A Steak in Genomics™

Decker explains the importance of utilizing hair shedding EPDs to increase animal adaptability. “Hair shedding is linked to milk production, reproduction and possibly animal welfare. Hair shedding is easy to collect and predict so it may play a role in selecting genetics with an improved adaptability to heat stresses,” said Jared Decker, University of Missouri associate professor. He gave his presentation “A Piece of the Adaptability Puzzle: Multi-breed Hair Shedding Genetic Effects and EPD” during the Beef Improvement Federation (BIF) Symposium June 23 in Des Moines, Iowa. Cow efficiency and adaptability is a multi-pronged and complicated puzzle. Researchers have pursued the identification of local adaptation and region-specific genomic predictions in beef cattle using hair shedding scores as an indicator of tolerance to heat stress. Hair shedding scores measure how early the winter hair is shed off in the spring and summer. Cattle tend to shed their winter hair from front to back an...

Larry Kuehn and Tara McDaneld U.S. Meat Animal Research Center Bovine Respiratory Disease may be hard to diagnosis. Have to keep in mind that prey animals, like ruminants, have evolved to hide being sick. What are the BRDC pathogens? Bacteria Mannheimia Haemolytica Pasteurella multocida Mycoplasma bovis Others Virus Parainfluencza-3 Infectious Bovine Rhinotracheitis Bovine Viral Diarrhea Bovine Respiratory Syncytial Virus Bovine Coronnavirus (implications relatively recent) Viruses typically aren't severe on their own, but they are often the gateway for bacteria infections to start. Difficulty of BRDC treatment records as phenotypes Disease incidence measured as 0 or 1 Subclinicals/shedders analyzed as healthy How do we overcome these difficulties? Large sample sizes are needed. USDA MARC is not using a subset of USMARC Germplasm Evaluation Program. MARC is also working to improve the quality of diagnoses/necropsy. They are also looking for indicato...

Jeremy Howard Smithfield Premium Genetics  Smithfield Premium Genetics is the nucleus that provides sows (over 1 million) for Smithfield and the sires of the terminal market pigs. At Smithfield, they mate a Landrace to a Large White to produce the commercial F1 sow. These sows are then breed to a Duroc. The terminal pig then has maximal heterosis (maternal heterosis and direct heterosis). SPG uses single sire semen of Durocs to mate to commerical farms in Missouri and North Carolina. They collect 60,000 carcass data points per year. On the maternal side, it is had to get stayability data because generations are turned over so quickly. They use commercial test herds to collect this data on sows. Howard said that genomic information on purebred animals prior to selection allows them to better predict performance in a commercial setting. This genomic data also allows them to figure out if problematic meat is produced at a company owned farm or an outside source. Big data is dri...

Mark Trotter Central Queensland University His research is outcome, not technology driven. It is not finding shiny new tools and asking how can I use it. Rather, it is looking at problems in the industry and finding solutions, including technology, to help it. Northern Australia is much more similar to central America that it is to the United States. Southern Australia is similar to the southern US. There are several tools for stocking rate management, but there is a need to get good tools into these systems. There is now high spatial and temporal satellite data  that is now basically available for free. There are emerging radar satellite systems. There's a lot of hype around "smart tags" and other agtech, but what's the actual need and value? There are three key bits of information producers would love to have from a sensor system: Location Behavior Health Producers see lots of applications for smart tags. Location We went from big backpacks on ca...

John Genho Neogen GeneSeek Why do we use a crossbreeding system? To gain the advantage of heterosis, the cross outperforming the parent average. Retained heterosis is the amount of this advantage that is maintained after multiple generations of mating crossbreed animals (not mating the purebred parents). Dominance, over dominance, and epistasis likely all contribute to heterosis. In general, traits with higher heritabilities have lower heterosis and traits with low heritability have higher heterosis. Why don't commercial producers use crossbreeding? The average herd size is 40 head and 9% of herds have >100 head. It is harder to implement a crossbreeding program in a smaller herd. Researchers in Canada have developed genomic indicators of retained heterosis. They use the genomic data to infer the breed proportion of the animals. They can then square these breed proportions, add them up, and subtract from zero to estimate the retained heterosis. Another approach is to...

Jeremy Taylor University of Missouri Taylor is going to cover several things: GGP-F250 Imputation Haplotype diversity Embryonic Lethals The GGP-F250 is a very unique assay compared to other SNP panels. All of the other available assays (SNP panels) use common variants. The GGP-F250 has many rare variants, most of which are located in genes or other functional elements. Why is rare variation important? Most of the variation in mammalian genomes, including the genomes of cattle, contain rare variation. Most of the DNA differences between different individuals are rare variants. We can't tag this rare variation with the common variants included in most SNP panels. To accurately measure genetic differences (and predict EPDs), we have to account for rare variation. Imputation is the process of: 1. Sorting DNA variants onto each chromosome (phasing) 2. Filling in missing genotypes We can impute from 50,000 SNPs to 700,000 SNPs to 15 million variants. But, we can'...

Alison Van Eenennaam UC-Davis United States beef cattle inventory has decreased since the 1970s. However, over that same time period, we have produced more beef. This means we are more efficiently producing more beef per cow. This is very different compared to other countries such as Brazil and India. We have seen inflection points in the genetic progress of beef production as various technologies have been adopted? Will gene editing be that next inflection point? Gene editing technologies are simply scissors that cut DNA. There are various types, such as Zinc Finger Nucleases, TALENS, and CRISPR/Cas9. CRISPR has become very popular recently because it uses a guide RNA to make the cut at a specific location. CRISPR can make site-specific variants (mutations) as the cell repairs the double stranded breaks. CRISPR can also be used to insert new sequence from a different animal, species, or kingdom. There are 13 papers that describe edits for 12 different traits in cattle. Gene...

