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