Genomic prediction using preselected DNA variants from a GWAS with whole-genome sequence data in Holstein–Friesian cattle

Table 3 Phenotypic variance (h²) explained in 2287 validation animals fitting GRM based on the selected set of variants for protein yield (PY), somatic cell score (SCS) and interval first–last insemination (IFL)

Trait	Selection criteria	ISQ	HD	50k
Trait	Selection criteria	Selected set of variants (GRM)
PY	All variants	0.83	0.82	0.81
	−log10(p) > 3	0.53^a	0.40	0.22
	−log10(p) > 5	0.60^a	0.43^a	0.22^a
	COJO3	0.21
	COJO5	0.19
	COJO5LD	0.19
	COJO#100	0.23
SCS	All variants	0.87	0.84	0.83
	−log10(p) > 3	0.57^a	0.45^a	0.19
	−log10(p) > 5	0.72^a	0.25^a	0.03^a
	COJO3	0.31
	COJO5	0.31
	COJO5LD	0.16
	COJO#100	0.22
IFL	All variants	0.72	0.70	0.69
	−log10(p) > 3	0.51^a	0.32	0.14
	−log10(p) > 5	0.50^a	0.15^a	0.03
	COJO3	0.25
	COJO5	0.23
	COJO5LD	0.13
	COJO#100	0.17

ISQ are all imputed sequence variants, and HD and 50k are the SNPs on the common HD and 50k panels. Variants were selected using GWAS results on 3469 discovery animals
^aInflated phenotypic variance (see Additional file 5: Table S1)

ISSN: 1297-9686