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

Table 2 Accuracy of genomic prediction for reproduction traits using different reference populations to predict 223 younger individuals of the LM population

Reference set^a (size of reference population)	Method	Trait
Reference set^a (size of reference population)	Method	NBA	TNB
LM (1418)	GBLUP_80K	0.453	0.450
	GBLUP_WGS	0.456	0.452
	GBLUP_LD	0.470	0.464
	GFBLUP_QTL	0.473	0.466
	GFBLUP_GWAS	0.464	0.459
	ssGBLUP_80K	0.649	0.664
	ssGBLUP_WGS	0.641	0.658
	ssGBLUP_LD	0.662	0.679
LM+XD (2180)	GBLUP_80K	0.459	0.460
	GBLUP_WGS	0.467	0.468
	GBLUP_LD	0.478	0.479
	GFBLUP_QTL	0.478	0.471
	GFBLUP_GWAS	0.462	0.455
	ssGBLUP_80K	0.646	0.664
	ssGBLUP_WGS	0.648	0.667
	ssGBLUP_LD	0.668	0.686
XD (762)	GBLUP_80K	0.026	− 0.016
	GBLUP_WGS	0.042	− 0.001
	GBLUP_LD	0.050	0.028
	GFBLUP_QTL	− 0.017	− 0.058
	GFBLUP_GWAS	− 0.008	− 0.009

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