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

Molecular Biology Reports

Volumn 37, Issue 1, 2010, Pages 603-611

  Zhou, Guoli ^a,b   Dudgeon, Crissy ^c   Li, Mei ^c   Cao, Yang ^d   Zhang, Lichun ^d   Jin, Haiguo ^d  

^a NORTHEAST AGRICULTURAL UNIVERSITY   (China)

^b LIAOCHENG UNIVERSITY   (China)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^d JILIN ACADEMY OF AGRICULTURAL SCIENCES   (China)

Author keywords

Association analysis; Cattle; HGD gene; Meat quality traits; Single nucleotide polymorphisms

Indexed keywords

AMINO ACID; COMPLEMENTARY DNA; GENOMIC DNA; HOMOGENTISATE 1,2 DIOXYGENASE; RNA;

AMINO ACID SEQUENCE; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CATTLE; CONTROLLED STUDY; EXON; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HAPLOTYPE; INTRON; MEAT; MOLECULAR CLONING; MUSCLE CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; QUANTITATIVE TRAIT LOCUS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION;

ANIMALS; CATTLE; CHINA; CLONING, MOLECULAR; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE FREQUENCY; HAPLOTYPES; HOMOGENTISATE 1,2-DIOXYGENASE; MEAT; MOLECULAR SEQUENCE DATA; ORGAN SPECIFICITY; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, MESSENGER; SEQUENCE ANALYSIS, PROTEIN;

BOS; BOVINAE;

EID: 77949262329     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-009-9860-4     Document Type: Article

References (27)

