Molecular cloning of the HGD gene and association of SNPs with meat quality traits in Chinese red cattle
- 174 Downloads
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 were polymorphisms of a bovine HGD gene have demonstrated a correlation with meat traits in Chinese red cattle.
KeywordsHGD gene Single nucleotide polymorphisms Meat quality traits Cattle Association analysis
This work was supported by the National High Technology Research and Development Project of China (No.2008aa101010), the National Fundamental Resources Platform of Science and Technology of P. R. China (2005DKA21101) and Natural Science fund of Shandong province of P. R. China (Y2007D33).
- 9.Chun J (2001) PHYDIT version 3.1. http://plaza.snu.ac.kr/~jchun/phydit/)
- 12.Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in human using restriction fragment length polymorphisms. Am J Hum Gene 32:314–331Google Scholar
- 14.AS S (1999) Statistical analysis system institute. Incorporation, Cary, NC, USAGoogle Scholar
- 23.Stone RT, Casas E, Smith TPL, Keele JW, Harhay G, Bennett GL, Koohmaraie M, Wheeler TLS, Shackelford D, Snelling WM (2005) Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: development of a low-density single nucleotide polymorphism map. J Anim Sci 83:2280–2288PubMedGoogle Scholar
- 26.Beltran-Valero de Bernabe D, Granadino B, Chiarelli I, Porfirio B, Mayatepek E, Aquaron R, Moore MM, Festen JJM, Sanmarti R, Penalva MA, Rodriguez de Cordoba S (1998) Mutation and polymorphism analysis of the human homogentisate 1, 2-dioxygenase gene in alkaptonuria patients. Am J Hum Genet 62:776–784CrossRefPubMedGoogle Scholar
- 27.Li JH, Yang MS, Xu NY (2008) Single nucleotide polymorphism of porcine HGD gene exon 14 and its association with carcass and meat quality traits. J Northwest AF Univ 36:22–26Google Scholar