A permutation test for validation of genomic estimated breeding values

• Published in: Journal of animal science Vol. 98; p. 8
• Main Authors: Karimi, Zahra, Sullivan, Brian, Jafarikia, Mohsen
• Format: Journal Article
• Language: English
• Published: Champaign Oxford University Press 01.11.2020
• Subjects: Animal breeding; Breeding; Breeding of animals; Genomics; Hogs; Litter size; Livestock; Permutations; Phenotypes; Standard error; Swine
• ISSN: 0021-8812; 1525-3163

Previous studies have shown that the accuracy of Genomic Estimated Breeding Value (GEBV) as a predictor of future performance is higher than the traditional Estimated Breeding Value (EBV). The purpose of this study was to estimate the potential advantage of selection on GEBV for litter size (LS) compared to selection on EBV in the Canadian swine dam line breeds. The study included 236 Landrace and 210 Yorkshire gilts born in 2017 which had their first farrowing after 2017. GEBV and EBV for LS were calculated with data that was available at the end of 2017 (GEBV2017 and EBV2017, respectively). De-regressed EBV for LS in July 2019 (dEBV2019) was used as an adjusted phenotype. The average dEBV2019 for the top 40% of sows based on GEBV2017 was compared to the average dEBV2019 for the top 40% of sows based on EBV2017. The standard error of the estimated difference for each breed was estimated by comparing the average dEBV2019 for repeated random samples of two sets of 40% of the gilts. In comparison to the top 40% ranked based on EBV2017, ranking based on GEBV2017 resulted in an extra 0.45 (±0.29) and 0.37 (±0.25) piglets born per litter in Landrace and Yorkshire replacement gilts, respectively. The estimated Type I errors of the GEBV2017 gain over EBV2017 were 6% and 7% in Landrace and Yorkshire, respectively. Considering selection of both replacement boars and replacement gilts using GEBV instead of EBV can translate into increased annual genetic gain of 0.3 extra piglets per litter, which would more than double the rate of gain observed from typical EBV based selection. The permutation test for validation used in this study appears effective with relatively small data sets and could be applied to other traits, other species and other prediction methods.