Journal of Biological Sciences1727-30481812-5719Asian Network for Scientific Information10.3923/jbs.2011.181.188WuZhen-Yang ZengSheng-Cheng LuoYu-Zhu HanJian-Lin 22011112Domestic duck production plays a very important role in producing meat, eggs and down. To support the conservation of closely related species of wild Mallard as well as Muscovy ducks and to understand the origin, domestication process, genetic diversity as well as differentiation of domestic ducks, the partial D-loop sequence of mitochondrial DNA has been employed as the most popular molecular marker. In this study, a total of four pairs of primers located in different D-loop portions were used to amplify and sequence the partial D-loop fragment from definite domestic Mallard and Muscovy ducks together with domestic duck samples of unknown species of origin. Intensive sequencing profiles identified a homoplasmic D-loop in domestic Muscovy ducks but heteroplasmic mtDNA D-loop fragments in domestic Mallard ducks. 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