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Mitochondrial DNA
The Journal of DNA Mapping, Sequencing, and Analysis
Volume 24, 2013 - Issue 5
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Full Length Research Paper

DNA barcode through cytochrome b gene information of mtDNA in native chicken strains

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Pages 528-537 | Received 30 Oct 2012, Accepted 23 Jan 2013, Published online: 06 Mar 2013

References

  • AOU (The American Ornithologists' Union). 1998. Check-list of North American birds. Lawrence, KS: AOU Press829.
  • Allendorf FW, Luikart G. 2006. Conservation and the genetics of populations. Malden, MA: Blackwell.
  • Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC. 1987. Intraspecific phylogeography: The mitochondrial bridge between population genetics and systematics. Annu Rev Ecol Syst. 18:489–522.
  • Avise JC, Glenn CJ. 1998. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol Evol. 15 11: 1481–1490.
  • Avise JC, Walker D. 1999. Species realities and numbers in sexual vertebrates: Perspectives from an asexually transmitted genome. Proc Natl Acad Sci USA. 96:992–995.
  • Avise JC, Zink RM. 1988. Molecular genetic divergence between avian sibling species: King and clapper rails, long-billed and short-billed dowitchers, boated-tailed and great-tailed grackles, and tufted and black-crested titmice. Auk. 105:516–528.
  • Banks RC, Cicero C, Dunn JL, Kratter AW, Ouellet H, Rasmussen PC, Remsen JV Jr, Rising JA, Stotz DF. 2000. Forty-second supplement to the Ornithologists' Union checklist of North American birds. Auk. 117:847–858.
  • Banks RC, Cicero C, Dunn JL, Kratter AW, Rasmussen PC, Remsen JV Jr, Rising JD, Stot DF. 2002. Forty-third supplement to the Ornithologists' Union checklist of North American birds. Auk. 119:897–906.
  • Banks RC, Cicero C, Dunn JL, Kratter AW, Rasmussen PC, Remsen JV Jr, Rising JD, Stot DF. 2003. Forty-fourth supplement to the Ornithologists' Union checklist of North American birds. Auk. 120:923–931.
  • Bates JM, Hackett SJ, Goerck JM. 1999. High levels of mitochondrial DNA differentiation in two lineages of Antbirds (Drymophila and Hypocnemis). Auk. 116:1093–1106.
  • Bellis C, Ashton KJ, Freney L, Blair B, Griffiths LR. 2003. A molecular genetic approach for forensic animal species identification. Forensic Sci Int. 134:99–108.
  • Blackburn TM, Cassey P, Gaston KJ. 2006. Variations on a theme: Sources of heterogeneity in the form of the interspecific relationship between abundance and distribution. J Anim Ecol. 75:1426–1439.
  • Bottero MT, Civera T, Nucera D, Rosati S, Sacchi P, Turi RM. 2003. A multiplex polymerase chain reaction for the identification of cows', goats' and sheep's milk in dairy products. Int Dairy J.. 13:277–282.
  • Brown WM, George M, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA. 76:1967–1971.
  • Brown WM, Prager EM, Wang A, Wilson AC. 1982. Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J Mol Evol. 18:225–239.
  • Cantatore P, Roberti M, Pesole G, Ludovico A, Milella F, Gadaleta MN, Saccone C. 1994. Evolutionary analysis of cytochrome b sequences in some Perciformes: Evidence for a slower rate of evolution than in mammals. J Mol Evol. 39:589–597.
  • Cheng GC, Liu KF, Zhang Q, Wang L, Duan ZX, Li XY, Liu RS, Yu Q. 1996. Studies on genetic relationship between red junglefowl (Gallus gallus) and domestic fowl (Gallus domesticus). Acta Genetica Sinica. 23:96.
  • Claridge MF, Dawah HA, Wilson MR. 1997. Species: The units of biodiversity. London: Chapman & Hall.
  • Esposti DM, De Vries S, Crimi M, Ghelli A, Patarnello T, Meyer A. 1993. Mitochondrial cytochrome b: Evolution and structure of the protein. Biochim Biophys Acta. 1143:243–271.
