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

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

Reference seta (size of reference population) Method Trait
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
  1. 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
  2. aYorkshire population LM, XD or LM plus the XD reference population