AGI implements updates to keep up with growing data store.
Often there’s not a noticeable difference in the condition of the vehicle you drive into the garage for routine maintenance and that same car on a return trip home. Yet, checking off the regular oil changes, tire rotations or coolant refills help ensure peak performance long-term.
Esther Tarpoff, director of performance programs, likens the upcoming American Angus Association genetic evaluation core updates to that: a behind-the-scenes tuneup to keep the database operating accurately and efficiency. They will take effect on May 24.
“We are very, very fortunate that the membership continues to see the importance of phenotypes and genotypes,” she says. “That creates the best kind of challenge for our team at Angus: how do we take all their information and continue to give them back tools?”
One of these tuneups is a core update, which is part of the algorithm used to build the genomic relationship matrix used to calculate the weekly expected progeny difference (EPD) releases.
“From the last core update in May of 2021 to now, we added more than 500,000 genotyped animals. As we continue to add genotyped animals at those rates, we need these updates to stay current with the current populations,” says André Garcia, senior geneticist for the American Angus Association.
Putting that into perspective, that’s an increase of 50% in the number of genotypes in the past three years.
Part of the background work Garcia and the team do leading up to the maintenance includes looking at correlations between the current EPDs and the updated numbers. Across the board, the current EPDs have a .99 correlation, where a 1.0 would be a perfect relationship.
“The AGI (Angus Genetics Inc.) team has spent a lot of time, hours upon hours, going through this and doing the research and running those correlations to quantify the change that the membership will see so that breeders can be prepared for it,” Tarpoff notes. “Across an entire population there will be some individual changes. But overall, there’s not going to be a lot of movement.”
Of course, there are other updates happening simultaneously, Garcia says, referring to the improvements to contemporary groups in the heifer pregnancy EPD. That could compound the amount of change on a small number of animals.
Younger sires or those with large numbers of genotyped progeny added in the last few years stand to see the most movement, Garcia explains.
“Animals with lower accuracy tend to show more change than those animals that have higher accuracies,” he says.
Garcia notes people often key in on shifts that are easier to quantify in their mind, such as weaning weight or birth weight, but the changes should be consistent across all traits.
“We see a similar magnitude of change across all traits, which is expected because the core update applies to the entire genetic evaluation,” Garcia says.
Better AND faster
Playing devil’s advocate, one might wonder why AGI would bother with the core update if the numbers won’t shift dramatically. Is it worth the effort?
“There are two reasons why these updates are important. One is keeping the genetic evaluation up to date, because of that large increase in the number of genotyped animals we need to ensure that the core accurately reflects the population,” Garcia explains. “The other one is that helps us reduce computing time quite a bit.”
Each trait in the genetic evaluation takes a different amount of time to calculate, but over time as breeders add more animals and more data, that calculation time has increased across the board. Today, when the carcass evaluation run starts on a Friday, it won’t be complete until late Wednesday night.
That’s a considerable increase in run time as compared to just two years ago, and doesn’t allow for any room to rerun the evaluation if there’s a hitch in the process.
“Being able to have those numbers updated on a weekly basis is a huge advantage,” Tarpoff says. “Members have gotten really used to having those EPDs every Friday. As it takes longer to compute all the statistical models because of the growing database, it takes longer to get results. We’re not to the point where we can’t deliver on that weekly expectation, but without the core updates, that could become an issue down the road.”
The Association has invested in faster computing power and regularly evaluates the best strategies for calculations of the EPDs. The core update is one of those strategies, and it’s one the team plans to complete on a regular basis.
“The number of animals, genotypes, and phenotypes will continue to increase, and this is a good thing,” Garcia says.
Nothing a little routine, preventative maintenance can’t address.