H. Y. Zhang
College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
W. J. Yang
College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
Y. Z. Luo
College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
J. L. Han
International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, Kenya
ABSTRACT
The widely expressed chicken UBTD2 gene in different types of tissues from embryonic to adult developmental stages implies its important role in regulating protein ubiquitination and delivery of ubiquitinated substrates, however, there is no specific study on the genomic DNA structure and function of chicken UBTD2 gene except a few invalidated SNPs derived from ESTs. In this study, a 1.2 kb long fragment within intron 2 of chicken UBTD2 gene was amplified and directly sequenced from a flock of 11 White Leghorn chickens. A total 15 sequences were identified from these birds, of which seven were homozygous but the remaining four were heterozygous. These new sequences were analyzed together with the homologous region in Gallus gallus reference genome version 71.4 (Chromosome 13: 8104760 - 8105979 in Galgal4). There were 10 polymorphic sites including seven transitions and three transversions, which defined four haplotypes in these 16 sequences. The Gallus gallus reference sequence formed a specific and distinct haplotype while the White Leghorn chickens carried three haplotypes at very similar frequencies of four, five and six sequences each. These data were the first piece of evidence of genetic polymorphisms present in the chicken UBTD2 gene which is therefore warranted for further investigation on the functional diversity in its complete genomic DNA sequence of different genetic backgrounds.
PDF References
How to cite this article
H. Y. Zhang, W. J. Yang, Y. Z. Luo and J. L. Han, 2013. Genetic Polymorphisms in a 1.2 kb Long Fragment within Intron 2 of Chicken
UBTD2 Gene. International Journal of Poultry Science, 12: 307-311.
DOI: 10.3923/ijps.2013.307.311
URL: https://scialert.net/abstract/?doi=ijps.2013.307.311
DOI: 10.3923/ijps.2013.307.311
URL: https://scialert.net/abstract/?doi=ijps.2013.307.311
REFERENCES
- Bandelt, H.J., P. Forster and A. Rohl, 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol., 16: 37-48.
PubMedDirect Link - Boardman, P.E., J. Sanz-Ezquerro, I.M. Overton, D.W. Burt and E. Bosch et al., 2002. A comprehensive collection of chicken cDNAs. Curr. Bio., 12: 1965-1969.
PubMed - Carninci, P., T. Kasukawa, S. Katayama, J. Gough and M.C. Frith et al., 2005. The transcriptional landscape of the mammalian genome. Science, 309: 1559-1563.
PubMed - Carre, W., X. Wang, T.E. Porter, Y. Nys and J. Tang et al., 2006. Chicken genomics resource: Sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index. Physiol. Genomics, 25: 514-524.
PubMed - Church, D.M., L. Goodstadt, L.W. Hillier, M.C. Zody and S. Goldstein et al., 2009. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol., Vol. 7.
CrossRef - Gerhard, D.S., L. Wagner, E.A. Feingold, C.M. Shenmen and L.H. Grouse et al., 2004. The status, quality and expansion of the NIH full-length cDNA project: The mammalian gene collection (MGC). Genome Res., 14: 2121-2127.
CrossRefPubMedDirect Link - Gibbs, R.A., J. Rogers, M.G. Katze, R. Bumgarner and G.M. Weinstock et al., 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316: 222-234.
CrossRef - Guyon, J.R., A.N. Mosley, S.J. Jun, F. Montanaro and L.S. Steffen et al., 2005. δ-Sarcoglycan is required for early zebrafish muscle organization. Exp. Cell Res., 304: 105-115.
CrossRef - Harhay, G.P., T.S. Sonstegard, J.W. Keele, M.P. Heaton and M.L. Clawson et al., 2005. Characterization of 954 bovine full-CDS cDNA sequences. BMC Genomics, Vol. 6.
CrossRef - Hillier, L.W., W, Miller, E. Birney, W. Warren1 and R.C. Hardison et al., 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432: 695-716.
CrossRef - Hubbard, S.J., D.V. Grafham, K.J. Beattie, I.M. Overton and S.R. McLaren et al., 2005. Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Res., 15: 174-183.
PubMed - Kimura, K., A. Wakamatsu, Y. Suzuki, T. Ota and T. Nishikawa et al., 2006. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res., 16: 55-65.
PubMed - Klein, S.L., R.L. Strausberg, L. Wagner, J. Pontius, S.W. Clifton and P. Richardson, 2002. Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. Dev. Dyn., 225: 384-391.
PubMed - Leon, A.J., D. Banner, L. Xu, L. Ran and Z. Peng et al., 2013. Sequencing, annotation and characterization of the influenza Ferret infectome. J. Virol., 87: 1957-1966.
PubMed - Li, X.X., L.X. Han and J.L. Han, 2010. No specific primer can independently amplify the complete exon 2 of chicken BLB1 or BLB2 genes. Int. J. Poult. Sci., 9: 192-197.
CrossRefDirect Link - Librado, P. and J. Rozas, 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.
CrossRefPubMedDirect Link - Ommeh, S., L.N. Jin, H. Eding, F.C. Muchadeyi and S. Sulandari et al., 2010. Geographic and Breed Distribution Patterns of an A/G Polymorphism resent in the Mx Gene Suggests Balanced Selection in Village Chickens Int. J. Poult. Sci., 9: 32-38.
CrossRefDirect Link - Ota, T., Y. Suzuki, T. Nishikawa, T. Otsuki and T. Sugiyama et al., 2004. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat. Genet., 36: 40-45.
CrossRefDirect Link - Rogers, A.R. and H. Harpending, 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol., 9: 552-569.
Direct Link - Schmutz, J., J. Martin, A. Terry, O. Couronne and J. Grimwood et al., 2004. The DNA sequence and comparative analysis of human chromosome 5. Nature, 431: 268-274.
CrossRefDirect Link - Shaw, I., T.J. Powell, D.A. Marston, K. Baker and A. van Hateren et al., 2007. Different evolutionary histories of the two classical class I genes BF1 and BF2 illustrate drift and selection within the stable MHC haplotypes of chickens. J. Immunol., 178: 5744-5752.
PubMed - Slatkin, M. and R.R. Hudson, 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129: 555-562.
Direct Link - Song, A.X., C.J. Zhou, X. Guan, K.H. Sze and H.Y. Hu, 2010. Solution structure of the N-terminal domain of DC-UbP/UBTD2 and its interaction with ubiquitin. Protein Sci., 19: 1104-1109.
Direct Link - Strausberg, R.L., E.A. Feingold, L.H. Grouse, J.G. Derge and R.D. Klausner et al., 2002. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Nat. Acad. Sci. USA., 99: 16899-16903.
PubMed - Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei and S. Kumar, 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol. Biol. Evol., 28: 2731-2739.
CrossRefPubMedDirect Link - Venter, I.C., M.D. Adams, E.W. Myers, P.W. Li and R.J. Mural et al., 2001. The sequence of the human genome. Science, 291: 1304-1351.
CrossRefDirect Link - Wong, G., B. Liu, J. Wang, Y. Zhang and X. Yang et al., 2004. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature, 432: 717-722.
CrossRefDirect Link