Thursday, December 20, 2012

Lower Prices, More Genotypes

I was really happy to see that 23andMe has lowered prices in an effort to genotype 1,000,000 people. Luckily the effective population size (a measure of genetic diversity) is much smaller in cattle breeds, so many fewer animals are needed to design genomic selection programs!

But, in an effort to increase the number of animals in its training population with high accuracy EPDs (genetic predictions), the American Hereford Association is offering a cost-sharing program to offset DNA test cost for breeders. If I was a breeder with a bull who meet the AHA's criteria, I would be jumping at the opportunity. (And, if I can scrounge up the money during the holidays, I will be taking advantage of 23andMe's deal!)

See message from the AHA below. 

High Accuracy Bulls Sought, Cost-Share Option Available

During the American Hereford Association (AHA) Board meeting the Board discussed its continued commitment to DNA testing more high accuracy sires. Hereford breeders who have a bull that does not have a genomic-enhanced expected progeny difference (GE-EPD), has a weaning weight accuracy of better than .50 and was born in 2001 or after, can contact Toni Shapiro at the AHA office, and the AHA will pay $40 of the fees to have the bull DNA tested.
A list of high-use Hereford sires that the Association would like tested has been generated. To see if a bull you own is on that list, contact Jack Ward, AHA chief operating officer and director of breed improvement, at or at 816-842-3757.
For more about Hereford DNA testing visit the Hereford YouTube channel (PDF). 

Beef Genomic Selection strategies

This past summer Hereford, Simmental, and Limousin breed associations announced genomic-enhanced EPD programs, following the lead of the Angus Association.  Two strategies have emerged, which I will call the commercial model and the genotype model.

The Commercial Model
In the commercial model, cattle producers send hair or other tissue samples to their breed association.  The association enters the identification information into its database, and sends the tissue sample to the DNA testing company (typically Pfizer or GeneSeek).  The DNA testing company extracts DNA from the tissue and runs a SNP assay.  These SNP tests contain hundreds or thousands of SNP markers, depending on the company.  The company then computes molecular breeding values (MBVs) based on the animals SNP genotypes.  A MBV is an estimated breeding value based solely on molecular markers.  The company then returns the MBVs to the breed association.  The breed association then uses these MBVs as an indicator trait to predict more accurate EPDs (see also Table 2 of "The Future is Here!").  The American Angus Association is currently using the commercial model.

The Genotype Model
This past summer the American Hereford Association, in partnership with the NBCEC, became the first breed association to develop and market its own genomic selection test. This means that the breed association manages the phenotypes and genotypes.  The process is as follows. Breeders let the breed association know they would like to test an animal (note, the animal must have a registration number).  The association then generates the test form with tracking bar code, and the breeder sends tissue samples and the test form to GeneSeek. This is when the process is fundamentally different.  GeneSeek then returns genotypes from the Bovine50K assay to the breed association, rather than a molecular breeding value. The breed association and the breeders now own more of the data associated with the genomic predictions. This also allows the American Hereford Association to routinely retrain and improve their genomic prediction models as increasing numbers of animals are genotyped. The North American Limousin Foundation and the American Simmental Association also have access to their genotypes.

For another take on the different paradigms in genomic selection strategies, see this video by Matt Spangler.

*Note: Article was updated on September 20th, 2013 to reflect that Limousin and Simmental have access to their genotypes resulting from Neogen's purchase of Igenity.