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 bovine autosomes for quantitative tt-ait loci (QTL) affecting estimated breeding value for milk protein percentage (EBVP%). Milk pools prepared from high and low daughters of each of seven sires were genotyped for 138 dinucleotide microsatellites. Shadow-corrected estimates of sire allele frequencies: were compared between high and low pools. hn adjusted false discovery rate (FDR) method was employed to calculate experimentwise significance levels and empirical power. Significant associations with milli protein percentage were 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 substitution effects of the putative QTL averaged 0.016 (0.009-0.028) in units 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 account 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.