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Table 4 Reliabilities from a pedigree 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 0.318
ssGBLUP a0.407a a0.398a a0.404a a0.395a
ssFGBLUP a0.401a a0.387a a0.369a
ssWGBLUP_bin1 a0.406a a0.398a a0.405a a0.396a
ssWGBLUP_bin30 a0.412a a0.398a a0.401a a0.389a
ssWGBLUP_bin100 a0.410a a0.405a a0.405a a0.406a
Non-genotyped PBLUP 0.126
ssGBLUP a0.139a a0.138a a0.140a a0.139a
ssFGBLUP a0.138a a0.141a a0.138a
ssWGBLUP_bin1 a0.140a a0.137a a0.139a a0.139a
ssWGBLUP_bin30 a0.138a a0.136a a0.139a a0.139a
ssWGBLUP_bin100 a0.139a a0.137a a0.140a a0.143a
IFLc Genotyped PBLUP 0.086
ssGBLUP a0.234a a0.229a a0.236a a0.230a
ssFGBLUP a0.213a a0.234a a0.218a
ssWGBLUP_bin1 a0.239a a0.232a a0.238a a0.234a
ssWGBLUP_bin30 a0.245a a0.239a a0.247a a0.236a
ssWGBLUP_bin100 a0.240a a0.233a a0.244a a0.240a
Non-genotyped PBLUP 0.108
ssGBLUP a0.088a a0.087a ab0.090a a0.089a
ssFGBLUP a0.083b a0.093a a0.089ab
ssWGBLUP_bin1 a0.086a a0.085a ab0.089a a0.087a
ssWGBLUP_bin30 a0.085a a0.083a b0.086a a0.084a
ssWGBLUP_bin100 a0.084a a0.083a ab0.084a a0.083a
ICF Genotyped PBLUP 0.031
ssGBLUP a0.140a a0.143a a0.143a a0.145a
ssFGBLUP a0.147a a0.149a a0.153a
ssWGBLUP_bin1 a0.140a a0.144a a0.142a a0.145a
ssWGBLUP_bin30 a0.138a a0.140a a0.142a a0.144a
ssWGBLUP_bin100 a0.140a a0.141a a0.142a a0.144a
Non-genotyped PBLUP 0.069
ssGBLUP a0.069c a0.070bc a0.071ab a0.072a
ssFGBLUP a0.073a a0.076a a0.078a
ssWGBLUP_bin1 a0.069b a0.070ab a0.071a a0.072a
ssWGBLUP_bin30 a0.069b a0.070b a0.071ab a0.072a
ssWGBLUP_bin100 a0.069b a0.071ab a0.072a a0.073a
  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. 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. Reliabilities with no common letter differ significantly (P < 0.05)