This paper examines some of the implied effects commonly assumed when building relationship matrices. We propose the inclusion of an additional 'individual' in the genomic relationship matrix which models the mean of the founder population. It is shown that this resolves the problem of inconsistent prediction error variances due to alternate allele coding schemes.

Bruce Tier, Karin Meyer, Andrew Swan

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Methods and Tools - Models and Computing Strategies 2, , 127, 2018
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