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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVING GENETIC PREDICTIONS FOR DAIRY ANIMALS USING PHENOTYPIC AND GENOMIC INFORMATION Title: Selection and Management of DNA Markers for Use in Genomic Evaluation


Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 18, 2010
Publication Date: May 1, 2010
Repository URL:
Citation: Wiggans, G.R., Van Raden, P.M., Bacheller, L.R., Tooker, M.E., Hutchison, J.L., Cooper, T.A., Sonstegard, T.S. 2010. Selection and management of DNA markers for use in genomic evaluation. Journal of Dairy Science. 93(5):2287-2292.

Interpretive Summary: A database was developed to store single-nucleotide polymorphisms (SNP) genotypes from the BovineSNP50 BeadChip. A usability indicator was included so that only sample genotypes consistent with pedigree are used in SNP selection and genomic evaluation. Historical data were reprocessed to obtain genotypes for 50,972 SNP, and a set of 43,385 SNP were selected for the Holstein, Jersey and Brown Swiss breeds. New edits included conflict rate and call rate for each SNP, and all edits except minor allele frequency were applied across breed. Including females, very old bulls, and the larger set of SNP in predictions had only small effects on reliability. Genomic predictions for all 3 breeds became official in 2009. Predictions had higher reliability than parent average by 30% for Holstein, 12% for Jersey, and 8% for Brown Swiss when averaged across traits indicating the benefit of genomic evaluation.

Technical Abstract: A database was constructed to store genotypes for 50,972 single-nucleotide polymorphisms (SNP) from the Illumina BovineSNP50 BeadChip for over 30,000 animals. The database allows storage of multiple samples per animal and stores all SNP genotypes for a sample in a single row. An indicator specifies if the genotype for that sample is used in genomic evaluation. Samples with low call rates or pedigree conflicts are marked not usable. Among acceptable samples, the one with the highest call rate is marked as usable. When more than 1 sample is stored for an animal, a composite is formed during extraction by using SNP genotypes from the other samples to fill in ones that are missing. Scanner output for nearly 19,000 samples was reprocessed, and all genotypes were edited using the editing system for the new database. Genomic evaluation in August 2009 used 43,385 SNP as compared to 38,416 for Holstein, 31,658 for Jersey, and 34,593 for Brown Swiss used previously, and SNP were selected if minor allele frequency was above 1% in any of the 3 breeds. A low number of parent-progeny conflicts (< 1%) and high call rate (> 90%) were additional requirements for SNP selection. Because monomorphic SNP did not degrade convergence, a single set of SNP was adopted for all breeds. November 2004 genomic predictions had higher reliability than parent average by 30.4% for Holstein, 11.6% for Jersey, and 8.3% for Brown Swiss when averaged across traits. Including females, very old bulls, and the larger set of SNP in predictions had only small effects on reliability. The use of a database for genotypes, detection of conflicts as genotypes are stored, and use of a single set of SNP for genomic evaluations have simplified genomic evaluation as a routine and official process.

Last Modified: 8/19/2014
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