A Steak in Genomics™

Written by Duane Dailey Beef cattlemen will gain insights into Show-Me-Select replacement heifers Friday, Jan. 4, at the start of their annual meeting in Columbia. The Missouri Cattlemen’s Association (www.mocattle.org) meeting runs Jan. 4-6, 2019, at the Holiday Inn Executive Center. The SMS group usually meets at the University of Missouri campus in Columbia. They will join on the first day for the heifer meetings. “Joining two groups benefits both,” says Dave Patterson, MU Extension beef reproduction specialist. “Both sides gain.” An educational seminar is planned for 2-5 p.m. on Jan. 4. Focus is on heifer development. Highlights are two SMS panels. The first covers “The Role of the Veterinarian in Heifer Development.” The other has five producers telling of success. Many veterinarians urge clients to follow breeding protocols of MU Extension for heifer development. A big SMS attraction to farmers is calving ease. Trouble-free calving also gains favor with veterinarians. Tha...

MANHATTAN, Kan. – Beef cattle producers have a wide range of selection tools available for use in selection of breeding stock. These range from visual appraisal to EPD (expected progeny differences) and selection indexes that leverage genomic technologies. Adoption of new technologies by the beef industry has dramatically changed beef cattle selection strategies and opportunities. Beef genetics and genomic tools continue to evolve at a rapid rate. To aid the development of new selection tools and their adoption by producers, researchers seek to understand current attitudes and perceptions of industry stakeholders. Producers and industry participants are encouraged to take part in an online survey to help inform the development of a new beef cattle selection decision support tool. This work is part of the activities funded through a recent USDA Agriculture and Food Research Initiative Critical Agriculture Research and Extension grant (2018-68008-27888) awarded to research and extension...

University of Missouri's Southwest Research Center near Mt. Vernon hosted an open house December 3rd that gave attendees a peek at the direction beef cattle research is taking at the 890 acre Center. Dr. Jordan Thomas, MU Extension beef reproduction specialist, led the presentations by asking if producers think they can afford not to use technology. Specifically, he mentioned estrus synchronization and artificial insemination. "The genetics of the AI bred calves allows producers to be competitive with the best herds in the country due to the use of elite bulls with higher accuracy expected progeny differences (EPD)," said Thomas. "The protocol results in more early-born heifers that are more likely to conceive earlier and remain in the herd longer." That longevity adds to herd profitability over the females lifetime. Their early-born steer mates will also be heavier than those out of a natural service sire that's born late in the calving season. Dr....

Matt Spangler University of Nebraska-Lincoln Are we done with changes? Releasing a single-step evaluation should allow us to focus attention on other topics and needs. EPD have been available to the U.S. beef industry for over 40 years. Survey results suggest that 30% of beef producers use EPDs or indexes as their primary selection criteria. Part of the lack of technology adoption is likely due to the confusion surrounding how best to use them. Also, some breed associations publish in excess of 20 EPD per animal. There are increasing number of EPDs, but we continue to publish indicator traits such as Birth Weight, when we have the economically relevant trait published, Calving Ease in this case. Selection indexes were first published in 1942, but the first breed-wide selection index for beef cattle was published in 2004. We have terminal and general purpose indexes in the beef industry. "We don't have any truely maternal indexes in the beef industry," Spangler sa...

Lee Leachman Leachman Cattle of Colorado Leachman's uses three indexes, $Ranch which is birth through weaning, $Feeder which is weaning to carcass, and $Profit which is $Ranch and $Feeder combined. "Most of us as breeders cannot look at 22 traits and compute a quadratic equation to identify the best combination of traits." Leachman said. On the female side they are adding $2 per cow per year using the $Ranch index. They have data from a cooperator showing an increase in pounds weaned per cow exposed. "We know we can make rapid change. We know it can be significant," Leachman said. With Lu Ranch, they added an inch to ribeye, doubled the number of cattle qualifying for CAB, and improved other traits included in the indexes. Leachman worked with his cooperators and after three years of discussion, they were able to share the indexes with other seedstock producers. Over 50 breeders are included in the evaluation. Over 38,000 records are added each year...

Shane Bedwell American Hereford Association Today is the 1 year plus 2 day anniversary of AHA's switch to single-step.This is the North American Hereford Genetic Evaluation including AHA and Canadian Hereford Association. They are currently working with Uruguay and Argentina are in the process of switching to the single-step approach. Part of the process was building a fully automated genomic pipeline to run the genetic evaluation weekly. They have been very happy with the quality controls measures that were built into this pipeline. AHA implemented a data pruning strategy to capitalize on their switch to whole-herd reporting in 2001. Animals that have data reported after 2001 plus 3 generations of their pedigree are included in the analysis. They have performance data on 2.3 million animals. They have genotypes on over 70,000 animals. Previously, all traits were fit in a single model. With the switch to single-step, AHA switched to 9 cluster models. They also re-paramet...

