title: Are evaluations on young genotyped animals benefiting from the past generations?
abstract: Data sets of US Holsteins, Israeli Holsteins, and pigs from PIC (a Genus company, Hendersonville, TN) were used to evaluate the effect of different numbers of generations on ability to predict genomic breeding values of young genotyped animals. The influence of including only 2 generations of ancestors (A2) or all ancestors (Af) was also investigated. A total of 34,506 US Holsteins, 1,305 Israeli Holsteins, and 5,236 pigs were genotyped. The evaluations were computed by traditional BLUP and single-step genomic BLUP, and computing performance was assessed for the latter method. For the 2 Holstein data sets, coefficients of determination (R(2)) and regression (δ) of deregressed evaluations from a full data set with records up to 2011 on estimated breeding values and genomic estimated breeding values from the truncated data sets were computed. The thresholds for data deletion were set by intervals of 5 yr, based on the average generation interval in dairy cattle. For the PIC data set, correlations between corrected phenotypes and estimated or genomic estimated breeding values were used to evaluate predictive ability on young animals born in 2010 and 2011. The reduced data set contained data up to 2009, and the thresholds were set based on an average generation interval of 3 yr. The number of generations that could be deleted without a reduction in accuracy depended on data structure and trait. For US Holsteins, removing 3 and 4 generations of data did not reduce accuracy of evaluations for final score in Af and A2 scenarios, respectively. For Israeli Holsteins, the accuracies for milk, fat, and protein yields were the highest when only phenotypes recorded in 2000 and later were included and full pedigrees were applied. Of the 135 Israeli bulls with genotypes (validation set) and daughter records only in the complete data set, 38 and 97 were sons of Israeli and foreign bulls, respectively. Although more phenotypic data increased the prediction accuracy for sons of Israeli bulls, the reverse was true for sons of foreign bulls. Also, more phenotypic data caused large inflation of genomic estimated breeding values for sons of foreign bulls, whereas the opposite was true with the deletion of all but the most recent phenotypic data. Results for protein and fat percentage were different from those for milk, fat, and protein yields; however, relatively, the changes in coefficients of determination and regression were smaller for percentage traits. For PIC data set, removing data from up to 5 generations did not erode predictive ability for genotyped animals for the 2 reproductive traits used in validation. Given the data used in this study, truncating old data reduces computation requirements but does not decrease the accuracy. For small populations that include local and imported animals, truncation may be beneficial for one group of animals and detrimental to another group.
authors.affiliation: Department of Animal and Dairy Science, University of Georgia, Athens 30602. Electronic address: danilino@uga.edu.
authors.forename: D A L
authors.initials: DA
authors.lastname: Lourenco
authors.affiliation: Department of Animal and Dairy Science, University of Georgia, Athens 30602.
authors.forename: I
authors.initials: I
authors.lastname: Misztal
authors.affiliation: Department of Animal and Dairy Science, University of Georgia, Athens 30602.
authors.forename: S
authors.initials: S
authors.lastname: Tsuruta
authors.affiliation: Instituto Nacional de Investigacion Agropecuaria, Las Brujas 90200, Uruguay.
authors.forename: I
authors.initials: I
authors.lastname: Aguilar
authors.affiliation: Holstein Association USA Inc., Brattleboro, VT 05302.
authors.forename: T J
authors.initials: TJ
authors.lastname: Lawlor
authors.affiliation: Genus PIC, Hendersonville, TN 37075.
authors.forename: S
authors.initials: S
authors.lastname: Forni
authors.affiliation: Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel.
authors.forename: J I
authors.initials: JI
authors.lastname: Weller
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D005260:Female; D023281:Genomics; D005838:Genotype; D007557:Israel; D008297:Male; D008957:Models, Genetic; D010375:Pedigree; D010641:Phenotype; D013552:Swine / Q000235:genetics*; D014481:United States
keywords: dairy cattle; genomic selection; pedigree depth; single-step genomic BLUP