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 |
- 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.
