02789naa a2200241 a 450000100080000000500110000800800410001902200140006002400270007410000160010124501040011726000090022150003670023052016990059765300130229665300240230965300130233370000210234670000150236770000180238270000160240077301310241610609212020-08-10       2020    bl uuuu     u00u1 u    #d  a0931-26687 a10.1111/jbg.124702DOI1 aAGUILAR, I.  aEffects of ignoring inbreeding in model-based accuracy for BLUP and SSGBLUP.h[electronic resource]  c2020  aArticle history: Received: 22 August 2019 / Revised: 10 December 2019 / Accepted: 11 January 2020 / First published:20 February 2020 Corresponding author: Aguilar, I.; email:iaguilar@inia.org.uy Funding information: FEDER; INRA; Universidad Nacional de Lomas de Zamora; European Unions' Horizon 2020 Research & Innovation Programme, Grant/Award Number: N°772787  aABSTRACT. Model-based accuracy, defined as the theoretical correlation between true and estimated breeding value, can be obtained for each individual as a function of its prediction error variance (PEV) and inbreeding coefficient F, in BLUP, GBLUP and SSGBLUP genetic evaluations. However, for computational convenience, inbreeding is often ignored in two places. First, in the computation of reliability = 1-PEV/(1 + F). Second, in the set-up, using Henderson's rules, of the inverse of the pedigree-based relationship matrix A. Both approximations have an effect in the computation of model-based accuracy and result in wrong values. In this work, first we present a reminder of the theory and extend it to SSGBLUP. Second, we quantify the error of ignoring inbreeding with real data in three scenarios: BLUP evaluation and SSGBLUP in Uruguayan dairy cattle, and BLUP evaluations in a line of rabbit closed for >40 generations with steady increase of inbreeding up to an average of 0.30. We show that ignoring inbreeding in the set-up of the A-inverse is equivalent to assume that non-inbred animals are actually inbred. This results in an increase of apparent PEV that is negligible for dairy cattle but considerable for rabbit. Ignoring inbreeding in reliability = 1-PEV/(1 + F) leads to underestimation of reliability for BLUP evaluations, and this underestimation is very large for rabbit. For SSGBLUP in dairy cattle, it leads to both underestimation and overestimation of reliability, both for genotyped and non-genotyped animals. We strongly recommend to include inbreeding both in the set-up of A-inverse and in the computation of reliability from PEVs.  © 2020 Blackwell Verlag GmbH  aBREEDING  aGenomic predictions  aGENOMICS1 aFERNÁNDEZ, E.N.1 aBLASCO, A.1 aRAVAGNOLO, O.1 aLEGARRA, A.  tJournal of Animal Breeding and Genetics, 1 July 2020, Volume 137, Issue 4, pp. 356-364. Doi: https://doi.org/10.1111/jbg.12470