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Research article2016Peer reviewed

Accuracy of genomic prediction of purebreds for cross bred performance in pigs

Hidalgo, André; Hidalgo, André Marubayashi; Bastiaansen, J.W.M.; Lopes, M.S.; Calus, Mario P.L.; De Koning, Dirk-Jan

Abstract

In pig breeding, as the final product is a cross bred (CB) animal, the goal is to increase the CB performance. This goal requires different strategies for the implementation of genomic selection from what is currently imple- mented in, for example dairy cattle breeding. A good strategy is to esti- mate marker effects on the basis of CB performance and subsequently use them to select pure bred (PB) breeding animals. The objective of our study was to assess empirically the predictive ability (accuracy) of direct geno- mic values of PB for CB performance across two traits using CB and PB genomic and phenotypic data. We studied three scenarios in which genetic merit was predicted within each population, and four scenarios where PB genetic merit for CB performance was predicted based on either CB or a PB training data. Accuracy of prediction of PB genetic merit for CB performance based on CB training data ranged from 0.23 to 0.27 for gestation length (GLE), whereas it ranged from 0.11 to 0.22 for total num- ber of piglets born (TNB). When based on PB training data, it ranged from 0.35 to 0.55 for GLE and from 0.30 to 0.40 for TNB. Our results showed that it is possible to predict PB genetic merit for CB performance using CB training data, but predictive ability was lower than training using PB training data. This result is mainly due to the structure of our data, which had small-to-moderate size of the CB training data set, low relationship between the CB training and the PB validation populations, and a high genetic correlation (0.94 for GLE and 0.90 for TNB) between the studied traits in PB and CB individuals, thus favouring selection on the basis of PB data.

Keywords

Cross breeding; genomic selection; reproduction traits; within-population prediction

Published in

Journal of Animal Breeding and Genetics
2016, Volume: 133, number: 6, pages: 443-451

      UKÄ Subject classification

      Genetics and Breeding

      Publication identifier

      DOI: https://doi.org/10.1111/jbg.12214

      Permanent link to this page (URI)

      https://res.slu.se/id/publ/77858