Brent Mason Mason-Knox Ranch Mason-Knox Ranch develops heifers to market bred heifers. They like to purchase the heifer calves back from their customers. They also like to breed heifers to producer heifer calves, because we know that heifer calves are lighter compared to bull calves. Mason also sees an opportunity to quick change a cow herd by using sex sorted semen. Mason said, "Those who know me, know I'm a nervous nelly." The first time they did split time AI, Mason looked at all of the heifers in the hold pen and was nervous. Dave Patterson told him to eat dinner. Mason ate dinner, came back, and still very few heifers in heat. Patterson said, "Just let them be." Next morning, lots of heifers were in heat. Mason also sees opportunity for sexed-semen in seedstock. Think about breeding that cow who always produces a great bull, to male select semen. "There is a difference between burlap and satin," Mason quoted a friend. Mason believes in us...

Jordan Thomas University of Missouri NAAB Symposium Why do we care about sex sorted semen? For any on mating, one sex of calf is always more valuable. This is due to genetic potential and your marketing program. What is the value difference? What is the true cost of using sex sorted semen? Does the value difference justify the cost? In a perfect world, pregnancy rates would be identical between conventional and sex-sorted semen. But, this is not true. Further, the bull you want to use may not have sex-sorted semen available due to sorting or fertility factors. Sex-sorted semen is also very sensitive to the timing of estrus in a timed synchronization program. Lastly, sex-sorted semen is not free! There are direct costs (cost per straw of semen) and indirect cost (lower pregnancy rates, estrus detection, more complicated protocols). Unlike the dairy industry, we have a fixed breeding season in the beef industry. If a dairy cow is not breed using sex-sorted semen, we just AI ...

George Perry South Dakota State University NAAB Symposium Assume that a cow breeds 30 cows per year for 4 years. Regardless of the year, bull price per calf sired was higher than the cost of semen. We could have different bulls for different groups of cows. Bulls for heifers, bulls for maternal calves, and bulls for terminal calves. Consider breeding a calving ease bull to mature cows- you are giving up additional growth with that mating. Sexed semen causes the differences in sexes of the calves that we would expect to see. The number of bulls and heifers in a calf crop can be skewed even if we do one round of artificial insemination followed by natural service. Perry's groups used 6 herds with 878 cows breed to 5 different bulls. They used conventional semen and sexed semen from each bull. Gender skewed semen had a pregnancy rate of 52.4% and conventional semen had a pregnancy rate of 67%. When cows have displayed estrus (been in heat) at time of AI, pregnancy rate was 6...

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...

Steve Miller Angus Genetics Inc has four research scientists. They do single-step genomic evaluations for Angus, Canadian Angus, Charolais, Canadian Charolais, and Maine-Anjou. Angus switched to single-step on July 7th, 2017. Miller feels like the switch to single-step was a monumental switch, should have made the Time Magazine year in review! When breeders see bulls re-rank, they then understand was a correlation of 0.9 really means! On July 7th, Steve Miller talked to two breeders. On July 8th he was feel cool and casual like Ferris Buller. The next week, then the calls came. "I've seen this before, in a couple of months it will all blow over" a friend told Miller. And that proved true. The switch to single-step was kind of like the stages of grief with getting a flat tire. Quiet phase: Listening, evaluating, asking yourself if you have a flat tire. Expressive phase: Cussing, kicking dirt, frustrated. Have to Move Forward phase: Fixing the tire and getting ...

Chuck Sattler Vice President, Genetic Programs, Select Sires Inc. Data is fuel for breed improvement programs. Data drives the machine. Noise in the data is like water in the fuel. Data has value! However, individual records have very little data. We have to share data for it to achieve its value. "We are not good at investing in data. It's not sexy," Sattler said. We need to invest in data collection. We need to share data thoughtfully. Have a written agreement and think strategically when sharing data. Genomic evaluations are a big data success story! "We marvel at the technology that makes this all possible," he said. As much as it is a story about DNA technology, it is also a story about bring large amounts of data together. It is also a success of big data. If we had to do it over again, dairy industry might re-think Dairy Recording Processing Centers. Dairy Recording Processing Centers control the data and sometimes the breeder's voice is no...

John Pollak Emeritus Professor, Cornell University 50 years is a milestone in time that provides an opportunity to reflect on accomplishments. It is also an opportunity to reset the clock. The process for selection Establish a goal Create a breeding objective Collect data for traits defined in the objective Utilize the data to predict genetic merit (other steps I missed) What was the goal to motivate selection we performed over the past 50 years? Pollak could not identify a consistent goal over the last 50 years. We can look at genetic trends and see that genetic change has been accomplished. Change has happened, but can we articulate the goal that lead to these changes? What goal should motivate the selection we perform ove the next 50 years? The temptation is to continue on perhaps the same path on before. Doing the same things better. We should avoid this. If Pollak were to define the goal for the beef industry's breeding objective it would be increase th...

Dorian Garrick Professor and Chief Scientist, Massey University This is a one bull or two bull meeting. This means it cost about the profit from one or two bulls to pay for the attendence of this meeting. Beef producers need to leave this meeting with information and thoughts about how they will change and improve their operation. We would like to think that you use index selection, but we know that you are probably using independent culling levels or phenotypic selection. However, we can look at genetic trends to see how traits have changed. Weaning weight and yearling weights have increased over time. However, the rate at which these growth traits were changing slowed in 1990, when ultrasound carcass measures were introduced. So, Hereford breeders were still selecting for growth, but were also putting emphasis on other traits. An average 2017-born daughter eats $57 more feed per year than an average 1980 daughter. This possibly outweighs improvement in terminal profitability...