G. R. Wiggans,*1 P. M. VanRaden,* L. R. Bacheller,* M. E. Tooker,* J. L. Hutchison,* M. V. Silva,† T. A. Cooper,* and T. S. Sonstegard*
*Agricultural Research Service, USDA,
Beltsville, MD 20705-2350
†Embrapa Dairy Cattle, Juiz de Fora, MG,
Brazil 36038-330
2009 J. Dairy Sci. (?)
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A database was constructed to store genotypes for 50,972 single-nucleotide polymorphisms (SNP) from the Illumina BovineSNP50 BeadChip for >30,000 animals. The database stores multiple samples per animal. It stores all SNP genotypes for a sample in a single row. An indicator specifies if the genotype for a sample qualifies to be used in genomic evaluation. Samples with low call rates or pedigree conflicts are marked as not usable. Among acceptable samples, the one with the highest call rate is marked as usable. When multiple samples are stored for an animal, a composite is formed during extraction by using SNP genotypes from other samples to fill in missing genotypes. To increase the number of SNP available, scanner output for nearly 19,000 samples was reprocessed. Any SNP with a minor allele frequency of >1% in any of the 3 breeds was selected. Few (<1%) parent-progeny conflicts and a high (>90%) call rate were additional requirements for SNP selection. Because monomorphic SNP did not degrade convergence, a single set of SNP was adopted for all breeds. Genomic evaluation in August 2009 used 43,385 SNP as compared with 38,416 for Holsteins, 31,658 for Jerseys, and 34,593 for Brown Swiss used previously. Reliabilities for prediction of 2009 evaluations from November 2004 data were higher than for parent average by 30.4 percentage units for Holsteins, 11.6 for Jerseys, and 8.3 for Brown Swiss when averaged across 25 traits. Inclusion of females, bulls born before 1986, and a larger SNP set 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 tracking of genotypes and genomic evaluation as a routine and official process.
(Key words: genomic prediction, genotyping, single nucleotide polymorphism, reliability)