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Effects of ignoring inbreeding in model‐based accuracy for BLUP and SSGBLUP
Author(s) -
Aguilar Ignacio,
Fernandez Eduardo N.,
Blasco Agustin,
Ravagnolo Olga,
Legarra Andres
Publication year - 2020
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12470
Subject(s) - inbreeding , best linear unbiased prediction , statistics , selection (genetic algorithm) , mathematics , population , computer science , demography , artificial intelligence , sociology
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.