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Table 3 Reliabilities from a pedigree-based BLUP (PBLUP) model and different ssGBLUP models using different SNP sets for milk production traits

From: Weighted single-step genomic best linear unbiased prediction integrating variants selected from sequencing data by association and bioinformatics analyses

Trait Population Model Pedigree SNP
54K 54K + DFS 54K + FRA 54K + DFS + FRA
Milk Genotyped PBLUP 0.225
ssGBLUP c0.595c b0.633ab b0.631b a0.637a
ssFGBLUP ab0.641a ab0.630a a0.637a
ssWGBLUP_bin1 a0.641a ab0.645a ab0.642a a0.645a
ssWGBLUP_bin30 a0.640b a0.648a a0.644ab a0.645ab
ssWGBLUP_bin100 b0.627b ab0.641a ab0.639a a0.640a
Non-genotyped PBLUP 0.200
ssGBLUP b0.240b b0.247a a0.247a a0.248a
ssFGBLUP ab0.248a a0.247a a0.247a
ssWGBLUP_bin1 a0.249a a0.250a a0.250a a0.250a
ssWGBLUP_bin30 a0.248a ab0.249a a0.249a a0.249a
ssWGBLUP_bin100 a0.247b ab0.249a a0.248ab a0.248ab
Fat Genotyped PBLUP 0.125
ssGBLUP a0.391 cd ab0.397ab a0.391bd a0.396ac
ssFGBLUP a0.405a a0.387b a0.398a
ssWGBLUP_bin1 a0.383a b0.387a a0.382a a0.386a
ssWGBLUP_bin30 a0.386b ab0.398a a0.390ab a0.396ab
ssWGBLUP_bin100 a0.389a ab0.386a a0.385a a0.384a
Non-genotyped PBLUP 0.121
ssGBLUP a0.191ab ab0.192a ab0.191b ab0.192ab
ssFGBLUP ab0.194a b0.189c ab0.191b
ssWGBLUP_bin1 a0.192b a0.194a a0.192b a0.193ab
ssWGBLUP_bin30 a0.190b a0.194a a0.194a a0.193a
ssWGBLUP_bin100 a0.192a b0.190ab b0.188c b0.188bc
Protein Genotyped PBLUP 0.152
ssGBLUP b0.428c a0.447ab a0.444b a0.450a
ssFGBLUP a0.457ab a0.442b a0.451a
ssWGBLUP_bin1 a0.449ab a0.452a a0.445b a0.448ab
ssWGBLUP_bin30 ab0.445b a0.455a a0.447ab a0.452ab
ssWGBLUP_bin100 ab0.437a a0.443a a0.442a a0.442a
Non-genotyped PBLUP 0.140
ssGBLUP b0.188b bc0.191a bc0.190a b0.191a
ssFGBLUP bc0.192a c0.188b bc0.189b
ssWGBLUP_bin1 a0.197a a0.197a a0.194b a0.194b
ssWGBLUP_bin30 b0.190a b0.192a ab0.192a b0.191a
ssWGBLUP_bin100 b0.191a c0.189a c0.187b c0.187b
  1. ssGBLUP models = a single-step genomic BLUP (ssGBLUP) model, a featured ssGBLUP (ssFGBLUP) model, and weighted ssGBLUP models with a region size of 1 (ssWGBLUP_bin1), 30 (ssWGBLUP_bin30), or 100 SNPs (ssWGBLUP_bin100)
  2. SNP sets = SNPs on the 54K-SNP chip (54K), SNPs on the 54K-SNP chip together with sequencing SNPs selected by Denmark-Finland-Sweden (54K + DFS), SNPs on the 54K-SNP chip together with sequencing SNPs selected by France (54K + FRA), and SNPs on the 54K-SNP chip together with both sets of selected sequencing SNPs (54K + DFS + FRA)
  3. a,b,csubscript letters to the left are for comparisons among models using the same SNP set, and superscript letters to the right are for comparisons among SNP sets using the same model. Reliabilities with no common letter differ significantly (P < 0.05)