Mahdi Saatchi International Genetic Solutions IGS has data from about 15 different breed associations. They have 180,000 genotyped animals in the evaluation. Two years ago, they have 65,000 animals genotyped in IGS. Most of these were males. So, in the last two years they have almost tripled this number and have added many more females, through programs such as Cow Herd Roundup. IGS uses the BOLT software developed by Theta Solutions. This software allows many different types of models to be fit. IGS fits the single-step hybrid model. In single-step BLUP, you blend the pedigree relationships with the genomic relationship to have a single relationship matrix. In single-step hybrid you blend the genotypes and pedigree to infer genotypes for every animal in the pedigree. They then use the marker effects to estimate breeding values. In their genetic evalution they use a subset of markers that they have identified as predictive in multiple breeds. This subset of markers provides more...

John Genho Neogen/GeneSeek Genho works with American breeds and smaller breed associations to provide them with genetic evaluations. He implemented single-step BLUP to use genomic information. Brangus and Santa Gertrudis have monthly genetic evaluations. Brangus has over 21,000 animals genotyped. Other clients range from 3,000 to 6,000 animals genotyped. A lot of the problems with genomic prediction is having lots of animals in the pedigree, but with relatively small proportion of animals genotyped. However, Genho works with commercial ranches who have genotyped every living animal. This simplifies many of the struggles with single-step BLUP. Genho wonders what the next iteration of models will look like given the entire dataset is genotyped. All of the American breeds have Bos indicus influence. However, there are very few pedigree connection between these breeds. Genho wonders if identifying marker effects that could be shared across breeds could be an opportunity to share ...

Steve Miller Angus Genetics Inc. Details of genetic evaluation are published in their Sire Evaluation Report. angus.org/nce  The first four papers of the report contains the details of the evaluation. Miller states that it actually functions as a nice animal breeding textbook. Angus Genetics, Inc. does evaluations for 6 clients, ranging from weekly to annual evaluations. The weekly evaluation of Angus is a bit like Groundhog Day, same thing week after week. The Angus Association uses an unweighted single-step approach, and the development of this method is the result of lots of research that has been peer-reviewed and published. When they switched to single-step they asked the question if the new evaluation was actually better. They compared to the independent evaluation done by USDA-MARC. The new evaluation performed better. Because the single-step model allowed them to fit more traits in the same model, they improved the carcass trait model. By adding in weaning weigh...

Dr. Sara Place Senior Director, Sustainable Beef Production Research, NCBA Presentation at Mountaineer Cattlemen's College Headlines are largely negative regarding beef and sustainability. Increased questions about beef's environmental impacts, animal welfare, and health/nutrition. Many companies are using these concerns to market their products. Unfortunately, there is a lot of misinformation regarding beef's impact. Sustainability is a complex topic influencing environmental, social, and economic issues. Most of beef's opponents focus on environmental impact. It is true that beef tends to have a larger biological impact, because they are ruminants and produce gas. They also have later maturity compared to other livestock species. However, there is a lot of variability across the world in terms of beef's environmental impact. United States beef production has some of the lowest environmental impacts of cattle production across the world. Americans eat ...

Dr. Robin Falkner Zoetis Beef Technical Services Talk at Mountaineer Cattlemen's College We have put a lot of the blame for high-risk feeder cattle on the cow-calf producer. However, Falkner says it is the system, not the producer, that is to blame. Pre- and postweaning factors affecting bovine respiratory disease (BRD) in beef cattle and the resulting outcomes of the disease. + = decreased incidence or consequence; − = increased incidence or consequence; ? = effects not fully understood based on the available data. BVD = bovine viral diarrhea virus. Figure 1 from  Duff & Galyean (2007) Journal of Animal Science , 85(3), 823-840 . Falkner described how as his time since graduating veterinary school has passed, that he knows less but understands more. When talking to Falkner, people want a recipe. He provides two recipes, one for Possumneck pudding and Biscuit pudding.  We spend a lot of time chasing the right "recipe" for cattle health. What we need to d...

Written by Duane Dailey Replacement heifers to upgrade cow-calf herds will be offered in six Show-Me-Select sales this fall. Also, owners can restock cow herds culled in the drought. With strength in beef demand and rains growing pastures, herd owners can rebuild. Dry weather’s impact on forages had farmers concerned. “Optimism of cow-calf herd owners should return,” says David Patterson, University of Missouri Extension beef specialist. “The sales can help them.” Patterson has developed Show-Me-Select for more than two decades. The marketing sales are a small part of a year-round education program. The main parts are reproduction management and genetics. This year the sales reach beyond Missouri. All will be broadcast online at LiveAuctions.TV. Buyers anywhere can bid in every sale. Sales start Nov. 16 at Joplin and Kirksville. Consignors north and south in the state offer heifers guaranteed pregnant. Many of those will be timed-AI bred, giving a calving date and uni...

