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 3 Top five predictive genomic features for mastitis, protein, milk and fat yield in Jersey cattle

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	9	10⁻¹⁰	>1	0.46	15.79	0.567	0.927	0.018
	12	10⁻²	NAⁱ	3.98	37.31	0.566	0.930	0.017
	9	10⁻¹⁰	NA	1.31	26.64	0.564	0.921	0.015
	12	10⁻¹⁰	<−1	0.71	16.15	0.564	0.925	0.015
	6	10⁻³	<−1	1.67	28.69	0.563	0.923	0.014
Protein	48	10⁻²	>2	0.02	6.42	0.576	0.807	0.046
	48	10⁻⁶	>2	<0.01	4.59	0.571	0.797	0.041
	48	10⁻¹⁰	>2	<0.01	4.11	0.569	0.787	0.039
	48	10⁻⁸	>2	<0.01	4.28	0.569	0.796	0.039
	48	5 × 10⁻²	>2	0.03	6.74	0.568	0.804	0.038
Milk	48	0.01	>2	0.02	2.19	0.608	0.805	0.011
	9	10⁻²	<−1	3.02	12.85	0.607	0.801	0.010
	12	10⁻⁸	<−1	0.88	10.39	0.606	0.809	0.009
	48	5 × 10⁻²	>2	0.03	1.38	0.605	0.805	0.008
	9	10⁻³	<−1	2.31	13.94	0.604	0.800	0.007
Fat	48	5 × 10⁻²	>1	0.30	4.04 × 10⁻⁷	0.438	0.672	0.005
	6	5 × 10⁻²	>1	2.57	2.00 × 10⁻⁷	0.437	0.672	0.004
	48	5 × 10⁻²	NA	0.35	2.24 × 10⁻⁶	0.437	0.672	0.004
	9	10⁻⁶	>2	0.32	5.93 × 10⁻⁷	0.437	0.672	0.004
	9	10⁻⁸	>2	0.28	5.68 × 10⁻⁷	0.437	0.672	0.004

^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