Identification of gametes and treatment of linear dependencies in the gametic QTL-relationship matrix and its inverse

Abstract

-The estimation of gametic effects via marker-assisted BLUP requires the inverse of the conditional gametic relationship matrix G. Both gametes of each animal can either be identified (distinguished) by markers or by parental origin. By example, it was shown that the conditional gametic relationship matrix is not unique but depends on the mode of gamete identification. The sum of both gametic effects of each animal -and therefore its estimated breeding value -remains however unaffected. A previously known algorithm for setting up the inverse of G was generalized in order to eliminate the dependencies between columns and rows of G. In the presence of dependencies the rank of G also depends on the mode of gamete identification. A unique transformation of estimates of QTL genotypic effects into QTL gametic effects was proven to be impossible. The properties of both modes of gamete identification in the fields of application are discussed. marker assisted selection / best linear unbiased prediction / linkage analysis / gametic relationship matrix

Refined mapping of quantitative trait loci for somatic cell score on BTA02 in the German Holstein

“…For all models discussed above, the (co)variance matrices for the additive effects of the QTL conditional on marker haplotypes were calculated by treating highly correlated haplotypes in the same way: if very close correlations between haplotypes occur, a predefined threshold (e.g. ɛ = 0.03) was given and all haplotypes with correlations above 0.97 were clustered together (Tuchscherer et al. 2004; Calus et al.…”