Dean Houghton Anyone who wants to protect soil, air and water is at ground zero. Houghton has been an observer of agriculture. He bought a 35mm camera and enrolled in journalism at the University of Missouri. He is also a farmer in Polo, Missouri. His wife loves baldie cattle and he raises sheep. When they first got married, Dean left the cattle alone and his wife left the sheep alone. But, they eventually realized it worked better if they managed the cattle and sheep together. They never leave anything uncovered using strip grazing, cover crops, and no-till. We need to recognize the benefits of cattle and livestock production including carbon sinks, soil health, and wildlife habitat. We can't sustain metropolitan areas without agriculture land. The year 1950 is the Great Acceleration point for the use of resources. We are now in the Anthropocene, which is defined as the earth's most recent geologic time frame. This is defined by human activity influencing geological p...

What does it mean to have a successful cow herd in the Ozarks? What should be the genetic focus? How do we select and manage cattle to perform on toxic endophyte-infected fescue? What technologies can be used profitably? What marketing opportunities could add value to the cattle? These are questions facing every beef operation in Southwest Missouri, including the University of Missouri Southwest Research Center. As the Center moves away from a focus on grazing dairy production, faculty and staff at the Southwest Research Center and on campus at the University of Missouri recognize there is now an opportunity to increase the emphasis placed on beef cattle Research and Extension at the Southwest Research Center. With support from the Southwest Research Center Advisory Board and key stakeholders in the regional and national beef industry, an effort to expand and improve the Southwest Research Center beef herd is now underway. A Beef Focus for Southwest Missouri A defined objective ...

Commercial beef producers will get more traits and selection index tools in the upgraded Igenity® Beef profile. The Igenity Beef Profile will offer 16 traits for $29, replacing Neogen’s 13-trait Igenity Gold ($40) and 6-trait Igenity Silver ($25) tests. The upgrade includes new predictions for weaning weight, yearling weight and hot carcass weight for a total of 16 traits scored on a 1–10 scale, plus two new selection indexes. “Our customers will be getting a powerful new profile at even greater value,” said Dr. Stewart Bauck, vice president of agrigenomics at Neogen. “The Igenity profile was designed and validated for crossbred or straightbred cattle with backgrounds of Angus, Red Angus, Simmental, Hereford, Limousin and Gelbvieh. “Most DNA profiles are breed-specific,” Bauck continued. “The novel design of Igenity Beef allows for the accurate prediction of performance in both crossbred or straightbred cattle among the target breeds. This lets cow-calf producers use a DNA profile t...

Megan Rolf Kansas State University What is genomic testing? We are looking at single base changes (SNPs) at thousands of locations across an animals DNA. We can use these DNA markers to predict genetic merit differences. We can also use these DNA markers for parentage. Other DNA test don't use markers, but they directly test the variant responsible for the phenotype. Examples of this are genetic defects or coat color testing. Genotyping in seedstock We collect a DNA sample, send it off to the breed assocation, and the data is incorporated into EPDs. DNA testing for genomic-enhanced EPDs is a breed improvement strategy. It is a way to make genetic progress faster. For a seedstock producer, it also provides customer service by providing more accurate EPDs. We can used DNA to improve EPDs using two approaches. First, we can use a DNA to create a prediction of the trait and blend this prediction with the EPD. Or, we can use the DNA to better estimate the relatedness between ...

Darrh Bullock University of Kentucky Crossbreeding should always be a consideration for commercial cattlemen. Crossbreeding has the greatest benefit for reproduction and other lowly heritable breeds. Practical Guide to Bull Buying Determine marketing strategy. Will heifers be retained? Make breeding decisions based on specific marketing plan. But, change marketing plan based on current situations. It's pretty easy to find a bull that will give you great feeder calves and market animals. When we are keeping replacement females, we are now asking a bull to create females and feeder calves. We've given him a new job. Determine your management level. What is your labor? How frequently do you visit your cattle? How much attention do you give to them? What is your level of nutritional management? Assure that bulls are reproductively sound with a BSE. Check for structural soundness. This is doubly important if you are retaining females. The tough one is to set performa...