  • FAO. 2004. Methodologies to identify, evaluate and conserve poultry genetic resources, Weigned, S., Romanov, M.N., Rath, D. World Poultry Congress 2004, June 8–13, Istanbul.
  • FAO. 2008. The structure and importance of the commercial and village based poultry systems in the Kingdom of Saudi Arabia. In: Shuaib MA. editors. Ministry of Agriculture, Veterinary Diagnostic Labs, KSA.
  • Frankel OH, Soulé ME. 1981. Conservation and evolution. Cambridge, UK: Cambridge University Press.
  • Frankham R, Ballou JD, Briscoe DA. 2002. Introduction to conservation genetics. Cambridge, UK: Cambridge University Press.
  • Frankham R, Ballou JD, Briscoe DA. 2010. Introduction to conservation genetics. Cambridge, UK: Cambridge University Press.
  • Funk DJ, Omland KE. 2003. Species-level paraphyly and polyphyly: Frequency, causes and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst. 34:397–423.
  • Gill FB, Slikas B. 1992. Patterns of mitochondrial DNA divergence in North American crested titmice. Condor. 94:20–28.
  • Granevitze Z, Hillel J, Feldman M, Six A, Eding H, Weigend S. 2009. Genetic structure of a wide-spectrum chicken gene pool. Anim Genet. 40:686–693.
  • Guillermo G, Claudio MB, Juan PL, Patricia MM, María VR, Pilar PG. 2004. A simple method for domestic animal identification in Argentina using PCR-RFLP analysis of cytochrome b gene. Legal Med. 6:246–251.
  • Hebert PDN, Cywinska A, Ball SL, de Waard JR. Biological identification through DNA barcodes. Proc Biol Sci. 2003a; 270:313–321.
  • Hebert PDN, Ratnasingham S, De Waard JR. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proc R SocLondon B. 2003b; 270:S96–S99.
  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. PLoS Biol. 2 10: e312 doi:10.1371/journal.pbio.0020312.
  • Hillis DM, Huelsenbeck JP. 1992. Signal, noise, and reliability in molecular evolutionary analyses. J Hered. 83:189–195.
  • Honeycutt RL, Nedbal MA, Adkins RM, Janecek LL. 1995. Mammalian mitochondrial DNA evolution: A comparison of the cytochrome b and cytochrome c oxidase II genes. J Mol Evol. 40:260–272.
  • Hsieh HM, Chiang HL, Tsai LC, Lai SY, Huang NE, Linacre A, Lee JCI. 2001. Cytochrome b gene for species identification of the conservation animals. Forensic Sci Int. 122:7–18.
  • Irwin DM, Kocher TD, Wilson AC. 1991. Evolution of cytochrome b gene inE mammals. J Mol Biol Evol. 2:13–34.
  • Johns GC, Avise JC. 1998. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol Evol. 15:1481–1490.
  • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 6:111–120.
  • Kirchman JJ, Whittingham LA, Sheldon FH. 2000. Relationships among cave swallow populations (Petrochelidon fulva) determined by comparisons of microsatellite and cytochrome b data. Mol Phy Evol. 14 1: 107–121.
  • Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablance FX, Wilson AC. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci USA. 86:6196–6200.
  • Kornegay JR, Kocher TD, Williams LA, Wilson AC. 1993. Pathways of lysozyme evolution inferred from the sequences of cytochrome b in birds. J Mol Evol. 37:367–379.
  • Kumazawa Y, Nishida M. 2000. Molecular phylogeny of osteoglossoids: a new model for Gondwanian origin and plate tectonic transportation of the Asian arowana. Mol Biol Evol. 17:1869–1878.
  • Li XY, Cheng GC, Duan ZX, Zhang Q, Liu KF, Wang L, Qi HS. 1996. Analysis on blood-group gene population genetics and plasma protein polymorphism of white layer. Acta Veterinaria et Zootechnica Sinica. 27:142–148.
  • Lovejoy NR, de Araújo MLG. 2000. Molecular systematics, biogeography, and population structure of Neotropical freshwater needlefishes of the genus Potamorrhaphis. Mol Ecol. 9 3: 259–268.
  • Lydeard C, Roe KJ. 1997. The phylogenetic utility of the mitochondrial cytochrome b gene for inferring relationships among Actinopterygian fishes. In: Kocher TD, Stepien CA. editors. Molecular systematic of fish. New York: Academic Press285–303.
