Broken Genes in the Age of Genomics) to the PowerPoint presentation I gave. I discussed the development of a genomic EPD based on the number of embryonic lethal variants (broken genes) that an animal carries that causes losses of embryos during pregnancy. DNA Sequencing Costs, Data from the NHGRI Genome Sequencing Program (GSP) http://www.genome.gov/sequencingcosts/  The cost of DNA sequencing has rapidly dropped in the last 15 years. In 2001 it cost about $10,000 to sequence a million base pairs of DNA. In 2014 it costs under 10 cents to sequence a million base pairs. This rapid drop in the price of DNA sequencing has enabled researchers to tackle questions that we previously could not address. With this sequencing data we are identifying loss-of-function variants (broken genes) that...

The "Bovine Respiratory Disease Symposium (BRDS) 2014: New Approaches to Bovine Respiratory Disease Prevention, Management and Diagnosis" is to be held at the Renaissance Denver Hotel in Denver, Colorado, USA from July 30th to July 31st, 2014. Registration is open and can be accessed, along with more information, at the Symposium website: http://www.brdsymposium.org The early registration deadline is June 15, 2014. The Symposium will include 2 days of presentations and discussions on a variety of topics relevant to BRDS. A research poster session will be held the first night. This meeting is being held in conjunction with the 2014  Summer Academy of Veterinary Consultants (AVC) meeting which will be held July 31st to August 2nd, 2014. We hope to see you there! As we previously noted , the Bovine Respiratory Disease Complex Coordinated Agricultural Project is using a variety of genetic analyses to better understand BRD and to predict an animal's genetic merit for...

The Tuesday and Wednesday prior to the 2014 BIF conference , the AICA will put on an event to discuss the development of genomic enhanced EPDs in the Charolais breed. Contact Dr. Robert Williams to RSVP for this event.