Brandon Smythe New Mexico State University Three species Smythe works on: Horn flies Stable flies House flies House flies become an issue when we upset our neighbors. Dairy in New Mexico dealt with litigation from their neighbors. Everyone knows that flies are horrible. Both horn fly males and females feed on blood. Horn flies feed 30 to 40 times a day. Stable flies feed once or twice and then find a place to rest. Horn flies almost never leave a cow. Only time they leave is to lay eggs on a manure patch. There can be 200 to 1000 flies per animal. Flies are reproductively efficient. Flies lay 10 to 200 viable eggs per female. This reproduction efficiency allows for population surges. Horn flies are a warm weather pest, thus during cattle breeding and growing. Flies go dormant in winter months. Horn flies reduce performance in feed efficiency, growth and milk production. Horn flies are number one in causing production losses. We see a $5 to $8 return for every $1 ...

Jared Decker, PhD University of Missouri One point must be clear from the very beginning: EPDs work . When we select parents based on EPDs the genetic merit for that trait increases in our herd. When we select the parents using EPDs the performance of the next generation improves. EPDs Defined EPD stands for Expected Progeny Difference. These three words are loaded with meaning, thus the need to define them here. The most loaded word is Expected. Here we use Expected the way a statistician would use the word. Expected means we are making a prediction of a future value. But, in this context, Expected also means we are describing the average of a group. What is the group for which we are predicting the average? We are predicting the average performance of the Progeny or calves out of an animal. An animal’s own performance and its EPD can be quite different, because that is not the purpose of an EPD. The EPD is predicting the average performance of that animal’s calf crop. Final...

Ky Pohler Texas A&M University Pohler will discuss many different methods of pregnancy diagnosis. Producers need to find a method that works for them. When do cows experience pregnancy loss? 95% of time fertilization occurs. By day 28, pregnancy has dropped to 70%, a 25% loss of pregnancies. This is referred to as early embryonic loss. By day 42, we lose 8% more pregnancies, the pregnancy rate is now around 62%. This is late embryonic loss. Cows all cost the same to manage. If they don't have a calf or have a calf born late in the calving season, they cost us money. Knowing pregnancy status of the herd helps make management decisions. They can help with drought management (sell open cows) and marketing decisions. Pregnancy diagnosis also helps us evaluate bull or semen fertility and breeding program success. Pregnancy diagnosis doesn't cost a lot, but provides a great economic benefit. What is the ideal pregnancy test? High sensitivity (correctly identify...

Joe Dalton University of Idaho Sperm attributes necessary for fertilitization: Acceptable morphology Metabolism for production of energy Progressive motility Capacity for hyperactive motility Stabilization of plasma and acrosomal membrane lipids Acrosomal enzymes Chromatin integrity More is not always better. 1/2 cc straws are not better than 1/4 cc straws. How many sperm cells are needed to get a female pregnant? It depends. Different bulls have different sperm fertility. There are compensable semen traits, such as mis-shaped sperm, that compromise sperm quality. Increasing sperm number can compensate for this. There are incompensable semen traits, such as genetic inviablity, that compromise sperm quality. Increasing sperm number cannont compensate for these traits. They used Angus bulls on Nelore cows to look at the effect of sperm dose. They used 10 million, 20 million, 20 million, and 40 million sperm per straw. They put each of these treatments in different ...

Adam Summers New Mexico State University What are some of the management things we do to help cows stay in the herd longer? Most literature says a cow needs to produce 3 to 5 calves to be profitable. This depends on your level of supplementation and inputs. Heifers that calve early stay in the herd longer. Cows that calve earlier produce more pounds of calf at weaning over their lifetime. Heifers that calve early produce 550 lbs more of calf over their lifetime. Calves that were in utero during good years (above average rain) had increased birth weights and weaning weights. Calves that were in utero during bad years (below average rain) had more calves when they became cows. Reduced body weight prior to breeding heifers did not change the rate at which those cows left the herd. We are not using estrus synchronization and artificial insemination as much as we should. Main concerns were labor, time, and facilities. However, we can use a PGF2 to increase the number of heife...

Eric Scholljegerdes New Mexico State University The number one limiting nutrient on rangeland, whether in a drought or winter, is going to be crude protein. We are feeding two organisms when we are feeding a beef cow. First is the rumen microbes. The second is the cow. We see improvement in low-quality forage intake in response to crude protein supplementation. However, in a drought year this can be an issue. When grass availability is limited, we don't want to waste that resource. This is when a conservative stocking rate comes into play. If forage crude protein is above 8%, we probably don't need to supplement protein as intake is not going to increase. If crude protein is above 8%, we may want to supplement energy instead. Increase in protein allows the bacteria in the rumen to more completely digest the fiber in the diet. By-pass protein provides key amino acids. Non-structural forms of energy, e.g. starch from cereal grains causes a substitution effect. Non-...