Wednesday, October 8, 2014

Brown Bagger EPD Updates

Jack Ward, Wade Shafer, and John Genho presented during todays NBCEC Brown Bagger seminar. They gave updates about how their breeds are utilizing genomic information.

Jack Ward
The American Hereford Association will release an Udder EPD in the Spring 2015 update, which is typically published in late December. They are also working on a Feed Efficiency EPD which could be released in December, but will more likely be in the Summer of 2015. In the Summer of 2015 the AHA will also publish a Sustained Cow Fertility EPD (similar to other breed's longevity EPDs) and a Heifer Calving Rate EPD (a measure of heifer fertility).

Ward also presented a nice analysis of price differences between bulls with and without genomic-enhanced EPDs. He set an upper limit of $15,000 to avoid high priced bulls that would skew the numbers. Bulls with traditional, low accuracy EPDs averaged $5,325. Bulls with genomic-enhanced EPDs averaged $7,475 at sale. More results can be seen in Ward's Hereford Genetic Summit presentation.

Wade Shafer
For the first training of Simmental genomic predictions, there were 2,800 animals with genotypes (DNA information) and phenotypes (trait measurements) available. This resulted in genomic predictions that gave the same amount of information as 1 to 9 progeny; which depends on the correlation between the genomic prediction and the trait, and the heritability of the trait. To avoid confusion, Shafer emphasized that they do not provide the genomic predictions to the producer only the genomic-enhanced EPD, which combines the genomic prediction and the traditional EPD. This is done to avoid confusion.

The American Simmental Association has created a collaborative genetic prediction service called International Genetic Solutions, which computes EPDs for 11 breed associations. The database contains records for over 15 million animals. During their last round of genomic prediction training they used 5,240 Simmental, 2,164 Angus, 1,604 Red Angus, 999 American Gelbvieh, 571 Maine-Anjou, and 85 Canadian Gelbvieh. For every trait the correlations stayed the same or increased. Progeny equivalents ranged from 1 to 28 progeny, Simmental specific weaning weight genomic predictions gave the same information as 5 progeny. The multiple-breed genomic predictions gave the same information as 8 progeny. For marbling, Simmental-specific genomic predictions gave the same information as 4 progeny, multiple-breed predictions gave the same information as 8 progeny.

In the current round of retraining they are using 56,116 animals from Simmental, Angus, Gelbvieh, Limousin, Red Angus, Maine-Anjou, and Shorthorn. They are currently looking at different ways to approach this training.

Researchers at Iowa State University have created a new approach to combine DNA genotypes and pedigree information in a single step. International Genetic Solutions is planning on using this method in the Spring of 2016. They are working with Bruce Golden and Dorian Garrick to completely rebuild the software used for EPD estimation. This software will use the new single-step method to incorporate DNA information, more robust accuracy estimates, and utilize modern computer hardware which allows multiple processes and faster calculations.

John Genho
Genho discussed the use of single-step  BLUP which simultaneously combines DNA genotypes and pedigree information. Every animal receives half of its chromosomes from its sire and half from its dam. On average an animal receives a quarter for it chromosomes from each grandparent, but these fractions can be quite different from a quarter in individual animals. Single-step BLUP uses DNA information to more precisely calculate relationships between animals rather than simply relying on averages. Genho's company Livestock Genetic Services, LLC uses this method for the Santa Gertrudis Association and several herd-specific genetic evaluations.

Post a Comment