Detection of putative loci affecting milk, health, and type traits in a US Holstein population using 70 microsatellite markers in a genome scan

Quantitative trait loci affecting milk yield, health, and type traits were studied for seven large U.S. Holstein grandsire families using the granddaughter design. Seventy microsatellite markers located throughout the genome were selected for the quantitative trait loci scan. Effects of marker alleles were analyzed for 30 traits (21 type traits, 5 milk traits, 2 calving ease traits, and somatic cell score and productive life) and 16 canonical traits derived from type and production traits. Previously ave reported results from 36 of these markers but have re-evaluated those results using a more robust analysis method. We report results from all 70 markers using permutation tests to calculate experiment-wise significance values, replacing the less stringent comparison-wise values previously reported. With this new methodology we detected 9 putative quantitative trait loci within specific families. Four markers were associated with effects on type traits on chromosomes 4, 5, 14, and 23. Two markers were associated with effects on protein percentage on chromosomes 6 and 14, and 3 markers were associated with effects on productive life on chromosomes 2, 21, and 23. Although these initial 70 microsatellite markers have been completed in the 7 Holstein families, additional markers will need to be added to allow interval analysis of areas where putative QTL have been identified and to increase marker density where needed.