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Table 6 Regression coefficients of yield deviation (YD) on prediction from a pedigree-based BLUP (PBLUP) model and different ssGBLUP models using different SNP sets for female fertility 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
IFLh Genotyped PBLUP 1.64
ssGBLUP a1.56a a1.54a a1.55a a1.53a
ssFGBLUP a1.55a a1.49a a1.46a
ssWGBLUP_bin1 a1.55a a1.54a a1.55a a1.53a
ssWGBLUP_bin30 a1.55a a1.53a a1.53a a1.51a
ssWGBLUP_bin100 a1.54a a1.53a a1.52a a1.53a
Non-genotyped PBLUP 1.08
ssGBLUP a1.10a a1.10a a1.10a a1.10a
ssFGBLUP a1.02a a1.09a a1.05a
ssWGBLUP_bin1 a1.10a a1.09a a1.10a a1.10a
ssWGBLUP_bin30 a1.10a a1.09a a1.10a a1.10a
ssWGBLUP_bin100 a1.10a a1.09a a1.10a a1.11a
IFLc Genotyped PBLUP 1.17
ssGBLUP a1.18a a1.17a a1.20a a1.18a
ssFGBLUP a1.11a a1.20a a1.14a
ssWGBLUP_bin1 a1.18a a1.16a a1.19a a1.17a
ssWGBLUP_bin30 a1.18a a1.16a a1.19a a1.16a
ssWGBLUP_bin100 a1.17a a1.15a a1.18a a1.17a
Non-genotyped PBLUP 1.32
ssGBLUP a1.03bc a1.02c a1.05a a1.04ab
ssFGBLUP b0.99c a1.07a ab1.04b
ssWGBLUP_bin1 b1.02b ab1.01b b1.04a b1.02ab
ssWGBLUP_bin30 b1.00a b0.99a c1.01a c1.00a
ssWGBLUP_bin100 b1.00a b0.99a bc1.00a bc0.99a
ICF Genotyped PBLUP 0.57
ssGBLUP a0.66a a0.67a a0.67a a0.67a
ssFGBLUP a0.67a a0.67a a0.68a
ssWGBLUP_bin1 a0.66a a0.67a a0.66a a0.67a
ssWGBLUP_bin30 a0.65a a0.66a a0.66a a0.67a
ssWGBLUP_bin100 a0.65a a0.66a a0.66a a0.66a
Non-genotyped PBLUP 0.89
ssGBLUP a0.71b a0.72ab a0.73a a0.73a
ssFGBLUP a0.74a a0.75a a0.76a
ssWGBLUP_bin1 a0.71b a0.72ab a0.73ab a0.73a
ssWGBLUP_bin30 a0.71b a0.72ab a0.73ab a0.73a
ssWGBLUP_bin100 a0.71b a0.72ab a0.73a a0.73a
  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 in the 54K-SNP chip (54K), SNPs in the 54K-SNP chip together with sequencing SNPs selected by Denmark–Finland–Sweden (54K + DFS), SNPs in the 54K-SNP chip together with sequencing SNPs selected by France (54K + FRA), and SNPs in the 54K-SNP chip together with both sets of selected sequencing SNPs (54K + DFS + FRA)
  3. IFLh the interval from first to last insemination in heifers, IFLc the interval from first to last insemination in cows, ICF the interval from calving to first insemination
  4. 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)
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