  • Ma JG, Lu XZ. 1993. Studies on the serum protein polymorphisms and the genetic relationships of the black bone chickens. Acta Veterinaria et Zootechnica Sinica. 24:12.
  • Matsunaga T, Chikuni K, Tanabe R, Muroya S, Shibata K, Yamada J, Shinmura Y. 1999. A quick and simple method for the identification of meat species and meat product by PCR assay. Meat Sci. 51:143–148.
  • Meyer A. 1994. Shortcomings of the cytochrome b gene as a molecular marker. Trend Ecol Evol. 9 8: 278–280.
  • Meyer A, Wilson C. 1990. Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish. J Mol Evol. 31:359–364.
  • Mindell DP, Sorenson MD, Huddleston CJ, Miranda HC, Knight A, Sawchuk SJ, Yuri T. 1997. Phylogenetic relationships among and within select avian orders based on mitochondrial DNA. In: Mindell DP. editors. Avian molecular evolution and systematics. San Diego: Academic Press213–247.
  • Moore WS. 1995. Inferring phylogenies from mtDNA variation: Mitochondrial-gene trees versus nuclear-gene trees. Evolution. 49:718–726.
  • Moore WS, DeFilippis VR. 1997. The window of taxonomic resolution for phylogenies based on mitochondrial cytochrome b. In: Mindell DP. editors. Avian molecular evolution and systematics. New York: Academic Press83–119.
  • Moritz C, Dowling TE, Brown WM. 1987. Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Ann Rev Ecol Syst. 18:269–292.
  • Murray BW, McGillivray WB, Barlow JC, Beech RN, Strobeck C. 1994. The use of cytochrome Bsequence variation in estimation of phylogeny in the Vireonidae. Condor. 96:1037–1054.
  • Niu D, Fu Y, Luo J, Ruan H, Yu Y, Chen G, Ya-Ping Zhang Y. 2002. The origin and genetic diversity of Chinese native chicken breeds. Biochem Genet. 40:163–174.
  • Normark BB, McCune AR, Harrison RG. 1991. Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences. Mol Biol Evol. 8:819–834.
  • Parson W, Pegoraro K, Niederstätter H, Föger M, Steinlechner M. 2000. Species identification by means of the cytochrome b gene. Int J Legal Med. 114:23–28.
  • Rocha-Olivares A, Rosenblatt RH, Vetter RD. 1999. Molecular evolution, systematics, and zoogeography of the rockfish subgenus Sebastomus (Sebastes, Scorpaenidae) based on mitochondrial cytochrome b and control region sequences. Mol Phy Evol. 11 3: 441–458.
  • Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406–425.
  • Shen XJ, Ito S, Mizutani M, Yamamoto Y. 2002. Phylogenetic analysis in chicken breeds inferred from complete cytochrome b gene information. Biochem Genet. 40:129–141.
  • Sturmbauer C, Meyer A. 1992. Genetic divergence, speciation, and morphological stasis in a lineage of African cichlid fishes. Nature (London). 358 6387: 578–58113.
  • Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA. 101:11030–11035.
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
  • Wan QH, Fang SG. 2003. Application of species-specific polymerase chain reaction in the forensic identification of Tiger species. Forensic Sci Int. 131:75–78.
  • William SM, Victor RD. 1997. The window of taxanomic resolution for phylogenies based on mitochondrial Cytochrome b. In: Mindell DP. editors. Avian molecular evolution and systematic. San Diego, CA: Academic Press83–119.
  • Yap FC, Yan YJ, Loon KT, Zhen JLN, Kamau NY, Kauran JVJ. 2010. Phylogenetic analysis of different breeds of domestic chickens in selected area of peninsular Malaysia inferred from partial cytochrome b gene information and RAPD markers. Anim Biotechnol. 21:226–240.
  • Zehner R, Zimmermann S, Mebs D. 1998. RFLP and sequence analysis of the cytochrome b gene of selected animals and man: Methodology and forensic application. Int J Legal Med. 111:323–327.

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