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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)