Genomic Prediction
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Genomic prediction

By Paul VanRaden*, George Wiggans*, Curt Van Tassell†, Tad Sonstegard†, and Leigh Walton*
*Animal Improvement Programs Laboratory, †Bovine Functional Genomics Laboratory 

Genomic predictions of genetic merit were released for the first time in April 2008. Predictions are based on genotypes derived from blood samples (or other DNA) provided by animal owners through arrangements made by participating artificial-insemination (AI) organizations. The DNA is extracted from the samples in most cases by GeneSeek (Lincoln, NE). The extracted DNA then is placed on a chip developed by Illumina (San Diego, CA), USDA's Bovine Functional Genomics Laboratory (Beltsville, MD), and other research partners. That chip provides genotypes on more than 50,000 single nucleotide polymorphisms (SNPs) evenly distributed across all 30 chromosomes; of those SNPs, nearly 40,000 are informative for Holsteins. The genotypes document which genes each animal inherited, and that completely new source of information can be included in genetic evaluations. Predicted transmitting abilities (PTAs) have used pedigrees to calculate probabilities that relatives share genes. With genotypes, the actual genes that are shared can be determined.

The DNA of proven Holstein bulls contributed by members of the National Association of Animal Breeders (Columbia, MO), Semex Alliance (Guelph, ON, Canada), and some other projects as well as DNA from a small number of cows is used in estimating genetic effects for each SNP. Each animal's PTA or parent average (PA) for each trait as well as its net merit index then is adjusted for the sum of the estimated genetic effects. The primary focus is to calculate genomic evaluations for young bulls and heifers nominated by the participating AI organizations. Evaluations of the nominated animals are distributed to the U.S. owners (see example mailer) and to the organizations that paid for genotyping to aid in selection decisions. The AI organizations that contributed to the research have a 5-year period of exclusive rights to obtain genomic evaluations of males. Evaluations of females are available to anyone who provides a genotype through a cooperating organization.

Two different evaluations predict the merit of an animal's daughters and sons separately. The difference is the sum of genetic effects on the X chromosome. The standard deviation of the difference between daughter and son merit is about one-tenth of the genetic standard deviation for most traits.

Genomic predictions should not be used in advertising until January 2009, when they become official. Statistical methods and results from both simulated and real genomic data have been reported by