Genomic PTA's Are Coming In 2009

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Bennet Cassell, Extension Dairy Scientist, Genetics & Management
(540) 231-4762, bcassell@vt.edu

I saw my first Genomic PTA’s today – October 15, 2008. A producer shared genomic proofs on a bull from a flush for an AI stud. Some genomic PTA’s are available to animal owners today, and will be released by USDA to the public for the first time in January 2009.

These genetic evaluations are predictions of genetic merit for different traits based on “dense SNP array” data from tissue samples on the animals being evaluated. A SNP or “single nucleotide polymorphism” is a change in a nucleotide—A:T or C:G—in DNA. Based on questions I have heard, there is a good deal of misunderstanding about genomic PTA’s.

Genomic data improves the accuracy of predictions of genetic merit over pedigree information alone, but the evaluations are still imperfect predictions. They are better than the pedigree data has been because they are based on the DNA animals actually inherit from parents. Parent average, which is the traditional pedigree estimate of genetic merit, predicts the expected average genetic merit of progeny of a sire - dam combination. But each individual offspring of such a mating gets a different gene sample from the average. For example, the evaluation that I saw today showed a Genomic PTA of 1.9 for daughter pregnancy rate on the bull calf, while his Parent Average was 1.3. This bull had inherited a slightly above average gene sample from his sire and dam, or maybe those PTA’s were lower than they should have been. The Reliability of the Genomic PTA for DPR was 55%, by no means a “highly reliable” proof, but certainly higher than the Reliability of 26% based on Parent Average.

I recently heard the first of what will certainly be a number of new marketing ideas using Genomic PTA’s. A “bundle” of semen consisting of equal amounts (10 or more units per bull) of sex sorted semen on three bulls would be sold. The bulls would be three year olds, still two years away from progeny test results. As I understand the plan, the average Genomic PTA of the three bulls will be published, rather than proofs on individuals, as the individual proofs are not of equal accuracy to proven bulls. The idea is for producers to be able to use sexed semen from young bulls with better prospects for high genetic merit than if the bundle had been selected on parent average. I like this concept. It would offer sexed semen on bulls that should be of exceptional genetic merit. It also spreads out the risk of change in proofs on individual bulls where the Reliabilities don’t justify heavy use of single individuals.