1. L Andersson M Georges 2004 Domestic-animal genomics: deciphering the genetics of complex traits Nat Rev Genet 5 202 212 10.1038/nrg1294 1:CAS:528:DC%2BD2cXht12itr0%3D 14970822 (Pubitemid 38294549)
2. JM Rodriguez DE Timm GP Titus D Beltran-Vale de Bernabe O Criado HA Mueller S Rodriguez de Cordoba MA Penalva 2000 Structural and functional analysis of mutations in alkaptonuria Hum Mol Genet 9 2341 2350 1:CAS:528:DC%2BD3cXnt1yntbs%3D 11001939
3. JM Fernandez-Canon B Granadino D Beltran-Valero de Bernabe M Renedo E Fernandez-Ruiz MA Pen alva S RodrIguez de Cordoba 1996 The molecular basis of alkaptonuria Nat Genet 14 19 24 10.1038/ng0996-19 1:CAS:528:DyaK28Xls1SqtL4%3D 8782815 (Pubitemid 26301542)
4. TP Yu L Wang CK Tuggle MF Rothschild 1999 Mapping genes for fatness and growth on pig chromosome 13: a search in the region close to the PIT1 gene J Anim Breed Genet 116 269 280 10.1046/j.1439-0388.1999.00198.x 1:CAS:528:DyaK1MXmsFOjtbo%3D
5. G Yue V Russo R Davoli I Sternstein C Brunsch D Schroffelova A Stratil G Moser H Bartenschlager G Reiner H Geldermann 2003 Linkage and QTL mapping for Sus scrofa chromosome 13 J Anim Breed Genet 120 Suppl 1 103 110 10.1046/j.0931-2668.2003.00430.x 1:CAS:528:DC%2BD2cXisFyksbs%3D (Pubitemid 38463659)
6. F Rouzaud J Martin PF Gallet D Delourme 2000 A first genotyping assay of French cattle breeds based on a new allele of the extension gene encoding the melanocortin-1 receptor (Mc1r) Genet Sel Evol 32 511 520 10.1186/1297-9686-32-5- 511 1:CAS:528:DC%2BD3cXosFynurY%3D 14736379
7. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410 1:CAS:528:DyaK3MXitVGmsA%3D%3D 2231712
8. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 24 4876 4882 10.1093/nar/25.24.4876 (Pubitemid 28022245)
9. Chun J (2001) PHYDIT version 3.1. http://plaza.snu.ac.kr/~jchun/phydit/ )
10. M Nei 1978 Estimation of average heterozygosity and genetic distance from a small number of individuals Genetics 89 583 590 17248844
11. HC Hines JP Zikakis GF Haenlein 1981 Linkage relationships among loci of polymorphisms in blood and milk of cattle J Dairy Sci 64 71 76 1:STN:280:DyaL3M3msVyquw%3D%3D 7264022
12. D Botstein RL White M Skolnick RW Davis 1980 Construction of a genetic linkage map in human using restriction fragment length polymorphisms Am J Hum Gene 32 314 331 1:CAS:528:DyaL3cXkvFamtbc%3D
13. JC Stephens JA Schneider DA Tanguay J Choi T Acharya SE Stanley R Jiang 2001 Haplotype variation and linkage disequilibrium in 313 human genes Science 293 489 493 10.1126/science.1059431 1:CAS:528:DC%2BD3MXlsFGjsbY%3D 11452081 (Pubitemid 32679076)
14. AS S (1999) Statistical analysis system institute. Incorporation, Cary, NC, USA
15. B Granadino D Beltran-Valero de Bernabe JM Fernandez-Canon MA Penalva S RodrIguez de Cordoba 1997 The human homogentisate 1, 2-dioxygenase (HGO) gene Genomics 43 115 122 10.1006/geno.1997.4805 1:CAS:528:DyaK2sXltVSltb8%3D 9244427 (Pubitemid 27335213)
16. R Breathnach P Chambon 1981 Organization and expression of eucaryotic split genes coding for proteins Annu Rev Biochem 50 349 383 10.1146/annurev.bi. 50.070181.002025 1:CAS:528:DyaL3MXkslGmtb0%3D 6791577
17. M Burset IA Seledtsov VV Solovyev 2000 Analysis of canonical and non-canonical splice sites in mammalian genomes Nucleic Acids Res 28 4364 4375 10.1093/nar/28.21.4364 1:STN:280:DC%2BD3crgvVahtg%3D%3D 11058137
18. JA Edwin FredericH Veldhuizen 2005 Steady-state kinetics and inhibition of anaerobically purified human homogentisate 1, 2-dioxygenase Biochem J 386 305 314 10.1042/BJ20041370 (Pubitemid 40343788)
19. XP He XW Xu B Liu 2009 Molecular characterization, chromosomal localization and association analysis with back-fat thickness of porcine LPIN2 and LPIN3 Mol Biol Rep 36 1819 1824 10.1007/s11033-008-9385-2 1:CAS:528:DC%2BD1MXptV2nurk%3D 18989753
20. CL Zhang YH Wang H Chen XY Lan CZ Lei XT Fang 2009 Association between variants in the 50-untranslated region of the bovine MC4R gene and two growth traits in Nanyang cattle Mol Biol Rep 36 1839 1843 10.1007/s11033-008-9388-z 1:CAS:528:DC%2BD1MXptV2ntbk%3D 18987992
21. XS Lai XY Lan H Chen XL Wang KY Wang M Wang H Yu M Zhao 2009 A novel SNP of the Hesx1 gene in bovine and its associations with average daily gain Mol Biol Rep 36 1677 1681 10.1007/s11033-008-9368-3 1:CAS:528:DC%2BD1MXptV2msr4%3D 18853282
22. DC Ciobanu JWM Bastiaansen SM Lonergan H Thomsen JCM Dekkers GS Plastow MF Rothschild 2004 New alleles in calpastatin gene are associated with meat quality traits in pigs J Anim Sci 82 2829 2839 1:CAS:528:DC%2BD2cXnvVWlurk%3D 15484933
23. RT Stone E Casas TPL Smith JW Keele G Harhay GL Bennett M Koohmaraie TLS Wheeler D Shackelford WM Snelling 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 2288 1:CAS:528:DC%2BD2MXhtVKqsLvN 16160037
24. A Marin J Bertranpetit JL Oliver JR Medina 1989 Variation in G + C-content and codon choice: differences among synonymous codon groups in vertebrate genes Nucleic Acids Res 17 6181 6189 10.1093/nar/17.15.6181 1:CAS:528:DyaL1MXlt1yisL8%3D 2570402
25. TD Porter 1995 Correlation between codon usage, regional genomic nucleotide composition, and amino acid composition in the cytochrome P-450 gene superfamily Biochim Biophys Acta 1261 394 400 7742368
26. D Beltran-Valero de Bernabe B Granadino I Chiarelli B Porfirio E Mayatepek R Aquaron MM Moore JJM Festen R Sanmarti MA Penalva S Rodriguez de Cordoba 1998 Mutation and polymorphism analysis of the human homogentisate 1, 2-dioxygenase gene in alkaptonuria patients Am J Hum Genet 62 776 784 10.1086/301805 1:STN:280:DyaK1c7pvVegtw%3D%3D 9529363 (Pubitemid 28194318)
27. JH Li MS Yang NY Xu 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 26