Detection of putative loci affecting milk, health, and conformation traitsin a US Holstein population using 105 microsatellite markers

Quantitative trait loci affecting milk yield, health, and conformation trai ts were studied for eight large US Holstein grandsire families by using the granddaughter design. A total of 105 microsatellite markers, located throu ghout the bovine genome, were selected for the scan. The data analyzed incl ude genotypes for 35 markers in eight families not previously reported and genotypes for 70 markers reported previously in seven of those families. An alyses of markers previously reported were updated. Effects of marker allel es were analyzed for 38 traits, including traits for milk production, somat ic cell score, productive life, conformation, calving ease, and 16 canonica l traits derived from conformation and production traits. Permutation tests were used to calculate empirical trait-wise error rates. A trait-wise crit ical value of P = 0.1 was used to determine significance. Eight putative qu antitative trait loci associated with 7 of the 35 new markers were identifi ed within specific families. Two of these markers were associated with diff erences in strength and rump angle on chromosomes 4 and 9, respectively. Di fferent markers were associated with protein percentage, milk yield, and so matic cell score on chromosomes 6, 7, and 10 in different families. Differe nces in the canonically transformed traits were associated with markers on chromosomes 5, 6, and 9. Additional marker-trait combinations were identifi ed in the across-family tests, including effects on chromosomes 3, 4, and 9 for protein percentage, body depth, and canonical conformation traits, res pectively. Additional markers are being added to allow interval analysis fo r putative quantitative trait loci that have been identified and to increas e marker density.