A Steak in Genomics™

The beef industry values sustainability. We value successful operations that are passed on to generation after generation. That is why beef producers support  youth programs. Those of you who know me personally, know I am way too busy for my own good.  I've learned to say no and am making strides in simplifying. When the beef project leader in my kid's 4-H club came open, I should have kept my mouth shut. Instead, I volunteered to be the leader, because I value educating youth. I wanted to pay it forward and help kids fall in love with cattle the way I did. On Friday July 8th will be our Sturgeon Beef Show . I hope those of you in mid-Missouri will come out and enjoy the successes of our youth. If you are interested in sponsoring a breed champion, please let me know. Thanks to those who have already sponsored. Watch the blog for pictures of my little ones falling in love with cattle. If you time driving by my house just right,  you might even catch a glimpse of a comp...

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)...

Dr. Mark Enns Colorado State University If we had the ability to improve maintenance feed consumption likely would improve profitiability of beef production. To make genetic improvement we need genetic variability. Is there variability for maintenance energy? Hotovy et al 1991 measured intake and fasting heat production on twins to estimate heritability of maintenance energy. The heritability was 0.51. But, putting a large number of cattle through metabolism chambers is not feasible. What tools are available to change maintenance energy? Mature weight and height Body condition scores Maintenance energy EPD For two beef breeds, we see an unfavorable trend for mature size. If we go from a 1000 pound cow to a 1500 pound cow, we have increased the maintenance requirement by 35.5%. But, maintenance energy is a function of both body weight and milk production. $EN index produced by the Angus Association is an economic index weighting both body weight and milk production. ...

Dr. Dave Lalman Oklahoma State University Lalman points out that we have made tremendous change for post weaning growth. Right now finished cattle weights are increasing at a rate of 9.4 pounds per year. Carcass weights are increasing by 5.7 pounds per year. Marbling has also increased over time. Compared with 1995, we have seen fewer yield grade 1s and 2s, but we have seen more yield grade 4s and 5s. The number of yield grade 3s has increased from 34.2% to 46.7%. The cow-calf sector and the entire industry have responded for the need for increased post-weaning performance and carcass quality. The increase in calf prices has increased by $5.25 per hundred weight (cwt) per year. The increase in costs has increase by $5 per year. Profitability appears to not have changed that much. Lalman discussed analyses by Pendell and coworkers published in 2015, in which they analyzed Kansas Farm Management Association data. The data had information from 79 operations with data from 201...

Dr. Matt Spangler University of Nebraska-Lincoln A seedstock producer's goal should be faster genetic progress ( breeders equation ). But, we need to balance this by the cost of the genetic progress. Although some of these traits are interesting to us as biologist (what Spangler termed "biological intrigue"), what really matters at the end of the day is improving cattle. What is the difference between an indicator trait and economically relevant traits? Economically relevant traits are traits that directly impact profit by either influencing revenues or expenses. Indicator traits are traits that are recorded because they allow us to more reliably predict economically relevant traits. An example of this would be calving ease direct and birth weight. No one gets paid for or has costs associated with birth weights. But, birth weight is a great indicator of calving ease, because calving ease can have economic impacts through labor, dead calves, cows that don't rebr...

Chip Ramsay Rex Ranch "I'm humbled to be in front of you." Ramsay said, "You all represent the most passionate and educated group of producers." Nirvana, what does that mean? In the Buddhist tradition, nirvana is described as the extinguishing of the fires that cause suffering and rebirth. These fires are typically identified as the fires of attachment, aversion, and ignorance. Rex Ranches and their feed yard face weather volatility. In 2012, calf cost was $635, in 2013 it increased to $876. They also face price volatility, there were swings in $241 of calf price over five years. There has to be trust between segments. Weighing conditions, changed to do what is best for the cattle instead of worry about who gets the advantage. Because of the integration of the cow-calf and feed yard, they can streamline vaccination protocol and reduce redundancy. This also requires sharing added value. Is it a zero sum game or can we add value? We need to have an abu...

