Trait
|
Population
|
Model
|
Pedigree
|
SNP
|
---|
54K
|
54K + DFS
|
54K + FRA
|
54K + DFS + FRA
|
---|
Milk
|
Genotyped
|
PBLUP
|
0.225
|
–
|
–
|
–
|
–
|
ssGBLUP
|
–
|
c0.595c
|
b0.633ab
|
b0.631b
|
a0.637a
|
ssFGBLUP
|
–
|
–
|
ab0.641a
|
ab0.630a
|
a0.637a
|
ssWGBLUP_bin1
|
–
|
a0.641a
|
ab0.645a
|
ab0.642a
|
a0.645a
|
ssWGBLUP_bin30
|
–
|
a0.640b
|
a0.648a
|
a0.644ab
|
a0.645ab
|
ssWGBLUP_bin100
|
–
|
b0.627b
|
ab0.641a
|
ab0.639a
|
a0.640a
|
Non-genotyped
|
PBLUP
|
0.200
|
–
|
–
|
–
|
–
|
ssGBLUP
|
–
|
b0.240b
|
b0.247a
|
a0.247a
|
a0.248a
|
ssFGBLUP
|
–
|
–
|
ab0.248a
|
a0.247a
|
a0.247a
|
ssWGBLUP_bin1
|
–
|
a0.249a
|
a0.250a
|
a0.250a
|
a0.250a
|
ssWGBLUP_bin30
|
–
|
a0.248a
|
ab0.249a
|
a0.249a
|
a0.249a
|
ssWGBLUP_bin100
|
–
|
a0.247b
|
ab0.249a
|
a0.248ab
|
a0.248ab
|
Fat
|
Genotyped
|
PBLUP
|
0.125
|
–
|
–
|
–
|
–
|
ssGBLUP
|
–
|
a0.391 cd
|
ab0.397ab
|
a0.391bd
|
a0.396ac
|
ssFGBLUP
|
–
|
–
|
a0.405a
|
a0.387b
|
a0.398a
|
ssWGBLUP_bin1
|
–
|
a0.383a
|
b0.387a
|
a0.382a
|
a0.386a
|
ssWGBLUP_bin30
|
–
|
a0.386b
|
ab0.398a
|
a0.390ab
|
a0.396ab
|
ssWGBLUP_bin100
|
–
|
a0.389a
|
ab0.386a
|
a0.385a
|
a0.384a
|
Non-genotyped
|
PBLUP
|
0.121
|
–
|
–
|
–
|
–
|
ssGBLUP
|
–
|
a0.191ab
|
ab0.192a
|
ab0.191b
|
ab0.192ab
|
ssFGBLUP
|
–
|
–
|
ab0.194a
|
b0.189c
|
ab0.191b
|
ssWGBLUP_bin1
|
–
|
a0.192b
|
a0.194a
|
a0.192b
|
a0.193ab
|
ssWGBLUP_bin30
|
–
|
a0.190b
|
a0.194a
|
a0.194a
|
a0.193a
|
ssWGBLUP_bin100
|
–
|
a0.192a
|
b0.190ab
|
b0.188c
|
b0.188bc
|
Protein
|
Genotyped
|
PBLUP
|
0.152
|
–
|
–
|
–
|
–
|
ssGBLUP
|
–
|
b0.428c
|
a0.447ab
|
a0.444b
|
a0.450a
|
ssFGBLUP
|
–
|
–
|
a0.457ab
|
a0.442b
|
a0.451a
|
ssWGBLUP_bin1
|
–
|
a0.449ab
|
a0.452a
|
a0.445b
|
a0.448ab
|
ssWGBLUP_bin30
|
–
|
ab0.445b
|
a0.455a
|
a0.447ab
|
a0.452ab
|
ssWGBLUP_bin100
|
–
|
ab0.437a
|
a0.443a
|
a0.442a
|
a0.442a
|
Non-genotyped
|
PBLUP
|
0.140
|
–
|
–
|
–
|
–
|
ssGBLUP
|
–
|
b0.188b
|
bc0.191a
|
bc0.190a
|
b0.191a
|
ssFGBLUP
|
–
|
–
|
bc0.192a
|
c0.188b
|
bc0.189b
|
ssWGBLUP_bin1
|
–
|
a0.197a
|
a0.197a
|
a0.194b
|
a0.194b
|
ssWGBLUP_bin30
|
–
|
b0.190a
|
b0.192a
|
ab0.192a
|
b0.191a
|
ssWGBLUP_bin100
|
–
|
b0.191a
|
c0.189a
|
c0.187b
|
c0.187b
|
- 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)
- 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)
- 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)