The objective of this study was to investigate methods and statistical power for mapping quantitative trait loci (QTL) using selective genotyping and Illumina's 50K BeadChip. A large unrelated population is recorded for a phenotypic trait. Animals with extreme phenotypes are used for genotyping with Illumina's arrays and QTL are mapped by linkage disequilibrium (LD). We carried out computer simulations to compute statistical power using this approach after varying QTL allele frequency, proportion selected in the extremes, and population size. For example, power for a population of 1,000 animals after genotyping the top and bottom 5% (QTL effect of 0.5 phenotypic standard deviations, alpha of 0.01 and allele frequency of 0.1) and assuming maximum LD, was 0.95. The method was tested in a Merino flock with 979 ewes in which fiber diameter (FD) was recorded. Illumina's 50K Bead Chip was used for simultaneous genotyping of 54,241 SNPs in selected animals (24 in each extreme) but only within a year class and breed. A total of 208 tests were significant out of 18,214 SNPs tested at significance level of 0.01. There were more significant tests than expected by chance. The highest significant results were obtained in Chromosomes 1, 14, 15, 21 and 26. Validation of the results must be confirmed in the unselected population
