A whole genome scan for quantitative trait loci affecting milk protein percentage in Israeli-Holstein cattle, by means of selective milk DNA pooling in a daughter design, using an adjusted false discovery rate criterion

Selective DNA pooling H as employed in a daughter design to screen all bovi ne autosomes for quantitative tt-ait loci (QTL) affecting estimated breedin g value for milk protein percentage (EBVP%). Milk pools prepared from high and low daughters of each of seven sires were genotyped for 138 dinucleotid e microsatellites. Shadow-corrected estimates of sire allele frequencies: w ere compared between high and low pools. hn adjusted false discovery rate ( FDR) method was employed to calculate experimentwise significance levels an d empirical power. Significant associations with milli protein percentage w ere found fur 61 of the markers (adjusted FDR = 0.10: estimated power. 0.68 ). The significant markers appear to he linked to 19-28 QTL. Mean allele su bstitution effects of the putative QTL averaged 0.016 (0.009-0.028) in unit s of the within-sire family standard deviation of EBVP% and summed to 0.460 EBVP%. Overall QTL heterozygosity was 0.40. The identified QTL appear to a ccount for all of the variation in EBVP% in the population. Through use of selective DNA pooling, 4400 pool data points provided the statistical power of 600,000 individual data points.