The aims of this study were (1) to confirm previously identified quantitative trait loci (QTL) on bovine chromosomes 6, 11, 14, and 23 in the Danish Holstein cattle population, (2) to assess the pleiotropic nature of each QTL on milk production traits by building multitrait and multi-QTL models, and (3) to include pedigree information on nongenotyped individuals to improve the estimation of genetic parameters underlying the random QTL model. Nineteen grandsire families were analyzed by single-trait (ST) and multitrait (MT) QTL mapping methods. The variance component-based QTL mapping model was implemented via restricted maximum likelihood (REML) to estimate QTL position and parameters. Segregation of the previously identified QTL was confirmed on bovine chromosomes 6, 11, and 14, but not on 23. A highly significant (1% chromosome-wise level) QTL was found on chromosome 6, between 37 and 73 cM. This QTL had a strong effect on protein percentage (PP) and fat percentage (FP) according to ST analyses, and effects on PP, FP, milk yield (MY), fat yield (FY), and protein yield (PY) in MT analyses. A QTL affecting PP was detected on chromosome 11 (at 70 cM) using ST analysis. The MT analysis revealed a second QTL (at 67 cM) approaching significance with an effect on MY. The ST analysis identified a QTL for MY and FP on chromosome 14, between 10 and 24 cM. The extended pedigree (nongenotyped animals) was included to estimate genetic parameters underlying the random QTL model; that is, additive polygenic and QTL variances. In general, the estimates of the QTL variance components were smaller but more precise when the extended pedigree was considered in the analysis.
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