Efficacy of alternative multivariate best linear unbiased prediction models for genetic evaluation of swine

A comparison of the accuracy of alternative BLUP evaluations of swine performance data is reported. A simulated data set of performance for days to market, backfat, number born alive, number weaned, and litter weight in six herds was used for the evaluation. The data structure was derived by using the performance records of six herds sampled from the American Yorkshire Club's STAGES (Swine Testing and Genetic Evaluation System) database. For growth traits, 10,360 pig records from 129 sires and 897 dams were recorded. For maternal traits, records on 2,598 litters of 1,209 sows from 147 sires and 585 dams were included. The actual observed performance of each record was removed and replaced with simulated performance. These simulated data were analyzed by within- and across-herd BLUP models using STAGES and Animal Model (AM) procedures. Results indicate that the alternative BLUP procedures produced similar estimates. Correlations between STAGES and AM EPD ranged from .84 to .95. Correlations between STAGES EPD and true genetic value (G) ranged from .41 to .74, and correlations between AM EPD and G ranged from .40 to .74. On average, AM EPD had a .04 larger correlation with G than did STAGES EPD, although the difference in the correlations was not significant (P greater than .05). Trends in EPD for sires, dams, and pigs or sows were the same. Likewise, standard errors of prediction for AM EPD averaged 4% smaller than those for STAGES EPD. Computationally, the AM procedures used 15 to 20 times as much processing time as did STAGES procedures.