03610naa a2200289 a 450000100080000000500110000800800410001902400320006010000150009224501770010726000090028450001020029352026380039565000120303365000090304565300160305465300230307065300320309370000160312570000160314170000160315770000160317370000210318970000200321070000170323077300730324710548392018-12-11       2016    bl uuuu     u00u1 u    #d7 a10.3168/jds.2015-105402DOI1 aMASUDA, Y.  aImplementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals.h[electronic resource]  c2016  aOPEN ACCESS. Received 19 October 2015, Accepted 1 December 2015, Available online 21 January 2016  aABSTRACT. The objectives of this study were to develop and evaluate an efficient implementation in the computation of the inverse of genomic relationship matrix with the recursion algorithm, called the algorithm for proven and young (APY), in single-step genomic BLUP. We validated genomic predictions for young bulls with more than 500,000 genotyped animals in final score for US Holsteins. Phenotypic data included 11,626,576 final scores on 7,093,380 US Holstein cows, and genotypes were available for 569,404 animals. Daughter deviations for young bulls with no classified daughters in 2009, but at least 30 classified daughters in 2014 were computed using all the phenotypic data. Genomic predictions for the same bulls were calculated with single-step genomic BLUP using phenotypes up to 2009. We calculated the inverse of the genomic relationship matrix View the MathML source based on a direct inversion of genomic relationship matrix on a small subset of genotyped animals (core animals) and extended that information to noncore animals by recursion. We tested several sets of core animals including 9,406 bulls with at least 1 classified daughter, 9,406 bulls and 1,052 classified dams of bulls, 9,406 bulls and 7,422 classified cows, and random samples of 5,000 to 30,000 animals. Validation reliability was assessed by the coefficient of determination from regression of daughter deviation on genomic predictions for the predicted young bulls. The reliabilities were 0.39 with 5,000 randomly chosen core animals, 0.45 with the 9,406 bulls, and 7,422 cows as core animals, and 0.44 with the remaining sets. With phenotypes truncated in 2009 and the preconditioned conjugate gradient to solve mixed model equations, the number of rounds to convergence for core animals defined by bulls was 1,343; defined by bulls and cows, 2,066; and defined by 10,000 random animals, at most 1,629. With complete phenotype data, the number of rounds decreased to 858, 1,299, and at most 1,092, respectively. Setting up View the MathML source for 569,404 genotyped animals with 10,000 core animals took 1.3 h and 57 GB of memory. The validation reliability with APY reaches a plateau when the number of core animals is at least 10,000. Predictions with APY have little differences in reliability among definitions of core animals. Single-step genomic BLUP with APY is applicable to millions of genotyped animals. © 2016, THE AUTHORS. Published by FASS and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).  aSsGBLUP  aTORO  aFINAL SCORE  aGENOMIC EVALUATION  aGENOMIC RELATIONSHIP MATRIX1 aMISZTAL, I.1 aTSURUTA, S.1 aLEGARRA, A.1 aAGUILAR, I.1 aLOURENCO, D.A.L.1 aFRAGOMENI, B.O.1 aLAWLOR, T.J.  tJournal of Dairy Science, 2016gv.99, no.3, p.1968-1974. OPEN ACCESS