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Sequences and Haplotypes Analysis of mtDNA D-loop in Duck

In order to seek tools for evaluating the breed characteristic among intergeneric and distinguishing different breeds, Beijing, Jinding, Lvtou, Banzui, and Muscovy duck(in total 40)were selected to amplifier the sequences of mtDNA D-loop. 616 bp sequence of domestic duck, 619 bp sequence of muscovy duck was obtained, respectively. In domestic ducks, 6 insertion/deletion, 114 times transversion and 94 times transition were detected, and in Muscovy duck, only 1 insertion/deletion and 4 times transition were found, but no transversion was detected. MEGA5. 0 and DnaSP V. 5.0 were used to compute the base compositions, mutations and haplotypes. The results showed that the mtDNA D-loop had the highest amount of base C, and showed the base composition of bias. 21 haplotypes were detected in all, and the Tajima's D value was-0.11344 which suggested that all mutations were in line with the neutral mutation. The nucleotide diversity(Pi) of Lvtou and Beijing duck were higher suggested abundant genetic diversity, the haplotype diversity(Hd=0.429)and nucleotide diversity(Pi=0.00139)in Muscovy duck were the lowest which declared low genetic diversity.