A Steak in Genomics™

  Beef Heifer Puberty and Fertility Genomic Research from American Hereford Association on Vimeo .

The University of Missouri is recruiting 2,500 Hereford heifers to participate in a heifer puberty and fertility genomic research project. Reserve a spot for the webinar on September 6th, 2022 at 7 p.m. CDT to hear from the team members conducting the project and learn how to get involved. RSVP for the event here:  https://hereford.ac-page.com/aha-mizzou-webinar  

DENVER - The bustling ballrooms of Kalispell, Montana, will soon be filled with innovative and forward-thinking cattlemen and women during the 69th annual National Red Angus Convention. The Commercial Cattlemen’s Symposium, hosted by the Red Angus Association of America, is sure to be a highlight of the convention and will offer beef producers the tools and knowledge they need to strengthen their operations and improve their profitability. This year’s symposium, held at the Hilton Garden Inn in Kalispell on Wednesday, Sept. 14, will feature a diverse, experienced group of speakers guaranteed to offer valuable insight to attendees. “We are thrilled to continue offering commercial cattlemen and women free educational events during the annual National Red Angus Convention. As the Commercial Marketing Team, it is always exhilarating to bring so many commercial operations – our customers – together for this event. Red Angus has always been focused on the cow, and with the release of our new...

 The Beef Reproduction Task Force invited me to present in their 2022 Webinar series. You can watch the webinar below or on Facebook. Thanks again to BRTF for the opportunity to present!

At the National Western Stock Show, I had a great discussion with the American Angus Association board and members. Angus Media put together a nice summary of that presentation.

My group has posted a new preprint on bioRxiv .  You can check it out here:  https://doi.org/10.1101/2020.03.11.988121 Warning, it is written for a technical audience, not in cowboy terms. So- what are the take-home messages for farmers and ranchers? We can identify the DNA variants responding to your selection decisions. You tend to select cattle that have better immune systems. Hormone production in the ovaries is under selection in Red Angus. Makes sense based on the breed's focus on fertility. Muscle development is under selection in Gelbvieh.  We can identify the DNA variants that lead to cattle adapted to their environment Blood vessel tightening or loosening is under environmental selection. The brain and neuron signaling is an important part of environmental adaptation. We are losing local adaptation in beef cattle. Check out this Twitter thread to see figures from the paper. https://twitter.com/pop_gen_JED/status/1258786262149808131 Regarding the last point, we c...

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 ...

In January, Angus Genetics, Inc. (AGI) announced the release of research Claw Set and Foot Angle EPDs. The development of a research EPD is the second step towards a production EPD. This followed research presented in the summer of 2017 which found heritabilities of 0.34 for foot angle and 0.21 for claw set. Estimating heritability (portion of the trait influenced by genetics) is the first step towards a production EPD. This research also found a genetic correlation of 0.22 between the two traits, indicating that both traits need to be reported and analyzed. Stephen Miller, AGI Director of Genetic Research stated, "“Angus breeders have completed a tremendous amount of data reporting in such a short period of time; this is truly a testament to their commitment toward genetic progress. We are absolutely thrilled to begin the process of rolling this breakthrough out to the membership.” Kelli Retallick, AGI Director of Genetic Services cautioned, “Though we are getting closer ...

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 ...

Reverend Bayes via Wikimedia Commons You are asking yourself, who is Reverend Bayes and what does he have to do with cattle? The answer to this question will answer a major misconception in cattle genetics. Reverend Bayes was an 18th century Presbyterian minister. He was also trained in logic. Due to Bayes’ work on probabilities, an approach to statistics called Bayesian statistics is named after him. In Bayesian statistics, we start with a prior belief (prior probability). As more information and data are gathered, we update this prior belief. We call this new update a posterior belief. We continue this process as we collect additional data. Further, a key tenant of Bayesian statistics is evaluating the methods (i.e. models) used in our analysis. Statisticians and scientists did not frequently use this system of statistics in the early 20th century. But, with increased computing power, Bayesian statistics has become very popular in the 21st century. By Lutz Koch CC BY-NC-ND...

Allen Moczygemba, CEO of American Angus Association announced in a memo  Monday August 14, 2017 that the price for Neogen GGP-LD and Zoetis i50K tests would be reduced to $37, effective immediately. The motivation for this price reduction is even more notable. In November of 2017 Angus Genetics Inc. (AGI) and Neogen will launch a new genomic test (SNP panel) called AngusGS™. This test will use 50,000 (50K) DNA variants, designed specifically for Angus cattle. DNA variants are included based on their frequency in the Angus breed, rather than across many breeds like most DNA panels currently used in the industry. Further, AGI has increased the number of DNA markers in stretches of DNA believed to be involved in fertility, feed efficiency and tenderness. The more detailed genotyping of these chromosome segments will enable more refined research of these important traits. For example, AGI could include increased markers in regions believed to harbor embryonic lethal DNA vari...

