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 4 Top five predictive genomic features for mastitis, protein, milk and fat yield in across-breed prediction

Trait	Time (h)^a	\({\text{FDR}}_{\exp }^{\text{b}}\)	Log₂(FC)^c	SNP_f (%)^d	\({\text{H}}_{\text{f}}^{2}\) (%)^e	\(r_{\text{GFBLUP}}^{\text{f}}\)	bias ^g	Δr ^h
Mastitis	6	10⁻³	<−1	1.94	9.98	0.063	0.277	0.121
	6	5 × 10⁻²	<−1	3.53	14.03	0.046	0.178	0.104
	6	10⁻²	<−1	2.72	12.68	0.044	0.171	0.102
	9	5 × 10⁻²	NAⁱ	6.99	25.98	0.034	0.115	0.092
	12	5 × 10⁻²	>1	2.34	12.84	0.034	0.112	0.092
Protein	48	10⁻⁶	>2	0.01	2.24	0.302	1.250	0.204
	48	10⁻⁸	NA	0.01	2.04	0.298	1.264	0.200
	48	10⁻⁸	>2	<0.01	2.09	0.295	1.265	0.197
	48	10⁻³	>2	0.01	2.66	0.292	1.245	0.194
	48	10⁻¹⁰	NA	<0.01	1.60	0.282	1.172	0.184
Milk	9	10⁻³	<−1	2.69	24.65	0.232	0.798	0.072
	9	10⁻⁶	NA	2.60	14.41	0.229	0.805	0.069
	9	10⁻⁶	<−1	1.67	8.20	0.228	0.808	0.068
	48	10⁻⁶	>2	0.01	0.25	0.222	0.826	0.062
	12	10⁻⁸	<−1	1.02	3.95	0.221	0.802	0.061
Fat	6	10⁻³	>1	1.98	19.66	0.117	0.577	0.047
	9	10⁻⁶	NA	2.61	24.48	0.104	0.477	0.034
	6	10⁻⁶	<−1	0.95	20.29	0.102	0.446	0.032
	3	5 × 10⁻²	>2	0.11	0.85	0.101	0.567	0.031
	3	10⁻²	>2	0.11	0.72	0.100	0.560	0.030

^aTime points post intra-mammary infection with E. coli LPS
^bFDR values used to define genomic features from RNA-Seq analysis
^cLog₂(fold-change) values used to define up- (down-) regulated genomic features from RNA-Seq analysis
^dProportion of SNPs in genomic features over the whole genome
^eProportion of the total genomic variance explained by genomic features
^fPrediction accuracy with GFBLUP
^gThe regression coefficient of de-regressed proofs (DRP) on predicted genomic breeding values (GEBV)
^hThe change of prediction accuracy with GFBLUP relative to GBLUP
ⁱThe genomic feature defined without log₂(fold-change)

ISSN: 1297-9686