1. Predictions of Breed Composition Using Holsteins, Jersey, and Brown Swiss Genotypes
K. M. Olson and P. M. VanRaden

2. Background
200 Breed-specific SNP were used to verify an animal received the correct breed code in the quality control data step
Several animals had fewer breed-specific SNP and lower genomic relationships and inbreeding
Wanted to investigate a more precise way to look at breed composition

3. Objective
Use a full and reduced SNP set to predict breed composition with Holstein, Jersey, and Brown Swiss genotypes

4. Materials & Methods Used both females and males
Y- Variable was breed of animal
A Holstein would receive a 1 for the Holstein analysis and a 0 for the Jersey and Brown Swiss analysis
Animal Breed
Holstein Analysis
Jersey Analysis
BSW Analysis
HOL 1
JER
BSW

5. Materials & Methods
3 different sizes of SNP sets were used for the genomic evaluation to compute SNP estimates for breed
The full 43,385 SNP set
The proposed 3 K SNP set
The 600 SNP set
Each breed has ~ 200 – used for the basic check currently not a genomic evaluation

6. Materials & Methods
Training data set – animal reliability set to 99% and parent average reliability set to 50%
Proven as of July 2009
Total of 14,039 animals across all breeds
Validation data set – reliabilities set to 0%
Unproven as of July 2009
15,809 animals across all breeds

7. Results
Means and standard deviations for given breed of the training (old animals) data set
SNP set/ Breed
43 K
3 K
600
Holstein
(N = 11,053)
1.000±0.007
0.997±0.041
0.999±0.021
Jersey
(N = 2,208)
1.000±0.016
0.990±0.069
0.989±0.047
Brown Swiss
(N = 778)
0.994±0.021
0.988±0.035
0.992±0.051

8. Results
Means and standard deviations for given breed of the validation
(young animals) data set
SNP set/ Breed
43 K
3 K
600
Holstein
(N = 14,794)
1.000±0.008
1.004±0.031
1.002±0.019
Jersey
(N = 919)
0.996±0.028
0.978±0.063
0.989±0.036
Brown Swiss
(N = 96)
0.994±0.021
0.992±0.051

9. Results
All three tests were able to determine a Holstein that was by pedigree 1/8 (12.5%) Jersey
43 K test predicted her as 85.9% Holstein and 13.3% Jersey
3 K predicted she was 84.4% Holstein and 15.5% Jersey
600 SNP set she was 83.0% Holstein and 16.6% Jersey

10. Conclusions
The 43 K set was the most accurate at prediction of breed composition (SD ranged from 0.8% - 2.8%)
The 3 K set could identify individuals that had large amounts (> 13%) of foreign DNA
The population of interest would need to be determined

11. Obstacles May not be accurate for animals from different populations
foreign animals
older animals
There is a patent
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