title: Short communication: Analysis of genomic predictor population for Holstein dairy cattle in the United States--Effects of sex and age.
abstract: Increased computing time for the ever-growing predictor population and linkage decay between the ancestral population and current animals have become concerns for genomic evaluation systems. The effects on reliability of US genomic evaluations from including cows and bulls in the Holstein predictor population and also from excluding older bulls from the predictor population were examined. Holstein data collected for December 2013 US genomic evaluations were used in cutoff studies to determine reliability gains, regression coefficients, and bias for 5 yield, 3 fitness, 2 fertility, and 18 conformation traits. Three predictor populations were examined based on animal sex: 30,852 cows with traditional evaluations as of August 2012, 21,883 bulls with traditional evaluations as of August 2012, and a combined group of all bulls and cows. Three subsets of the bull predictor population were examined to determine effect of age: bulls born before 1996 excluded (25% of bulls excluded), bulls born before 2001 excluded (50%), and bulls born before 2005 excluded (75%). The validation set for all predictor populations was either bulls or cows first receiving a traditional evaluation between August 2012 and December 2013. Across all traits, the addition of cows to the bull predictor population increased reliability gains by 0.4 percentage points for validation bulls and 4.4 points for validation cows. Across all traits, excluding bulls born before 1996 from the bull-only predictor population decreased gains in genomic reliability by 1.8 percentage points. For 19 of 28 traits, excluding bulls born before 2005 from the predictor population resulted in lower bias in genomic evaluations of validation bulls. Although the contribution of cows and older bulls to improved accuracy of US genomic evaluations is small, a plateau of achievable gain has not yet been reached.
authors: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350. Electronic address: Tabatha.Cooper@ars.usda.gov.
authors: T A
authors: TA
authors: Cooper
authors: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350.
authors: G R
authors: GR
authors: Wiggans
authors: Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350.
authors: P M
authors: PM
authors: VanRaden
mesh_terms: D000375:Aging; D000818:Animals; D002417:Cattle / Q000235:genetics*; D003142:Communication; D005260:Female; D008040:Genetic Linkage; D016678:Genome; D023281:Genomics / Q000379:methods*; D005838:Genotype; D008297:Male; D036801:Parturition / Q000235:genetics; D012737:Sex Factors; D014481:United States
keywords: dairy cattle; genomic evaluation; single nucleotide polymorphism