Segregation of paternal marker alleles in the progeny of a single boar was used to estimate linkage between the marker genes and associations of these genes with quantitative trait loci (QTL). The sire was heterozygous at four polymorphic marker loci, haptoglobin (HP), glucosephosphate isomerase (GPI), phosphogluconate dehydrogenase (PGD), and esterase D (ESD), and sired 30 litters during an 8-mo period. Glucosephosphate isomerase and PGD were linked (θ = .09; P < .005). The phase of these two loci in the sire was determined to be GPI A - PGD B, GPI B - PGD A. No other linkages were detected. Growth (135 ≤ n ≤ 172) and carcass data (70 ≤ n ≤ 80) were analyzed assuming a fixed linear model. Least squares means were compared for differences in growth and carcass traits between pigs that inherited alternative paternal marker alleles. Pigs that inherited the GPI A allele from the sire had a 22-g higher daily live weight gain postweaning and reached 103 kg live weight in 2.6 fewer days than did pigs that inherited the GPI B allele (P < .05), indicative of the presence of gene(s) that affect rate of gain linked to the GPI locus. Pigs that inherited the PGD B allele had a .14 unit higher score for muscle firmness (score ranged from 1 to 3 units) than pigs that inherited the PGD A allele (P < .05). Pigs that inherited the HP 3 allele had a .06-kg higher weaning weight and a .11 lower ham muscle mass score than did pigs that inherited the HP 2 allele from the sire (P < .05). No associations with quantitative traits were detected for ESD.