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

Milk

Genotyped

PBLUP

0.225

–

–

–

–

ssGBLUP

–

_c0.595^c

_b0.633^ab

_b0.631^b

_a0.637^a

ssFGBLUP

–

–

_ab0.641^a

_ab0.630^a

_a0.637^a

ssWGBLUP_bin1

–

_a0.641^a

_ab0.645^a

_ab0.642^a

_a0.645^a

ssWGBLUP_bin30

–

_a0.640^b

_a0.648^a

_a0.644^ab

_a0.645^ab

ssWGBLUP_bin100

–

_b0.627^b

_ab0.641^a

_ab0.639^a

_a0.640^a

Non-genotyped

PBLUP

0.200

–

–

–

–

ssGBLUP

–

_b0.240^b

_b0.247^a

_a0.247^a

_a0.248^a

ssFGBLUP

–

–

_ab0.248^a

_a0.247^a

_a0.247^a

ssWGBLUP_bin1

–

_a0.249^a

_a0.250^a

_a0.250^a

_a0.250^a

ssWGBLUP_bin30

–

_a0.248^a

_ab0.249^a

_a0.249^a

_a0.249^a

ssWGBLUP_bin100

–

_a0.247^b

_ab0.249^a

_a0.248^ab

_a0.248^ab

Fat

Genotyped

PBLUP

0.125

–

–

–

–

ssGBLUP

–

_a0.391 ^cd

_ab0.397^ab

_a0.391^bd

_a0.396^ac

ssFGBLUP

–

–

_a0.405^a

_a0.387^b

_a0.398^a

ssWGBLUP_bin1

–

_a0.383^a

_b0.387^a

_a0.382^a

_a0.386^a

ssWGBLUP_bin30

–

_a0.386^b

_ab0.398^a

_a0.390^ab

_a0.396^ab

ssWGBLUP_bin100

–

_a0.389^a

_ab0.386^a

_a0.385^a

_a0.384^a

Non-genotyped

PBLUP

0.121

–

–

–

–

ssGBLUP

–

_a0.191^ab

_ab0.192^a

_ab0.191^b

_ab0.192^ab

ssFGBLUP

–

–

_ab0.194^a

_b0.189^c

_ab0.191^b

ssWGBLUP_bin1

–

_a0.192^b

_a0.194^a

_a0.192^b

_a0.193^ab

ssWGBLUP_bin30

–

_a0.190^b

_a0.194^a

_a0.194^a

_a0.193^a

ssWGBLUP_bin100

–

_a0.192^a

_b0.190^ab

_b0.188^c

_b0.188^bc

Protein

Genotyped

PBLUP

0.152

–

–

–

–

ssGBLUP

–

_b0.428^c

_a0.447^ab

_a0.444^b

_a0.450^a

ssFGBLUP

–

–

_a0.457^ab

_a0.442^b

_a0.451^a

ssWGBLUP_bin1

–

_a0.449^ab

_a0.452^a

_a0.445^b

_a0.448^ab

ssWGBLUP_bin30

–

_ab0.445^b

_a0.455^a

_a0.447^ab

_a0.452^ab

ssWGBLUP_bin100

–

_ab0.437^a

_a0.443^a

_a0.442^a

_a0.442^a

Non-genotyped

PBLUP

0.140

–

–

–

–

ssGBLUP

–

_b0.188^b

_bc0.191^a

_bc0.190^a

_b0.191^a

ssFGBLUP

–

–

_bc0.192^a

_c0.188^b

_bc0.189^b

ssWGBLUP_bin1

–

_a0.197^a

_a0.197^a

_a0.194^b

_a0.194^b

ssWGBLUP_bin30

–

_b0.190^a

_b0.192^a

_ab0.192^a

_b0.191^a

ssWGBLUP_bin100

–

_b0.191^a

_c0.189^a

_c0.187^b

_c0.187^b