Wednesday, October 26, 2016

NBCEC Brown Bagger: Implementation of single step methodologies at Angus Genetics, Inc.

Steve Miller
AGI

Angus Genetic Services provides evaluations for AAA, CAA, and Charolais breed associations.

"The ship has sailed on using genomics. Breeders are using it now, and seeing the benefits of it," said Miller.

Previously at AGI, they have been using a two-step approach. In this method, a genomic prediction is created and then is used as an indicator trait for EPD estimation. The calibration data set size has increased dramatically as Angus breeders have used genomic-enhanced EPDs.

The orgininal method of incorporting genomic predictions as correlated trait.

In the future, we will stop referring to genomic-enhanced EPDs. We don't refer to EPDs as pedigree-enhanced or performance-enhanced, we simply refer to them as EPDs. In the future use of genomic data in genetic prediction will become so routine that we will simply call them EPDs.

Is the Animal Model Obsolute?


In single-step genomic prediction, we combine the measures of relatedness from pedigree data with the measures of relatedness from the genomic data. In comparison to pedigree data, genomic data captures more variation is relationships.

Consider 6 full sibs. Their pedigree relationship is 0.59 (slightly higher than 0.5 due to inbreeding in the pedigree). But with genomic data the relationships vary from 0.49 to 0.65.

Single-step
 eliminates the need for periodic calibration.
utilizes all available data

The migration to single-step genomic evaluation is not unique to beef cattle. This has happened in multiple breeds and species on multiple continents.

One of the keys that makes single-step genomic evaluation is APY.

The Angus association has 7.6 million birth weight records and 254,000 genotyped animals.

The move to single-step required more computing power at AGI; they have purchased 4 new servers.

Between the previous correlated evaluation and single-step evaluation, for  200 proven sires the correlation between the current and new EPDs were 0.99.

AGI is currently in the process of changing horses on the fly. They are currently running two genetic evaluations, the current two-step correlated genetic evaluation and the new single-step evaluation. They are looking at the consistency of these predictions over weekly runs.

Right now, when we recalibrate a genomic prediction, we can see big jumps in EPDs. But, with weekly evaluations as data is added, AGI sees  incremental changes in EPDs as phenotype data is added.

Single-step BLUP will allow progressive breeders to leverage all of their data. Phenotype and genotype information will be utilized together in a single step.

Angus Association has also started a sire progeny testing program to get carcass data on proven, popular sires.

The Angus Association has not yet identified a time to completely switch to single-step BLUP. They are evaluating single-step, and when they are confident that the program is ready, they will switch.
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