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Table 5 Regression coefficients of yield deviation (YD) on prediction 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 0.89
ssGBLUP a0.84a a0.83a a0.83a a0.83a
ssFGBLUP a0.83a b0.81a a0.82a
ssWGBLUP_bin1 c0.80a b0.80a c0.79a b0.80a
ssWGBLUP_bin30 b0.81a b0.80b bc0.80b b0.80b
ssWGBLUP_bin100 b0.81a b0.81ab c0.80b b0.80b
Non-genotyped PBLUP 0.87
ssGBLUP a0.87a a0.87a a0.86a a0.86a
ssFGBLUP ab0.87a a0.86b a0.86ab
ssWGBLUP_bin1 b0.85a c0.85a b0.84a b0.85a
ssWGBLUP_bin30 ab0.85a c0.85a b0.85a b0.85a
ssWGBLUP_bin100 a0.86a bc0.86a ab0.85ab b0.85b
Fat Genotyped PBLUP 0.77
ssGBLUP a0.74a a0.74a a0.73a a0.73a
ssFGBLUP a0.75a a0.72b a0.73b
ssWGBLUP_bin1 b0.68a b0.68a b0.68a b0.68a
ssWGBLUP_bin30 b0.69a b0.70a b0.69a b0.70a
ssWGBLUP_bin100 b0.70a b0.69a b0.69a b0.68a
Non-genotyped PBLUP 0.77
ssGBLUP a0.78a a0.78a a0.77b a0.77b
ssFGBLUP a0.79a ab0.77b a0.77b
ssWGBLUP_bin1 b0.76a b0.76a bc0.76a b0.76a
ssWGBLUP_bin30 b0.76b b0.77a ab0.77a ab0.76ab
ssWGBLUP_bin100 b0.76a b0.76ab c0.75bc c0.74c
Protein Genotyped PBLUP 0.81
ssGBLUP a0.76a a0.77a a0.76a a0.76a
ssFGBLUP a0.78a a0.75b a0.76b
ssWGBLUP_bin1 b0.73a b0.73a b0.72a b0.72a
ssWGBLUP_bin30 b0.73a b0.74a b0.72a b0.73a
ssWGBLUP_bin100 b0.74a b0.73ab b0.72ab b0.72b
Non-genotyped PBLUP 0.80
ssGBLUP a0.77a ab0.77a a0.77a a0.77a
ssFGBLUP a0.78a ab0.76b a0.77ab
ssWGBLUP_bin1 a0.77ab ab0.77a ab0.76ab ab0.76b
ssWGBLUP_bin30 a0.76a b0.76a ab0.76a a0.76a
ssWGBLUP_bin100 a0.77a b0.76ab b0.75bc b0.75c
  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. Regression coefficients with no common letter differ significantly (P < 0.05)