Guest post by Tamar Crum, University of Missouri Tom Brink Red Angus Association of America Fitting that the Georgia peach is in the logo for this year’s BIF, as we have learned throughout the conference that the industry has been provided with many types of “fruit” to choose form when it comes to our technology and genetic tools. Do EPDs work?  Are you a skeptic? If so, you are not alone! Believe it or not there are still skeptics out there. Numerous studies have been completed on carcass traits, milk, and weaning weight EPDs in the late 1990s and 2000s.  After that period, the research coming out proving EPDs worth got a little sparse.  Why? We convinced ourselves and our scientists that EPDs work, but skeptics remained in the industry.  They wanted to belief in EPDs but still need to see more. This study was in conducted in conjunction with Gardiner Angus Ranch, Zoetis, and Top Dollar Angus. The field test wanted to make comparisons between high...

Angus Genetics Inc will switch to single-step genomic prediction on July 7th. Since 2010 they have been using multi-step genomic prediction. In multi-step, genomic predictions are treated as correlated traits to produce GE-EPDs. In single-step, all genomic, pedigree, and performance data is analyzed in one model. The key to calculating EPDs is measuring genetic similarity. Traditional EPDs used pedigree data to estimate genetic similarity. In single-step, genomic data more accurately measures relatedness, i.e. genetic similarity. The pedigree and genomic relationship measures are combined. Since November, AGI has evaluated multi-step vs single-step. They have seen very similar accuracies between the two methods. But, single-step tends to have slightly higher accuracies. Further, there are several advantages to single-step. These advantages include removing the need to recalibrate and using all of the data simultaneously. Watch for further information from Angus about the switch t...

Matt Spangler University of Nebraska-Lincoln In the past, the only way we made improvement was through visual appraisal. Photo from Harlan Ritchie's Beef Review. Difference between 1835 and 1937 champion. As the picture above shows, we can make a change, but how many of us want to wait 100 years? Improvement can be accomplished through management and genetics. In the past we (animal breeding scientist) have probably done a disservice to the industry by producing lots of EPDs, then dumping those in beef producers lap and then expect you all to make meaningful decisions with them. In some situations, this may be as valuable as a free cat. There are many factors that can influence an animals record, for example a weaning weight. Weaning weight may be affected by age of the calf, age of the dam, how much it was feed, and other environmental factors. So, we need to compare animals to their contemporaries, Contemporaries are animals of the same sex, raised at the same ra...

The application of genomics to improve the accuracy of EPDs is a rapidly developing field. There are ongoing improvements in genotyping and sequencing technologies, statistical methods to increase the correlation between genomic predictions and true genetic merit, and the computing systems to handle the large datasets associated with animal breeding. One thing still remains true in the genomic age and that is the need to collect accurate phenotypic records. It is essential to ensure performance data, pedigree, and DNA information are recorded and reported accurately. Genomic predictions will only be as reliable as the data upon which they are based.  Although it might seem like the genomics era could signal the end of performance recording, the opposite is true. Now more than ever, it is important that producers accurately report data, and ensure that animals which are genotyped are correctly identified so that their information can contribute towards improving the accuracy of the ...

The application of genomics to improve the accuracy of EPDs is a rapidly developing field. There are ongoing improvements in genotyping and sequencing technologies, statistical methods to increase the correlation between genomic predictions and true genetic merit, and the computing systems to handle the large datasets associated with animal breeding. One thing still remains true in the genomic age and that is the need to collect accurate phenotypic records. It is essential to ensure performance data, pedigree, and DNA information are recorded and reported accurately. Genomic predictions will only be as reliable as the data upon which they are based.  Although it might seem like the genomics era could signal the end of performance recording, the opposite is true. Now more than ever, it is important that producers accurately report data, and ensure that animals which are genotyped are correctly identified so that their information can contribute towards improving the accuracy of the ...

The application of genomics to improve the accuracy of EPDs is a rapidly developing field. There are ongoing improvements in genotyping and sequencing technologies, statistical methods to increase the correlation between genomic predictions and true genetic merit, and the computing systems to handle the large datasets associated with animal breeding. One thing still remains true in the genomic age and that is the need to collect accurate phenotypic records. It is essential to ensure performance data, pedigree, and DNA information are recorded and reported accurately. Genomic predictions will only be as reliable as the data upon which they are based.  Although it might seem like the genomics era could signal the end of performance recording, the opposite is true. Now more than ever, it is important that producers accurately report data, and ensure that animals which are genotyped are correctly identified so that their information can contribute towards improving the accuracy of the ...

Here are videos from the American Simmental Association's Facebook livestream of my presentation titled "Taking Technology Home to the Farm and Ranch." Tradition Intuition Legacy Seedstock Producers as Educators Decker's Rants EPDs and Environment  Q&A Loading...