Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection

Table 5 GFBLUP analyses of 34 genes detected in the comparison 48 h vs. −22 h (FDR < 10⁻⁶; log₂(fold-change) > 2) for mastitis, protein, milk and fat yield

Scenario	Trait	\({\text{H}}_{\text{f}}^{2}\) (%)^a	\(r_{\text{GFBLUP}}^{\text{b}}\)	bias ^c	Δr ^d
Within HOL	Mastitis	0.44	0.505	0.865	0.001
	Protein	1.84	0.622	0.783	0.020
	Milk	0.32	0.643	0.863	0.008
	Fat	0.15	0.607	0.809	0.000
Within JER	Mastitis	0.50	0.550	0.918	0.001
	Protein	4.59	0.571	0.797	0.041
	Milk	0.00	0.596	0.789	−0.001
	Fat	0.00	0.434	0.671	0.001
Across-breed	Mastitis	0.46	−0.063	−0.373	−0.005
	Protein	2.24	0.302	1.250	0.204
	Milk	0.25	0.222	0.826	0.062
	Fat	0.09	0.079	0.491	0.009

^aProportion of total genomic variance explained by the genomic feature
^bPrediction accuracy with GFBLUP
^cRegression of coefficient of de-regressed proofs (DRP) on predicted genomic breeding values (GEBV)
^dChange in prediction accuracy with GFBLUP relative to GBLUP

ISSN: 1297-9686