Selective DNA pooling was employed in a daughter design to screen all bovineautosomes for quantitative trait loci (QTL) affecting estimated breeding valuefor milk protein percentage (EBVP%). Milk pools prepared from high and lowdaughters of each of seven sires were genotyped for 138 dinucleotidemicrosatellites. Shadow-corrected estimates of sire allele frequencies werecompared between high and low pools. An adjusted false discovery rate (FDR)method was employed to calculate experimentwise significance levels andempirical power. Significant associations with milk protein percentage werefound for 61 of the markers (adjusted FDR = 0.10; estimated power, 0.68). Thesignificant markers appear to be linked to 19--28 QTL. Mean allele substitutioneffects of the putative QTL averaged 0.016 (0.009--0.028) in units of thewithin-sire family standard deviation of EBVP% and summed to 0.460 EBVP%.Overall QTL heterozygosity was 0.40. The identified QTL appear to account forall of the variation in EBVP% in the population. Through use of selective DNApooling, 4400 pool data points provided the statistical power of 600,000individual data points.