By Jared E. Decker Many of you have probably noticed that things have been a lot less active on the A Steak in Genomics™ blog, but you probably haven't known why. In January 2021, I was named the Wurdack Chair in Animal Genomics at Mizzou, and I now focus on research, with a little bit of teaching. I no longer have an extension appointment. But, with exciting news, the blog is about to become a lot more active! Jamie Courter began as the new MU Extension state beef genetics specialist in the Division of Animal Sciences on September 1, 2023. I have known Jamie for several years, meeting her at BIF when she was a Masters student. I have been impressed by Jamie in my interactions with her since that time. Dr. Courter and I have been working closely together the last 6 weeks, and I am excited to work together to serve the beef industry for years to come! Jamie holds a bachelor’s degree in animal science from North Carolina State University and earned a master's degree in animal...
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Doctor Bovine Genome or: How I Learned to Stop Worrying and Fix the Assembly
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I know, this is a very strange title for a post. More about that later...
USDA Fellowship
In this post I want to introduce you to part of my day-to-day research. In August of this year, I was awarded a USDA NIFA Postdoctoral Fellowship. I was awarded this fellowship for two reasons: to prepare to become a leader in agricultural science and to complete a specific project. My project is reassembly of the bovine reference genome sequence.
Motivation: Why are we reassembling the bovine genome?
The completion of the draft human genome sequence was announced to much fanfare in 2000. But, the work of finishing the human genome still continues. Two versions of the bovine reference sequence, by the Baylor College of Medicine and the University of Maryland, were published in 2009. At that time the bovine genomics community began discussing how to improve the draft assembly. Key players suggested that more sequence data on L1 Dominette 01449, the cow on whom the reference sequence is based, would be the best step to improve the assembly. Subsequently, this additional data was generated.
L1 Dominette 01449, courtesy Michael MacNeil, USDA
My Experience
Scientists who work with draft genomes know to watch for errors in the reference. As part of my Ph.D. training, I did a local assembly of a 400,000 base pair region to identify a DNA rearrangement which controls a phenotypic trait. When I finished, the Baylor reference, Maryland reference, and my assembly had numerous disagreements about the sequence of this region. I decided that if I was going to be successful in identifying variants which underlie phenotypic variation, I was going to need a better reference.
Volunteering
Last winter, I wrote a USDA NIFA Postdoctoral Fellowship proposal in which I volunteered to take the existing data that was waiting to be analyzed and lead the reassembly of the bovine reference genome sequence. Leaders in the bovine genomics community supported my application and agreed to share sequence data for the reassembly effort. Fortunately, Uncle Sam accepted my proposal and will be paying my salary for the next two years.
In Conclusion, Dr. Strangelove
The title of this post is inspired by one of my advisor's favorite movies. And just like a doomsday device, the value of a scientific project is lost if you don't tell the world! Check back here for more updates about the progress of the bovine genome reassembly.
*Finally, two disclaimers. First, I don't consider myself "Doctor Bovine Genome", I simply needed a catchy title. Second, I don't know of any similarities between myself and Dr. Strangelove. If you know of any, feel free to leave them in the comments section. Enjoy!
All bulls purchased after February 1st, 2019 for use as natural service sires in the Show-Me-Select Replacement Heifer Program ™ must be DNA tested to have genomic-enhanced EPDs. All bulls used as natural service sires after February 1st, 2020 must have genomic-enhanced EPDs, regardless of when they were purchased. Seedstock producers classifying bulls as Show-Me-Select qualified in sale books must have genomic-enhanced EPDs on those lots. Bulls purchased prior to February 1st, 2019 will be grandfathered into the program, as is the common practice with all natural service sires. However, this grandfather grace period will end February 1st, 2020. At that time for a bull to qualify for use in the program, it must have genomic-enhanced EPDs. Why the change? The Show-Me-Select Replacement Heifer Program has the goal of producing premium heifers that perform predictably as 2 year olds. The program has a history of requiring Show-Me-Select producers to go beyond typical...
At the January 4th Show-Me-Select Board of Directors meeting, new service sire EPD requirements were approved. All sires, artificial insemination and natural service, must meet minimum Calving Ease Direct (CED) EPD requirements. In addition to yearly updates, two changes were made. First, no Birth Weight EPD requirement will be published. All commonly used breeds now have CED EPDs available. Second, all breeds in the International Genetic Solutions (IGS) genetic evaluation are now set to a common requirement. In the summer of 2018, breeds within the International Genetic Solutions switched to a single-step BOLT multi-breed genetic evaluation. The EPDs for animals in the IGS genetic evaluation are directly comparable across breeds. In 2017, the Red Angus requirement for CED was a CED of 8, which represents the 30th percentile. Less than 5% percent of heifers breed to a bull with a CED EPD of 8 or larger had calving difficulty. We feel that this require is meeting the need to re...
Bob Hough recently posted the following comment on Facebook (posted with his permission): Early in my career at a breed association, the much beloved American Angus breed executive told me that the secret to success running a breed association was to have a top junior program, keep the books straight, and make sure the numbers (EPDs) don't change. This philosophy meant Angus valued stability in their genetic predictions over keeping them up-to-date with the latest science. The Angus Association also marketed extremely effectively the infallibility of their EPDs because of the size of their database. I will start with the later. Yes, a database needs certain critical mass to make sure the animals are tied, but that can be achieved in a modest size database. After that, data quality far and away outweighs data quantity in assuring the most precise and reliable EPDs possible. On the former point, Angus breeders are simply not use to change. This is not the case in most breed associ...
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