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Published byAndreas Gunnarsson Modified over 6 years ago
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Predictions of Breed Composition Using Holsteins, Jersey, and Brown Swiss Genotypes
K. M. Olson and P. M. VanRaden
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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
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Objective Use a full and reduced SNP set to predict breed composition with Holstein, Jersey, and Brown Swiss genotypes
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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
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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
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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
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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
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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
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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
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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
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Obstacles May not be accurate for animals from different populations
foreign animals older animals There is a patent Located at
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