Using imputation-based whole-genome sequencing data to improve the accuracy of genomic prediction for combined populations in pigs

Table 3 Accuracy of genomic prediction for reproduction traits using different reference populations to predict 196 younger individuals of the XD population

Reference set^a (size of reference population)	Method	Trait
Reference set^a (size of reference population)	Method	NBA	TNB
XD (566)	GBLUP_80K	0.392	0.431
	GBLUP_WGS	0.390	0.425
	GBLUP_LD	0.396	0.435
	GFBLUP_QTL	0.398	0.435
	GFBLUP_GWAS	0.378	0.425
	ssGBLUP_80K	0.441	0.465
	ssGBLUP_WGS	0.439	0.457
	ssGBLUP_LD	0.440	0.462
LM+XD (2207)	GBLUP_80K	0.387	0.439
	GBLUP_WGS	0.407	0.454
	GBLUP_LD	0.403	0.455
	GFBLUP_QTL	0.407	0.458
	GFBLUP_GWAS	0.429	0.494
	ssGBLUP_80K	0.451	0.480
	ssGBLUP_WGS	0.455	0.481
	ssGBLUP_LD	0.453	0.483
LM (1641)	GBLUP_80K	0.121	0.214
	GBLUP_WGS	0.204	0.275
	GBLUP_LD	0.152	0.228
	GFBLUP_QTL	0.163	0.232
	GFBLUP_GWAS	0.221	0.282

GBLUP_80K genomic BLUP based on the 80K SNP panel; GBLUP_WGS GBLUP based on imputed whole-genome sequencing (WGS) data; GBLUP_LD GBLUP based on WGS after LD pruning; GFBLUP_QTL genomic feature BLUP with a genomic feature matrix constructed based on QTL prior information; GFBLUP_GWAS genomic feature BLUP with a genomic feature matrix constructed based on GWAS prior information; ssGBLUP_80K, ssGBLUP_WGS, ssGBLUP_LD For ssGBLUP, the H matrix was constructed based on the different genomic relationship matrices of the 80K chip panel, WGS data and WGS data after LD pruning and termed ssGBLUP_80K, ssGBLUP_WGS and ssGBLUP_LD, respectively; NBA number of piglets born alive; TNB total number of piglets born
^aYorkshire population LM, XD or LM plus the XD reference population

ISSN: 1297-9686