Holly Neibergs Washington State University Neibergs lead an effort to identify key genes within the network of genes that influence feed efficiency differences. In this analysis they analyzed over 700,000 DNA variants in about 800 Hereford steers. For these Hereford steers they calculated the residual feed intake. Residual feed intake is how much the observed feed intake differs from the expected feed intake based on average daily gain and body weight. For over 19,000 genes, they identified the DNA marker within 8,000 base pairs of the gene that had the largest effect. These effects were assigned as the effect for that gene. They could then analyze networks of genes to look for gene networks that were significantly involved in feed efficiency differences. Gene networks involved in cell division, including cytoskeleton organization, influenced differences in feed efficiency. There were also genes involved in the formation and regulation of peroxisomes found to influence feed effi...

Dan Shike University of Illinois The correlation between the growing dry matter intake (DMI) and finishing dry matter intake was 0.56. This means 56% of the variation is shared between the two feeding periods. Average daily gain is not that repeatable. The correlation between average daily gain in the growing period and the finishing period is only 0.11. However, residual feed intake (RFI), a measure of efficiency, is  repeatable between feeding periods, with a correlation of 0.63. Using 35 days on feed accounts for about 95% of the variation in feed intake from a 70 day feeding trial. Intake seems to be very repeatable across stages of life and on different diets. The residual feed intake (RFI) repeatability was 0.42 when comparing a forage diet to a grain diet. Intake is repeatable. Gain is not repeatable between test periods. Shorter duration intakes are strongly correlated to total feeding period intake. Intake of forage is correlated to intake of grain, furthe...

Jerry Taylor University of Missouri The project assembled DNA samples, individual feed intake, growth and carcass data for 8,000 animals from 8 major beef breeds.The project has various objectives, including identifying genes with different levels of expression between high-efficiency and low-efficiency animals, create genomic predictions for feed efficiency, and identify DNA variants responsible for differences in feed efficiency (causal variants). The project collected 12 Angus sired steers, 12 Charolais sired heifers and steers, and 12 Hereford sired steers, half of which had poor feed efficiency and good feed efficiency. They collected over 15 tissues per animal. In the Hereford RNA sequencing data, the team found genes that are involved in metabolism. In the Angus and Charolais data they found many genes involved with immune function. This is likely due to the poor feed efficient animals having subclinical illness which led to them having poorer performance and less efficie...

Slides from my presentation at the GeneSeek meeting prior to the Beef Improvement Federation meetings. The Value Of Genomic Predictions in Beef Cattle from Jared Decker Slides can be downloaded here:  https://missouri.box.com/s/cls1uj42xcxf17aum1su516x39tsxy9q

Dr. Keith Belk spoke at BIF this morning. Belk suggested we should select based on the microbiome. Should we be selecting based on the microbiome? No. First, our current understanding of the microbiome is very incomplete. Second, the microbiome is not perfectly inherited. Every calf inherits 50% of its DNA from its sire and its dam. DNA can be used for prediction because it is inherited in a predictable manner. The microbiome is not inherited to the same level of predictability. The highest heritibility for a bacterial family is below 40% ( DOI: 10.1126/science.aab3958 ) in human twin studies. In other words, the microbiome is more influenced by the environment, then by inheritance. The microbiome may be a trait that we want to select, but I do not believe it is the tool to make selection decisions. Swapping genes between symbionts and their hosts are very rare events. Animals have developed mechanisms to stop this from happening. Animals strive to stop other organisms from ...

Dr. John Stika Certified Angus Beef Sometimes we think about beef production from a cow based focused. We think about our brand, the brand on the side of our cattle. Stika states we have seen a shift toward thinking about branded beef programs. Stika states, "The only sustainable flow of dollars from which to continue to build the beef business comes from the consumer." Sometimes we see a bull sell for high dollars, and we hear questions about if that was "real money." The dollars that come from consumers is absolutely real money. CAB's pull-through strategy: Exceed consumer expectations Build repeat business create benefit across the entire chain Strengthen demand for beef (increase supply and price at the same time) When consumers make purchase choices, taste is still king. The comparative retail price of beef is increasing relative to poultry and pork. To keep consumers happy, we have to provide them with better beef. Would you buy the same ...

