Breeding organisations generally estimate breeding values to identify the most appropriate individuals to become parents of the next generation, and one million genotyped animals is realistic. Three methods to specify genetic similarity between individuals, as implemented in MiXBLUP, were compared in a routine genetic evaluation of age at first calving of beef cattle in Ireland using genotypes of 50,240 SNP on 613,984 animals. The methods were pedigree BLUP, single-step genomic BLUP using genomic recursions to approximate the inverse genomic relationship matrix (ssGBLUP-APY) and single-step ridge-regression BLUP (ssRRBLUP). Inclusion of genomic information dramatically increased memory requirement and number of IO operations. Convergence of ssRRBLUP is slower than pedigree BLUP and ssGBLUP-APY. Time per iteration was similar for ssRRBLUP and ssGBLUP-APY. Correlations between solutions of different methods varied from 0.35 to 0.80 for genotyped and from 0.70 to 0.94 for non-genotyped animals. Also slope and intercept between any two methods differed for genotyped and non-genotyped animals. Overall, utilising a large number of genotyped animals in routine genetic evaluations with ssRRBLUP is possible, but as yet very slow due to slower convergence and a large number of IO operations. BLUP with regression on SNP covariates seems to be the most suitable method when convergence and IO problems have been resolved. Keywords: genomic selection, mixed model, computer program, relationship matrix, beef cattle

Jan ten Napel, Andrew Cromie, Ghyslaine Schopen, Jérémie Vandenplas, Roel F Veerkamp

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Electronic Poster Session - Methods and Tools - Software, , 905, 2018
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