Friday, June 20, 2014

Breed Updates on Genomic Prediction

Several of the breed associations gave reports on their progress to implement genomic-enhanced EPDs. When a breed is small it is difficult to obtain genotypes of animals with reliable EPD estimates. More on this later.

The American Gelbvieh Association has implemented and released genomic-enhanced EPDs. See page 30 of the April 2014 Gelbvieh World for more information. Gelbvieh has implemented a solution unique to beef breeds in which a beef producer can either purchase a low density or high density SNP test. The SNPs not genotyped on the low density tests are implemented based on inheritance patterns in the populations. This process is referred to as imputation.

This September, the American Hereford Association will be adding a low-density SNP test that will be marketed at half the cost of the complete SNP test. The SNPs not genotyped on this assay will be imputed from the genotyped DNA variants, the same as the Gelbvieh strategy. When first introduced, AHA genomic predictions had a correlation of 0.33 with calving ease. Now, after training with 10,000 animals across multiple continents, the correlation is now up to 0.84. This means 70% of the variation in calving ease will be explained by the genomic predictions.

John Genho of Livestock Genetic Services reported on the development of genomic-enhanced EPDs for Santa Gertrudis. Because small breeds have a significant challenge in obtaining enough genotypes and phenotypes to implement a genomic prediction, Santa Gertrudis Breeders International has implemented a single-step genomic BLUP where a genomic relationship matrix is merged with a pedigree relationship matrix. Because SNP effects are not estimated, genomic-enhanced EPDs can be produced when many fewer animals are genotyped. Genho looked at ultrasound data from the King Ranch to evaluate the value of the genomic BLUP. Without genomics, correlation between pedigree EPDs and the actual ultrasound intramuscular fat measurements was 0.22. When genomics were added to the genetic estimate, the correlation between EPD prediction and ultrasound measurements increased to 0.34.
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