Genomic relationships based on X chromosome markers and accuracy of genomic predictions with and without X chromosome markers

Table 5 Regression coefficients of deregressed proofs on genomic predictions based on four datasets ^a with or without X chromosome markers, using different models ^b and averaged over 15 traits

Datasets	G(A)	G(A + X)	G_c(A + X)	G(A) + G(X)	G(A) + Pol	G_c(A + X) + Pol
54K_real	0.881	0.885	0.885	0.885	0.918	0.919
IMP_test	0.881	0.885	0.885	0.885	0.918	0.919
IMP_0.5ref	0.881	0.886	0.885	0.886	0.920	0.922
LD_real	0.834	0.835	0.837	0.838	0.914	0.915

^a54K_real: all animals with marker data from the 54K chip; IMP_test: for the test animals in genomic prediction, the 54K marker data were imputed from LD marker data; IMP_0.5ref: for half (randomly chosen) of the reference animals, the 54K marker data were imputed from LD marker data; LD_real: all animals had LD marker data without extension to the 54K marker data; ^bG(A): model with a G matrix built using autosomal markers only; G(A + X): model with a G matrix built using all markers and treating X-specific markers as autosomal markers; G_c(A + X): model with a G matrix built using all markers and specifying sex-linked inheritance of X-specific markers; G(A) + G(X): model with an autosome G matrix and an X chromosome G matrix; G(A) + Pol: model G(A) plus a residual polygenic effect; G_c(A + X) + Pol: model G_c(A + X) plus a residual polygenic effect.

ISSN: 1297-9686