Skip to main content

Table 4 Reliability (%) of genomic predictions based on four datasets a with or without X chromosome markers, using different models b and averaged over 15 traits

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

Dataset G(A) G(A + X) Gc(A + X) G(A) + G(X) G(A) + Pol Gc(A + X) + Pol
54K_real 38.0 38.5 38.5 38.5 38.9 39.3
IMP_test 37.9 38.3 38.3 38.4 38.9 39.2
IMP_0.5ref 37.8 38.3 38.3 38.3 38.8 39.1
LD_real 33.0 33.5 33.6 33.6 35.5 35.9
  1. 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; Gc(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; Gc(A + X) + Pol: model Gc(A + X) plus a residual polygenic effect.