Allelic and genotypic distributions of polymorphisms in the uncoupling protein 3 (UCP3) and forkhead box O1 (FOXO1) genes were assessed in 491 Chinese Qinchuan cattle. Single-locus genotype effects and the combined effect of polymorphisms within those two genes were probed to determine possible association with the carcass quality traits. Using DNA sequencing, in total three novel single nucleotide polymorphisms (SNPs) were identified, including a SNP in the intron 1 of UCP3 (NC_037339.1: g.6821C>T), and two SNPs within the 3’UTR of FOXO1 (NC_037342.1: g.93063G>A and g.93280A>G). Statistical analyses indicated that the g.6821C>T (UCP3) and g.93280A>G (FOXO1) polymorphisms were significantly associated with intramuscular fat content (P < 0.05 or P < 0.01). So, the results obtained in this study constitute a valuable information about the markers applicable in marker-assisted selection (MAS) used in improving carcass quality traits.
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