Dr. Glynn Tonsor Dr. Ted Schroeder Kansas State University The comparative advantages of North American beef industry is world trust and premium prices. North America is the leader in grain-finished production. North America has a sound and effective infrastructure; feed grain base, processing, safety, transportation, genetics and meat quality expertise, research discovery and education. Some of the comparative disadvantages of North American beef production is that it is not the lowest price per pound producer. Further, there is limited communication, coordination, and signaling between sectors of beef production. There is fragmented support of traceability systems and focus on future beef demand. Schroeder stated it is important to remember that the value of beef production comes from supplying demands of beef consumers. We need to make sure that the domestic consumer market accepts what we are doing. The United States population is changing, and we need to make sure we are m...

Matt Barten Founder, EMBRUON We can now biopsy an embryo to extract a small number of cells. We can then extract DNA from that cell. In order to test that DNA with a SNP chip, it has to be copied (amplified) 2,100 times. This is like taking a bushel of corn and amplifying it to a trailer load of corn. Biopsying an embryo only decreases embryo pregnancy rates by about 10%. One of the straight forward applications of embryo biopsy is to look for carrier status of genetic abnormalies. We can now do a full GE-EPD test on these biopsies. This means we can actually decide which embryos to implant based on the embryo's genetic merit! We can know earlier and earlier what the genetic merit is, allowing us a new way to shrink the generation interval. Barten's company flushes a day early at 6.5 days, then send embryos back out at 7.5 days. They currently use human IVF tools to ship the embryos the same day. He biopsies the embryo and sends back the frozen embryos. The biggest ...

Jerry Taylor University of Missouri Why did we create a new SNP chip? There have been four large USDA research grants that Taylor has been a part of. From theses grants, there has actually been a synergy, the sum has been greater than the individual parts. In one grant they planned to genotype 4,000 variants in 10,000 cattle to look for variants causing embryo losses due to broken genes. The feed efficiency project and the bovine respiratory disease complex projects both budgeted to test 1,000 variants in 2,000 cattle. With a fourth project, they won additional funds to create a SNP chip to look at 200,000 DNA variants in over 17,000 cattle, thus tying all four projects together. If a DNA variant is lethal, meaning it causes an embryo which carries two copies of the variant to be aborted, then we will never see an animal carrying two copies of that DNA variant. We can look at the inheritance of DNA variants through pedigrees and identify DNA variants that we should observe anim...

Bruce Golden Theta Solutions Over the last 50 years we have had evolution of the statistical methods used to calculate genetic predictions, EPDs, for livestock. What drove the evolution of these methods? Knowledge of statistical models? New methods? Data? Enabling computer technology? Golden states that he believes the drive for better models has been a desire to increase the accuracy of prediction. Golden and Garrick had written grants to write genetic prediction software in the past. This avenue appears to have dried up, so they decided to start a company, Theta Solutions, in order to fund the development of genetic prediction. The latest genetic prediction runs contained 46,000 animals with genomic data. Theta Solutions uses graphical processing units, originally built for video gaming, to have a high performance computer at a relatively low cost. The BOLT software focuses on custom turnkey analyses, once the system is set up all one needs to do is feed it data. Using non-G...

EPDs represent the genetic components of an animal’s phenotype that are expected to be passed on to the next generation. Studies have shown that using EPDs are seven to nine times more effective than selecting based on actual phenotypes. This fact sheet will assist readers in understanding how to interpret EPDs and breed averages, and be able to use percentile ranks in order to identify potential sires that fit the desired breeding objective. Please see the fact sheet for more information. http://articles.extension.org/pages/73314/epd-basics-and-definitions#