Detection of Putative Loci Affecting Milk, Health, and Conformation Traits in a US Holstein Population Using 105 Microsatellite Markers

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Abstract
Quantitative trait loci affecting milk yield, health, and conformation traits were studied for eight large US Holstein grandsire families by using the granddaughter design. A total of 105 microsatellite markers, located throughout the bovine genome, were selected for the scan. The data analyzed include genotypes for 35 markers in eight families not previously reported and genotypes for 70 markers reported previously in seven of those families. Analyses of markers previously reported were updated. Effects of marker alleles were analyzed for 38 traits, including traits for milk production, somatic cell score, productive life, conformation, calving ease, and 16 canonical traits derived from conformation and production traits. Permutation tests were used to calculate empirical trait-wise error rates. A trait-wise critical value of P = 0.1 was used to determine significance. Eight putative quantitative trait loci associated with 7 of the 35 new markers were identified within specific families. Two of these markers were associated with differences in strength and rump angle on chromosomes 4 and 9, respectively. Different markers were associated with protein percentage, milk yield, and somatic cell score on chromosomes 6, 7, and 10 in different families. Differences in the canonically transformed traits were associated with markers on chromosomes 5, 6, and 9. Additional marker-trait combinations were identified in the across-family tests, including effects on chromosomes 3, 4, and 9 for protein percentage, body depth, and canonical conformation traits, respectively. Additional markers are being added to allow interval analysis for putative quantitative trait loci that have been identified and to increase marker density.