Molecular cloning of the HGD gene and association of SNPs with meat quality traits in Chinese red cattle.

Homogentisate 1, 2 dioxygenase (HGD) is one of six enzymes required for the catabolism of the aromatic amino acids phenylalanine and tyrosine. Here we present the nucleotide sequence of transcripts of the bovine HGD gene. The full length cDNA of bovine HGD has been identified, encoding a deduced protein of 445 amino acids (Accession No. FJ515744). The bovine HGD gene comprises 14 exons and 13 introns. This is the first published cDNA bovine sequences that share high sequence similarity with other species. Semi-quantitative RT-PCR analysis demonstrated that the bovine HGD transcript was mainly expressed in liver and kidney tissues. Nine single nucleotide polymorphisms (SNPs) were identified, five in the coding region and four intronic. Four of the SNPs change an amino acid in the HGD protein sequence. Genotype and allelic frequencies were determined in Chinese red cattle breeds. Ten haplotypes were determined based upon the genotype of 9 SNPs. Moreover, for the first time an association was reported between HGD gene polymorphism and meat quality traits in Chinese red cattle (n = 224). Marker-trait association analyses showed that the HGD/PvuII genotypes showed a significant effect on meat cooking rate, muscle fiber diameter, and shear force (P < 0.05). The HGD DraIII genotypes showed a significant effect on muscle fiber diameter, shear force, and drip loss (P < 0.05). The HGD/AluI genotypes showed a significant effect on meat cooking rate, shear force, and drip loss (P < 0.05). The HGD/DraI genotypes showed a significant effect on meat cooking rate and shear force (P < 0.05). The HGD/EcoRV genotypes showed a significant effect on meat cooking rate, muscle fiber diameter, and shear force (P < 0.05). In all loci, no statistically significant differences were observed for pHu (P > 0.05). This is the first incidence where polymorphisms of a bovine HGD gene have demonstrated a correlation with meat traits in Chinese red cattle.