How to Use Fewer Markers in Admixture Studies

Sa？etak Swiss Fleckvieh has been established from 1970 as a composite of Simmental and Red Holstein Friesian cattle. Breed composition is currently reported based on pedigree information. Information on ancestry informative molecular markers potentially provides more accurate information. For the analysis Illumina Bovine SNP50 Beadchip data for 495 bulls were used. Markers were selected based on difference in allele frequencies in the pure populations, using FST as an indicator. Performance of sets with decreasing number of markers was compared. The scope of the study was to see how much we can reduce the number of markers based on FST to get a reliability that is close to that with the full set of markers. On these sets of markers hidden Markov models (HMM) and methods used in genomic selection (BayesB, partial least squares regression, LASSO variable selection) were applied. Correlations of admixture levels were estimated and compared with admixture levels based on pedigree information. FST chosen SNP gave very high correlations with pedigree based admixture. Only when using 96 and 48 SNP with the highest FST, correlations dropped to 0.92 and 0.90, respectively