COVARIANCE BETWEEN RELATIVES FOR A MARKED QUANTITATIVE TRAIT LOCUS

Best linear unbiased prediction (BLUP) can be applied to marker-assisted selection. This application requires computation of the inverse of the conditional covariance matrix (G(upsilon)) of additive effects for the quantitative trait locus (QTL) linked to the marker locus (ML), given marker genotypes. This paper presents theory and algorithms to construct G(upsilon) and to obtain its inverse efficiently. These algorithms are sufficiently general to accommodate situations (1) where paternal or maternal origin of marker alleles cannot be determined and (2) where the marker genotypes of some individuals in the pedigree are unknown.